SINGLE-VECTOR TYPE I VECTORS

Abstract
The invention relates to the production and use of Cas-encoding sequences and vectors comprising these. Aspects of the invention provide products, vectors, delivery vehicles, uses and methods for producing Cas-encoding sequences in bacterial or archaeal cells.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to Great Britain Patent Application No. 1816700.7, filed Oct. 14, 2018, and Great Britain Patent Application No. 1817509.1, filed Oct. 27, 2018, the contents of each of which are hereby incorporated herein by reference in their entirety.


SUBMISSION OF SEQUENCE LISTING ON ASCII TEXT FILE

The content of the following submission on ASCII text file is incorporated herein by reference in its entirety: a computer readable form (CRF) of the Sequence Listing (file name: 786212000600SEQLIST.TXT, date recorded: Nov. 26, 2018, size: 6 KB).


TECHNICAL FIELD

The invention relates to the production and use of Cas-encoding sequences and vectors comprising these. Aspects of the invention provide products, vectors, delivery vehicles, uses and methods for producing Cas-encoding sequences in bacterial or archaeal cells.


BACKGROUND

The state of the art describes vectors and uses of these that employ CRISPR/Cas systems. For example, reference is made to WO2017/118598, US20180140698, US20170246221, US20180273940, US20160115488, US20180179547, US20170175142, US20160024510, US20150064138, US20170022499, US20160345578, US20180155729, US20180200342, WO2017112620, WO2018081502, PCT/EP2018/066954, PCT/EP2018/066980, PCT/EP2018/071454 and U.S. Ser. No. 15/985,658 and equivalent publications by the US Patent and Trademark Office (USPTO) or WIPO, the disclosures of which are incorporated herein by reference.


SUMMARY OF THE INVENTION

The invention provides the following configurations.


In a First Configuration A nucleic acid vector for introduction into a host cell, the vector comprising a first nucleotide sequence encoding a Type I Cas3 and a second nucleotide sequence encoding one or more Cascade proteins, wherein the first and second sequences are under the control of one or more promoters comprised by the vector for expression of the proteins in the cell.


In an example, the vector comprises an operon for expression in the cell of the Cas3 and Cascade proteins from a Cas module, the module comprising the nucleotide sequences encoding the Cas3 and Cascade proteins, and the operon comprising the Cas module under the control of a promoter for controlling the expression of both the Cas3 and Cascade proteins.


The invention also provides a delivery vehicle comprising the vector, as well as a pharmaceutical composition comprising the vector or vehicle and a pharmaceutically acceptable diluent, excipient or carrier.


The invention also provides a method of treating or reducing the risk of a disease or condition in a human or animal subject, the method comprising administering the vector, vehicle or composition to the subject, and introducing the vector into target host bacterial or archaeal cells in the subject (eg, in a gut microbiota, lung, eye or blood of the subject), wherein the Cas cuts (or otherwise modifies) one or more target sequences in the target cells and the cells are killed or growth or proliferation of the cells is reduced.


In a Second Configuration


A method of amplifying copies of a DNA encoding a functional Cas protein (optionally a Cas nuclease) in a bacterial or archaeal production strain of cells, the method comprising

    • (a) Providing production strain cells, each cell comprising a copy of said DNA, wherein each DNA comprises a nucleotide sequence encoding said Cas, wherein the nucleotide sequence is under the control of a promoter for controlling the expression of the Cas in the production strain cell, the DNA comprising an origin of replication that is operable in the cell for replication of the DNA;
    • (b) Culturing the cells to allow replication of the DNA, whereby the DNA is amplified; and
    • (c) Optionally isolating copies of the DNA,
    • Optionally wherein the promoter is an attenuated constitutive promoter.


In a Third Configuration


Use of an attenuated promoter in a DNA construct comprising a nucleotide sequence encoding a functional Cas protein (optionally a Cas nuclease) that is under the control of the promoter, in a method of amplifying copies of the DNA in a population of bacterial or archaeal production strain cells, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, for enhancing the yield of amplified DNA produced by the production host cells.


In a Fourth Configuration


Use of an attenuated promoter in a DNA construct comprising a nucleotide sequence encoding a functional Cas protein (optionally a Cas nuclease) that is under the control of the promoter, in a method of amplifying copies of the DNA in a population of bacterial or archaeal production strain cells, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, for reducing toxicity of the Cas in the production strain.


In a Fifth Configuration


Use of an attenuated promoter in a DNA construct comprising a nucleotide sequence encoding a functional Cas protein (optionally a Cas nuclease) that is under the control of the promoter, in a method of amplifying copies of the DNA in a population of bacterial or archaeal production strain cells, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, for reducing mutation of the DNA (optionally the Cas-encoding sequence) in the production strain.


In a Sixth Configuration


Use of an attenuated promoter in a DNA construct comprising a nucleotide sequence encoding a functional Cas protein (optionally a Cas nuclease) that is under the control of the promoter, in a method of amplifying copies of the DNA in a population of bacterial or archaeal production strain cells, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, for promoting production cell viability during the amplification of the DNA.


In a Seventh Configuration


Use of an attenuated promoter in a DNA construct comprising a nucleotide sequence encoding a functional Cas protein (optionally a Cas nuclease) that is under the control of the promoter, in a method of amplifying copies of the DNA in a population of bacterial or archaeal production strain cells, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, for reducing the occurrence of Cas cutting of DNA.


In an Eighth Configuration


A method for enhancing the yield of amplified copies of a DNA construct in a population of bacterial or archaeal production strain cells, wherein the construct comprises a nucleotide sequence encoding a functional Cas protein (optionally a Cas nuclease) that is under the control of a promoter, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, wherein the promoter is an attenuated promoter.


In a Ninth Configuration


A method for reducing toxicity of a functional Cas protein (optionally a Cas nuclease) in a population of bacterial or archaeal production strain cells in a process of amplifying copies of a DNA construct, wherein the construct comprises a nucleotide sequence encoding the Cas and the sequence is under the control of a promoter, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, wherein the promoter is an attenuated promoter.


In a Tenth Configuration


A method for reducing mutation of a DNA construct encoding a functional Cas protein (optionally a Cas nuclease) in a population of bacterial or archaeal production strain cells in a process of amplifying copies of the construct, wherein the construct comprises a nucleotide sequence encoding the Cas and the sequence is under the control of a promoter, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, wherein the promoter is an attenuated promoter.


In an Eleventh Configuration


A method for promoting production cell viability of a population of bacterial or archaeal production strain cells in a process of amplifying copies of a DNA construct comprised by the cells, wherein the construct comprises a nucleotide sequence encoding a functional Cas protein (optionally a Cas nuclease) and the sequence is under the control of a promoter, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, wherein the promoter is an attenuated promoter.


In a Twelfth Configuration


A method for reducing the occurrence of Cas nuclease cutting of a DNA construct in a population of bacterial or archaeal production strain cells in a process of amplifying copies of the construct, wherein the construct comprises a nucleotide sequence encoding the Cas and the sequence is under the control of a promoter, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, wherein the promoter is an attenuated promoter.





BRIEF DESCRIPTION OF THE DRAWINGS


FIGS. 1A-1C. Type I CRISPR-Cas system of C. difficile targeting E. coli MG1655. (FIG. 1A) Layout of the CRISPR Guided Vector™, CGV™. Plasmid 1: pSC101 or pBAD promoter (induced by arabinose), cas3 and cascade genes. Plasmid 2: pCloDF13 ori, pTac promoter (induced by IPTG), CRISPR array. (FIG. 1B) Dilution series (101-106) of drop spots (5 μI) of E. coli MG1655 harboring the CGV on LB agar plates with and without inducers. (FIG. 1C) CRISPR induction killed 99.9% of the population (grey bar). Growth in absence of induction is shown in black. CGV™ refers to a CRISPR Guided Vector™, which is a nucleic acid vector comprising nucleotide sequences encoding CRISPR/Cas components.



FIGS. 2A-2C. Type I CRISPR-Cas system of C. difficile targeting E. coli MG1655. (FIG. 2A) Layout of the CRISPR Guided Vector™, CGV™. pSC101 or pTac promoter (induced by IPTG), CRISPR array, pBAD promoter (induced by arabinose), cas3 and cascade genes. (FIG. 2B) Dilution series (101-106) of drop spots (5 μl) of E. coli MG1655 harboring the CGV on SM agar plates with and without inducers. (FIG. 2C) CRISPR induction killed 99% of the population (grey bar). Growth in absence of induction is shown in black. CGV™ refers to a CRISPR Guided Vector™, which is a nucleic acid vector comprising nucleotide sequences encoding CRISPR/Cas components.



FIGS. 3A-3B. Time-kill curves for E. coli MG1655 harboring the CGV. (FIG. 3A) CRISPR induction killed 99% of the population in 60 minutes (dashed line). Growth in absence of induction is shown in black lines. CRISPR/Cas was induced at time-point 0 and monitored until 120 minutes. (FIG. 3B) Dilution series (101-106) of drop spots (5 μl) on SM agar plates of E. coli MG1655 after 60 minutes of induction.



FIGS. 4A-4B. Specific killing of E. coli MG1655 with type I-B CRISPR-Cas system of C. difficile in a synthetic microbial consortium. (FIG. 4A) Bacteria count of a synthetic population composed of three different strains. CRISPR was induced at time-point 0 and monitored for 60 minutes. Growth in absence of induction is shown in black. CRISPR induction prompted 1-log10 reduction in viable cells of target strain E. coli MG1655, while leaving E. coli Top10 and L. lactis NZ9000 populations intact (dark grey bars). (FIG. 4B) Dilution series (101-106) of drop spots (5 μl) of the bacterial community mixture after 60 minutes of induction. E. coli MG1655 grows selectively on BHI+streptomycin, E. coli Top10 on ampicillin, and L. lactis NZ9000 on chloramphenicol.



FIGS. 5A-5B. Killing of E. coli MG1655 with type I-B CRISPR-Cas system of C. difficile in a synthetic microbial consortium compared to a pure culture of E. coli MG1655. (FIG. 5A) CRISPR induction generated 4-log10 reductions in viable cells of target strain E. coli MG1655, both in the pure culture and in the community mixture (grey bars). Growth in absence of induction is shown in black. (FIG. 5B) Dilution series of a pure culture of E. coli MG1655 and the bacterial community mixture on streptomycin plates with and without inducers.



FIGS. 6A-6B. Type I CRISPR-Cas system of E. coli targeting E. coli MG1655. (FIG. 6A) Dilution series (101-106) of drop spots (5 μl) of E. coli MG1655 harboring the CGV on SM agar plates with and without inducers. (FIG. 6B) CRISPR induction killed 99% of the population (grey bar). Growth in absence of induction is shown in black. CGV™ refers to a CRISPR Guided Vector™ which is a nucleic acid vector comprising nucleotide sequences encoding CRISPR/Cas components.





DETAILED DESCRIPTION

The invention relates to the production and use of Cas-encoding sequences and vectors comprising these. Aspects of the invention provide products, vectors, delivery vehicles, uses and methods for producing Cas-encoding sequences in bacterial or archaeal cells.


An aspect of the invention provides for the control of expression of Cas and optionally also Cascade proteins from single vectors, such as by regulated use of Cas modules in an operon and/or using attenuated promoters.


Concepts:


An aspect of the invention provides nucleic acid vectors that are useful for introducing into target host cells of any eukaryotic or prokaryotic species (eg, ex vivo or in vitro) for expressing Type I Cas and optionally other components of a Type I CRISPR/Cas system. Usefully, the vector may in some examples therefore provide a single-vector means for introducing a complete exogenous Type I CRISPR/Cas system into a target cell for modification (eg, cutting by Cas3) of DNA in the target cell. In an example, a chromosomal target sequence (ie, protospacer that is cognate with the Cas3) is modified. In another example, an episomal DNA sequence is modified, for example a plasmid sequence or a DNA that has been introduced into the cell. The latter may be useful in a recombineering method of the invention wherein exogenous DNA in the target cell is cut by the Cas3 and optionally this produces one or more recombinogenic ends for recombination of the cut DNA with a further DNA of interest, thereby producing a recombination product in the cell. For example, in such a recombineering method, the target cell is a recombinogenic E coli cell, eg, comprising a red/ET system. In another example, the target cell is an undesired cell (eg, a cell of a species or strain that is pathogenic to humans or animals, such as a bacterial disease-causing species or strain) and the cutting by Cas3 kills the cell. This may be useful for treating or preventing an infection in a human or animal harbouring target cells. The provision of single-vector means that express minimally a Cas endonuclease (eg, Cas3), cognate accessory proteins (eg, Cascade proteins) and at least one CRISPR array (or nucleotide sequence encoding a guide RNA (eg, a single guide RNA)), wherein the Cas, accessory proteins and array (or nucleotide sequence) comprise a functional CRISPR/Cas system is more convenient and the inventors believe more efficient for introducing into a target cell and effecting CRISPR/Cas modification of a target sequence therein than the use of 2 or 3 or more separate vectors (eg, a vector encoding the Cas nuclease and a different vector encoding the accessory proteins, and possibly a further vector comprising the array (or gRNA-encoding nucleotide sequence) which all need to transform the target cell for the system to function). This may provide one or more benefits, therefore, such as simplifying delivery (and thus the design of delivery vehicles), simplifying construction of the vector and vehicle and/or providing for better cutting or killing efficiencies. Conveniently, an example of the invention therefore uses an operon for the coordinated expression in the target cells of the Cas and accessory proteins (and optionally also the array or gRNA-encoding sequence(s)). Whilst not wishing to be bound by any particular theory, the introduction of a single vector (eg, using an operon) as per the invention may advantageously coordinate the expression of the Cas and accessory proteins (and optionally production of cRNAs or gRNAs) so that these are available to operate together without undue delay in the target cell. This may be important to tip the balance between, on the one hand the target cell using its endogenous anti-restriction, endogenous Cas or other endogenous mechanisms that seek out and degrade invading phage and DNA, and on the other hand efficient cell killing or deactivation of such mechanisms by the invading CRISPR components of the vector of the invention. In such an arms race, concerted and early operation of the CRISPR components in the cell are likely to be important to gain the upper hand and effect cell killing. The invention provides means to assist this.


By way of example, the invention thus provides the following Concepts:—

  • 1. A nucleic acid vector for introduction into a host cell, the vector comprising a first nucleotide sequence encoding a Type I Cas3 and a second nucleotide sequence encoding one or more Cascade proteins, wherein the first and second sequences are under the control of one or more promoters comprised by the vector for expression of the proteins in the cell.
  • 2. The vector of concept 1, wherein the vector comprises an operon for expression in the cell of the Cas3 and Cascade proteins from a Cas module, the module comprising the nucleotide sequences encoding the Cas3 and Cascade proteins, and the operon comprising the Cas module under the control of a promoter for controlling the expression of both the Cas3 and Cascade proteins.
  • 3. The vector of concept 2, wherein
    • (a) the first sequence is between the promoter and the second sequence in the operon;
    • (b) the operon comprises no Cas-encoding nucleotide sequences between the promoter and the first nucleotide sequence; and/or
    • (c) the operon comprises (in 5′ to 3′ direction) the promoter, the first sequence and the second sequence.
  • 4. The vector of any preceding concept, wherein each promoter is a constitutive promoter.
  • 5. The vector of any one of concepts 1 to 3, wherein the promoter is repressible (optionally repressible by a tetracycline repressor or lac repressor).
  • 6. The vector of any one of concepts 1 to 3, wherein the promoter is inducible.
  • 7. The vector of any preceding concept, wherein the first sequence is under the control of a medium strength promoter.
  • 8. The vector of any preceding concept, wherein the first sequence is under the control of a promoter that has an Anderson Score (AS) of 0.5>AS>0.1.
  • 9. The vector of any preceding concept, wherein the first sequence (and optionally the second sequence) is under the control of a promoter and translation initiation site (TIS) combination that is capable of producing expression of green fluorescent protein (GFP) from a first expression operating unit (EOU) in E. coli strain BW25113 cells with a fluorescence of from 0.5 to 4 times the fluorescence produced in E. coli strain BW25113 cells using a second EOU comprising a P10 promoter (SEQ ID NO: 1) combined with a BCD14 TIS (SEQ ID NO: 2), wherein the EOUs differ only in their promoter and TIS combinations, wherein each EOU comprises (in 5′ to 3′ direction) an upstream initiator, the respective promoter, the respective TIS, a nucleotide sequence encoding GFP, a 3′ UTR, a transcription terminator and a downstream insulator.
  • 10. The vector of concept 9, wherein fluorescence using the first EOU is 0.5 to 2 times the fluorescence using the second EOU.
  • 11. The vector of any preceding concept, wherein the vector comprises an origin of replication that is operable in the host cell.
  • 12. The vector of any preceding concept, wherein the vector comprises an origin of replication that is operable in a bacterial cell of a vector production strain, wherein the Cas3 is not operable in the production strain cell to target and cut a chromosomal sequence thereof.
  • 13. The vector of concept 12, wherein the first sequence is under the control of a promoter that is capable of controlling expression of the Cas3 at a level that is not toxic to the production strain cell.
  • 14. The vector of any preceding concept, wherein the vector is a high copy number vector.
  • 15. The vector of any preceding concept, wherein the first nucleotide sequence or operon is comprised by a mobile genetic element.
  • 16. The vector of any preceding concept, wherein the vector is devoid of a Cas adaption module.
  • 17. The vector of any preceding concept, wherein the vector is devoid of nucleotide sequence encoding one, more or all of a Cas1, Cast, Cas4, Cas6, Cas7 and Cas 8.
  • 18. The vector of any preceding concept, wherein the vector comprises (optionally in 5′ to 3′ direction) nucleotide sequence encoding one, more or all of Cas11, Cas7 and Cas8a1.
  • 19. The vector of concept 18, wherein the vector comprises nucleotide sequence encoding Cas3′ and/or Cas3″.
  • 20. The vector or concept 19, wherein the nucleotide sequences encoding the Cas3′ and/or Cas3″ are between the promoter and the sequence(s) recited in concept 18.
  • 21. The vector of any one of concepts 18 to 20, wherein the host cell comprises a Type IA CRISPR array that is cognate with the Cas3.
  • 22. The vector of any one of concepts 18 to 20, wherein the host cell comprises an endogenous Type TB, C, U, D, E or F CRISPR/Cas system.
  • 23. The vector of any one of concepts 1 to 17, wherein the vector comprises (optionally in 5′ to 3′ direction) nucleotide sequence encoding one, more or all of Cas8b1, Cas7 and Cas5.
  • 24. The vector of concept 23, wherein the vector comprises a nucleotide sequence encoding Cas3 between the promoter and the sequence(s) recited in concept 23.
  • 25. The vector of concept 23 or 24, wherein the host cell comprises a Type IB CRISPR array that is cognate with the Cas3.
  • 26. The vector of concept 23 or 24, wherein the host cell comprises an endogenous Type IA, C, U, D, E or F CRISPR/Cas system.
  • 27. The vector of any one of concepts 1 to 17, wherein the vector comprises (optionally in 5′ to 3′ direction) nucleotide sequence encoding one, more or all of Cas5, Cas8c and Cas7.
  • 28. The vector of concept 27, wherein the vector comprises a nucleotide sequence encoding Cas3 between the promoter and the sequence(s) recited in concept 27.
  • 29. The vector of concept 27 or 28, wherein the host cell comprises a Type IC CRISPR array that is cognate with the Cas3.
  • 30. The vector of concept 27 or 28, wherein the host cell comprises an endogenous Type IA, B, U, D, E or F CRISPR/Cas system.
  • 31. The vector of any one of concepts 1 to 17, wherein the vector comprises (optionally in 5′ to 3′ direction) nucleotide sequence encoding one, more or all of Cas8U2, Cas7, Cas5 and Cas6.
  • 32. The vector of concept 31, wherein the vector comprises a nucleotide sequence encoding Cas3 between the promoter and the sequence(s) recited in concept 31.
  • 33. The vector of concept 31 or 32, wherein the host cell comprises a Type IU CRISPR array that is cognate with the Cas3.
  • 34. The vector of concept 31 or 32, wherein the host cell comprises an endogenous Type IA, B, C, D, E or F CRISPR/Cas system.
  • 35. The vector of any one of concepts 1 to 17, wherein the vector comprises (optionally in 5′ to 3′ direction) nucleotide sequence encoding one, more or all of Cas10d, Cas7 and Cas5.
  • 36. The vector of concept 35, wherein the vector comprises a nucleotide sequence encoding Cas3′ and/or Cas3″.
  • 37. The vector of concept 36, wherein the nucleotide sequences encoding the Cas3′ and/or Cas3″ are between the promoter and the sequence(s) recited in concept 35.
  • 38. The vector of any one of concepts 35 to 37, wherein the host cell comprises a Type ID CRISPR array that is cognate with the Cas3.
  • 39. The vector of any one of concepts 35 to 37, wherein the host cell comprises an endogenous Type IA, B, C, U, E or F CRISPR/Cas system.
  • 40. The vector of any one of concepts 1 to 17, wherein the vector comprises (optionally in 5′ to 3′ direction) nucleotide sequence encoding one, more or all of Cas8e, Cas11, Cas7, Cas5 and Cas6.
  • 41. The vector of concept 40, wherein the vector comprises a nucleotide sequence encoding Cas3 between the promoter and the sequence(s) recited in concept 40.
  • 42. The vector of concept 40 or 41, wherein the host cell comprises a Type IE CRISPR array that is cognate with the Cas3.
  • 43. The vector of concept 40 or 41, wherein the host cell comprises an endogenous Type IA, B, C, D, U or F CRISPR/Cas system.
  • 44. The vector of any one of concepts 1 to 17, wherein the vector comprises (optionally in 5′ to 3′ direction) nucleotide sequence encoding one, more or all of Cas8f, Cas5, Cas7 and Cas6f.
  • 45. The vector of concept 44, wherein the vector comprises a nucleotide sequence encoding Cas3 between the promoter and the sequence(s) recited in concept 44, wherein the vector is devoid of nucleotide sequence encoding further Cas between the promoter and the sequence encoding the Cas3.
  • 46. The vector of concept 44 or 45, wherein the host cell comprises a Type IF CRISPR array that is cognate with the Cas3.
  • 47. The vector of concept 44 or 45, wherein the host cell comprises an endogenous Type IA, B, C, D, U or E CRISPR/Cas system.
  • 48. The vector of any one of concepts 1 to 17, wherein the Cas and Cascade are
    • (a) Type IA Cas and Cascade proteins;
    • (b) Type IB Cas and Cascade proteins;
    • (c) Type IC Cas and Cascade proteins;
    • (d) Type ID Cas and Cascade proteins;
    • (e) Type IE Cas and Cascade proteins;
    • (f) Type IF Cas and Cascade proteins; or
    • (g) Type IU Cas and Cascade proteins.
  • 49. The vector of any preceding concept, wherein the Cas and Cascade are E coli (optionally Type IE or IF) Cas and Cascade proteins.
  • 50. The vector of concept 49, wherein the E coli is ESBL-producing E. coli or E. coli ST131-O25b:H4.
  • 51. The vector of any preceding concept, wherein the Cas and Cascade are
    • (a) Clostridium (eg, C dificile) Cas and Cascade proteins, optionally C dificile resistant to one or more antibiotics selected from aminoglycosides, lincomycin, tetracyclines, erythromycin, clindamycin, penicillins, cephalosporins and fluoroquinolones;
    • (b) Pseudomonas aeruginosa Cas and Cascade proteins, optionally P aeruginosa resistant to one or more antibiotics selected from carbapenems, aminoglycosides, cefepime, ceftazidime, fluoroquinolones, piperacillin and tazobactam; or
    • (c) Klebsiella pneumoniae (eg, carbapenem-resistant Klebsiella pneumoniae or Extended-Spectrum Beta-Lactamase (ESBL)-producing K pneumoniae) Cas and Cascade proteins.
  • 52. The vector of any preceding concept, wherein the Cas and Cascade are E coli, C difficile, P aeruginosa, K pneumoniae, P furiosus or B halodurans Cas and Cascade proteins.
  • 53. The vector of any preceding concept, wherein the Cas3 is a Cas3 of a CRISPR/Cas locus of a first bacterial or archaeal species, wherein the distance between the Cas3-encoding sequence of the locus and its cognate promoter is further than the distance between the Cas3-encoding sequence and the respective promoter comprised by the vector.
  • 54. The vector of any preceding concept, wherein the distance between the promoter and the Cas3-encoding sequence and/or Cascade protein-encoding sequence(s) is shorter than in a corresponding wild-type Type I locus.
  • 55. The vector of any preceding concept, wherein the vector comprises (i) a CRISPR array for producing crRNAs in the host cell and/or (ii) one or more nucleotide sequences encoding one or more guide RNAs (gRNAs or single gRNAs), wherein the crRNAs or gRNAs are cognate to the Cas3 (and optionally cognate to the Cascade proteins).
  • 56. The vector of concept 55 when dependent from concept 2, wherein the array or gRNA-encoding sequence(s) are comprised by the operon and under the control of the promoter.
  • 57. The vector of concept 56, wherein the array or gRNA-encoding sequence(s) are under the control of a promoter that is different from the promoter that controls the expression of the Cas3.
  • 58. The vector of concept 56 or 57, wherein one or more of the crRNAs or gRNAs comprises a spacer sequence that is capable of hybridising to a target nucleotide sequence of the host cell, wherein the target sequence is adjacent a PAM, the PAM being cognate to the Cas3.
  • 59. The vector of concept 58, wherein the target sequence is a chromosomal sequence of the host cell.
  • 60. The vector of concept 58 or 59, wherein the Cas3 is operable to cut the target sequence.
  • 61. The vector of any preceding concept, wherein the vector is a plasmid or phagemid.
  • 62. A delivery vehicle comprising the vector of any preceding concept, wherein the delivery vehicle is capable of delivering the vector into the host cell.
  • 63. The vehicle of concept 62, wherein the delivery vehicle is a phage, non-replicative transduction particle, nanoparticle carrier, bacterium or liposome.
  • 64. The vector or vehicle of any preceding concept, wherein the host cell is a bacterial or archaeal cell, optionally, the host cell is a C dificile, P aeruginosa, K pneumoniae (eg, carbapenem-resistant Klebsiella pneumoniae or Extended-Spectrum Beta-Lactamase (ESBL)-producing K pneumoniae), E coli (eg, ESBL-producing E. coli, or E. coli ST131-025b:H4), H pylori, S pneumoniae or S aureus cell.
  • 65. The vector or vehicle of any preceding concept for administration to a human or animal subject for treating or reducing the risk of a disease or condition in the subject.
  • 66. The vector or vehicle of concept 65, wherein the disease or condition is an infection of the subject with host cells (eg, bacterial cells), or wherein the disease or condition is mediated by host cells (eg, bacterial cells).
  • 67. A pharmaceutical composition comprising the vector or vehicle of any preceding concept and a pharmaceutically acceptable diluent, excipient or carrier.
  • 68. A method of treating or reducing the risk of a disease or condition in a human or animal subject, the method comprising administering the vector, vehicle or composition of any preceding concept to the subject, and introducing the vector into target host bacterial or archaeal cells in the subject (eg, in a gut microbiota, lung, eye or blood of the subject), wherein the Cas cuts (or otherwise modifies) one or more target sequences in the target cells and the cells are killed or growth or proliferation of the cells is reduced.
  • 69. The method of concept 68, wherein the target cells are cells of a disease pathogen species.
  • 70. The method of concept 68 or 69, wherein the target cells are C dificile, P aeruginosa, K pneumoniae (eg, carbapenem-resistant Klebsiella pneumoniae or Extended-Spectrum Beta-Lactamase (ESBL)-producing K pneumoniae), E coli (eg, ESBL-producing E. coli, or E. coli ST131-025b:H4), H pylori, S pneumoniae or S aureus cells.


Embodiments

An aspect of the invention provides improved ways of amplifying DNA constructs in bacterial and archaeal production strain cells. For example, the DNA may be a high copy number plasmid or phagemid comprising a constitutive promoter for controlling the expression of one or more Cas proteins when the DNA has been introduced into a target host bacterial or host cell. It is desirable, according to an aspect of the invention, to consider attenuating the promoter activity during amplification of the DNA in the production strain. This is useful, since the inventors have found that Cas expression in production strains may be toxic to production strain cells, thereby reducing the yield of amplified DNA. Toxicity may be due, for example, to off-target cutting of the production strain chromosomal DNA when the Cas is a nuclease (such as Cas9 or Cas3) and/or due to relatively high levels of expression of the Cas in the cells. Additionally or alternatively, undesirably the Cas expression or activity may impose a selective pressure that favours mutation and propagation of mutated DNA constructs (such as mutation in one more or all of a CRISPR/Cas operon, Cas-encoding gene, Cascade-encoding gene, CRISPR array and gRNa-encoding sequence of the DNA construct) in production cells, thereby reducing the yield of desired amplified constructs and imposing an undesired step of separating desired from mutated DNA constructs for further formulation into useful compositions. Such compositions may be pharmaceutical compositions, herbicides, pesticides, environmental remediation compositions etc. In one example, the promoter attenuation in production strains is achieved by using a medium strength (not high or low) promoter to control the Cas-encoding nucleotide sequence of the DNA constructs. A medium level of Cas expression may be tolerable in the production strains, and yet once the DNA is subsequently introduced into target host cells the Cas is expressed at sufficiently high levels to produce desired activity to modify (eg, cut) target sequences in target cells. In an alternative, the invention uses a repressible promoter, wherein the promoter is repressed in production strain, but not repressed in target host cells. For example, aspects of the invention use a tetracycline repressor (tetR) expressed in production strain cells that represses the promoter.


Thus, the yield can be enhanced by one or more of

    • (a) reducing toxicity of the Cas in the production strain;
    • (b) reducing mutation of the DNA (optionally the Cas-encoding sequence) in the production strain;
    • (c) promoting production cell viability during the amplification of the DNA; and
    • (d) reducing the occurrence of Cas cutting of DNA (optionally cutting of production host cell chromosomal DNA or said DNA construct).


To this end, the invention provides Embodiments as follows:—

  • 1. A method of amplifying copies of a DNA encoding a functional Cas protein (optionally a Cas nuclease) in a bacterial or archaeal production strain of cells, the method comprising
    • (a) Providing production strain cells, each cell comprising a copy of said DNA, wherein each DNA comprises a nucleotide sequence encoding said Cas, wherein the nucleotide sequence is under the control of a promoter for controlling the expression of the Cas in the production strain cell, the DNA comprising an origin of replication that is operable in the cell for replication of the DNA;
    • (b) Culturing the cells to allow replication of the DNA, whereby the DNA is amplified; and
    • (c) Optionally isolating copies of the DNA,
    • wherein the promoter is an attenuated constitutive promoter.


In an example, promoter is a medium strength promoter. In another example, the promoter is repressed in the production strain cell. Hence, the promoter is an attenuated promoter in these examples.

  • 2. Use of an attenuated promoter in a DNA construct comprising a nucleotide sequence encoding a functional Cas protein (optionally a Cas nuclease) that is under the control of the promoter, in a method of amplifying copies of the DNA in a population of bacterial or archaeal production strain cells, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, for enhancing the yield of amplified DNA produced by the production host cells.
  • 3. The use of paragraph 2, wherein the use is for enhancing said yield by
    • (a) reducing toxicity of the Cas in the production strain;
    • (b) reducing mutation of the DNA (optionally the Cas-encoding sequence) in the production strain;
    • (c) promoting production cell viability during the amplification of the DNA; and/or
    • (d) reducing the occurrence of Cas cutting of DNA (optionally cutting of production host cell chromosomal DNA or said DNA construct).
  • 4. Use of an attenuated promoter in a DNA construct comprising a nucleotide sequence encoding a functional Cas protein (optionally a Cas nuclease) that is under the control of the promoter, in a method of amplifying copies of the DNA in a population of bacterial or archaeal production strain cells, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, for reducing toxicity of the Cas in the production strain.
  • 5. Use of an attenuated promoter in a DNA construct comprising a nucleotide sequence encoding a functional Cas protein (optionally a Cas nuclease) that is under the control of the promoter, in a method of amplifying copies of the DNA in a population of bacterial or archaeal production strain cells, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, for reducing mutation of the DNA (optionally the Cas-encoding sequence) in the production strain.
  • 6. Use of an attenuated promoter in a DNA construct comprising a nucleotide sequence encoding a functional Cas protein (optionally a Cas nuclease) that is under the control of the promoter, in a method of amplifying copies of the DNA in a population of bacterial or archaeal production strain cells, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, for promoting production cell viability during the amplification of the DNA.
  • 7. Use of an attenuated promoter in a DNA construct comprising a nucleotide sequence encoding a functional Cas protein (optionally a Cas nuclease) that is under the control of the promoter, in a method of amplifying copies of the DNA in a population of bacterial or archaeal production strain cells, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, for reducing the occurrence of Cas cutting of DNA.
  • 8. A method for enhancing the yield of amplified copies of a DNA construct in a population of bacterial or archaeal production strain cells, wherein the construct comprises a nucleotide sequence encoding a functional Cas protein (optionally a Cas nuclease) that is under the control of a promoter, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, wherein the promoter is an attenuated promoter.
  • 9. A method for reducing toxicity of a functional Cas protein (optionally a Cas nuclease) in a population of bacterial or archaeal production strain cells in a process of amplifying copies of a DNA construct, wherein the construct comprises a nucleotide sequence encoding the Cas and the sequence is under the control of a promoter, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, wherein the promoter is an attenuated promoter.
  • 10. A method for reducing mutation of a DNA construct encoding a functional Cas protein (optionally a Cas nuclease) in a population of bacterial or archaeal production strain cells in a process of amplifying copies of the construct, wherein the construct comprises a nucleotide sequence encoding the Cas and the sequence is under the control of a promoter, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, wherein the promoter is an attenuated promoter.
  • 11. A method for promoting production cell viability of a population of bacterial or archaeal production strain cells in a process of amplifying copies of a DNA construct comprised by the cells, wherein the construct comprises a nucleotide sequence encoding a functional Cas protein (optionally a Cas nuclease) and the sequence is under the control of a promoter, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, wherein the promoter is an attenuated promoter.
  • 12. A method for reducing the occurrence of Cas nuclease cutting of a DNA construct in a population of bacterial or archaeal production strain cells in a process of amplifying copies of the construct, wherein the construct comprises a nucleotide sequence encoding the Cas and the sequence is under the control of a promoter, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, wherein the promoter is an attenuated promoter.
  • 13. The use of paragraph 5 or 7, or the method of paragraph 10 or 12, wherein the mutation or cutting is mutation or cutting of host cell chromosomal DNA or the construct DNA.
  • 14. The method or use of any one of paragraphs 2 to 13, wherein the promoter is a constitutive promoter.
  • 15. The method or use of any preceding paragraph, wherein the promoter is repressed in the production strain cells (optionally repressed by a tetracycline repressor or a lac repressor).
  • 16. The method or use of paragraph 15, wherein the promoter is PLtetO-1, PLlaco-1 or a repressible homologue thereof.


Other examples of suitable repressible promoters are Ptac (repressed by lad) and he Leftward promoter (pL) of phage lambda (which repressed by the λcI repressor). In an example, the promoter comprises a repressible operator (eg, tetO or lacO) fused to a promoter sequence. The corresponding repressor is encoded by a nucleic acid in the production strain (eg, a chromosomally-integrated sequence or a sequence comprised by an episome) and the repressor is expressed during the DNA or vector amplification method of the invention, whereby the promoter controlling Cas expression is repressed. In delivery vehicles that are subsequently produced from isolated amplified DNA/vector, the vehicle is devoid of an expressible nucleotide sequence encoding the repressor, whereby the promoter is functional when the DNA/vector is introduced into a target host cell. For example, in the absence of the repressor the promoter is constitutively ON for expression of the Cas. The system is therefore primed to work once the DNA/vector is introduced into the host cells, and this effect can be enhanced further by using a high copy number DNA/vector comprising an origin of replication that is operable in the host cell. A high copy number vector or DNA is also desirable in the production strain cells for enhancing yield of the DNA/vector, and by use of an attenuated promoter as described herein (eg, medium strength promoter and/or repressed promoter in the production strain cells) one can minimise Cas toxicity whilst culturing to maximise amplification and thus yield of the DNA/vector.

  • 17. The method or use of any preceding paragraph, wherein the promoter is a medium strength promoter.
  • 18. The method or use of any preceding paragraph, wherein the promoter has an Anderson Score (AS) of 0.5>AS>0.1.
  • 19. The method or use of any preceding paragraph, wherein the nucleotide sequence encoding said Cas is under the control of a promoter and translation initiation site (TIS) combination that is capable of producing expression of green fluorescent protein (GFP) from a first expression operating unit (EOU) in E. coli strain BW25113 cells with a fluorescence of from 0.5 to 4 times the fluorescence produced in E. coli strain BW25113 cells using a second EOU comprising a P10 promoter (SEQ ID NO: 1) combined with a BCD14 TIS (SEQ ID NO: 2), wherein the EOUs differ only in their promoter and TIS combinations, wherein each EOU comprises (in 5′ to 3′ direction) an upstream initiator, the respective promoter, the respective TIS, a nucleotide sequence encoding GFP, a 3′ UTR, a transcription terminator and a downstream insulator.
  • 20. The method or use of paragraph 19, wherein fluorescence using the first EOU is 0.5 to 2 times the fluorescence using the second EOU.
  • 21. The method or use of any preceding paragraph, wherein the nuclease is Cas3 and optionally the DNA or cell encodes cognate Cascade proteins.
  • 22. The method or use of any one of paragraphs 1 to 20, wherein the Cas is a Cas9.
  • 23. The method or use of any preceding paragraph, wherein the production strain cells comprise a helper phage genome that is inducible to produce phage coat proteins in the cells, wherein the method further comprises inducing production of the phage proteins and causing packaging of the amplified DNA into phage particles or non-self-replicative transduction particles, and further isolating the phage or transduction particles and optionally formulating the particles into a pharmaceutical composition for administration to a human or animal subject for treating or reducing the risk of a disease or condition in the subject.
  • 24. The method or use of paragraph 23, wherein the particles are capable of infecting target host cells in the subject and transducing the cells with the DNA, wherein the Cas and crRNAs (or guide RNAs, gRNAs) encoded by the DNA are expressed in the cells, the crRNAs or (gRNAs) being operable to guide the Cas to a target nucleotide sequence (optionally a chromosomal sequence) comprised by the cells, wherein the Cas cuts the target sequences in the cells, thereby killing host cells and treating or reducing the risk of the disease or condition.
  • 25. The method or use of paragraph 24, wherein the host cells are bacterial or archaeal cells, optionally, the host cells are C dificile, P aeruginosa, K pneumoniae (eg, carbapenem-resistant Klebsiella pneumoniae or Extended-Spectrum Beta-Lactamase (ESBL)-producing K pneumoniae), E coli (eg, ESBL-producing E. coli, or E. coli ST131-025b:H4), H pylori, S pneumoniae or S aureus cells.
  • 26. The method or use of any preceding paragraph, wherein each DNA is comprised by a high copy number plasmid or phagemid.
  • 27. The method or use of any preceding paragraph, wherein the DNA construct comprises one or more nucleotide sequences for producing crRNAs or gRNAs that are operable for Cas nuclease targeting in target host cells.


Paragraphs & Generally Applicable Features:


The invention provides the following Paragraphs, which are supported by the Examples below. Any features of the Concepts are combinable with any features of the Embodiments. Any features of the Concepts are combinable with any features of the Embodiments. Any features of the Paragraphs are combinable with any features of the Embodiments.


Any cell herein (eg, a production strain cell or target host cell) may be a bacterial cell, archaeal cell, algal cell, fungal cell, protozoan cell, invertebrate cell, vertebrate cell, fish cell, bird cell, mammal cell, companion animal cell, dog cell, cat cell, horse cell, mouse cell, rat cell, rabbit cell, eukaryotic cell, prokaryotic cell, human cell, animal cell, rodent cell, insect cell or plant cell. Preferably, the cell is a bacterial cell. Alternatively, the cell is a human cell. Optionally, the production strain cell(s) and target host cell(s) are of the same phylum, order, family, genus, species or strain.

  • 1. A nucleic acid vector for introduction into a host cell, the vector comprising a first nucleotide sequence encoding a Type I Cas3, wherein the sequence is under the control of a promoter comprised by the vector for expression of the Cas3 in the cell.


In an example, the vector is a DNA vector, eg, ssDNA vector or dsDNA vector.

  • 2. The vector of paragraph 1, wherein the vector comprises a second nucleotide sequence encoding one or more Cascade proteins, wherein the first and second sequences are under the control of one or more promoters comprised by the vector for expression of the proteins in the cell.
  • 3. The vector of paragraph 2, wherein the Cascade protein(s) are cognate with the Cas3.


In an example, the Cas3 is cognate with Cascade proteins encoded by the host cell and/or encoded by a second operon. Optionally, the second operon is comprised by the vector. Optionally, the second operon is comprised by a second vector that is capable of introducing the second operon into the host cell, whereby the Cas3 and Cascade proteins are expressed from the operons in the host cell and are operable with crRNA or gRNA to target the Cas to a host cell target sequence, wherein the Cas3 is capable of modifying the target sequence.

  • 4. The vector of paragraph 2 or 3, wherein the vector comprises an operon for expression in the cell of the Cas3 and Cascade proteins from a Cas module, the module comprising the nucleotide sequences encoding the Cas3 and Cascade proteins, and the operon comprising the Cas module under the control of a promoter for controlling the expression of both the Cas3 and Cascade proteins.


The term “operon” is known to the skilled person such as relating to a functioning unit of DNA containing at least expressible 2 nucleotide sequences respectively encoding for an expression product (eg, a respective translatable mRNA), wherein the sequences are under common promoter control.

  • 5. The vector of paragraph 4, wherein the first sequence is between the promoter and the second sequence in the operon.
  • 6. The vector of paragraph 4 or 5, wherein the operon comprises no Cas-encoding nucleotide sequences between the promoter and the first nucleotide sequence.


Optionally, the Cas3 is a Cas3 encoded by a CRISPR/Cas locus of a first bacterial or archaeal species, wherein in the locus the Cas3-encoding sequence is 3′ of Cascade protein-encoding sequences (ie, the latter are between the Cas3 and the 5′-most promoter of the locus).


Optionally, the Cas3 is a ygcB protein (eg, wherein the production strain cell and/or host target cell is an E coli).


Optionally, the Cascade proteins comprise or consist of


cas5 (casD, csy2)


cas6 (cas6f, cse3, casE)


cas7 (csc2, csy3, cse4, casC)


cas8 (casA, cas8a1, cas8b1, cas8c, cas10d, cas8e, cse1, cas8f, csy1).


Optionally herein the promoter and the Cas3-encoding sequence are spaced no more than 150, 100, 50, 40, 30, 20 or 10 bp apart, eg, from 30-45, or 30-40, or 39 or around 39 bp apart.


Optionally herein a ribosome binding site and the Cas3-encoding sequence are spaced no more than 20, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 4 or 3 bp apart, eg, from 10-5, 6 or around 6 bp apart.

  • 7. The vector of any one of paragraphs 4 to 6, wherein the operon comprises (in 5′ to 3′ direction) the promoter, the first sequence and the second sequence.
  • 8. The vector of any preceding paragraph, wherein each promoter is a constitutive promoter.
  • 9. The vector of any one of paragraphs 1 to 7, wherein the promoter is repressible (optionally repressible by a tetracycline repressor or lac repressor).
  • 10. The vector of any one of paragraphs 1 to 7, wherein the promoter is inducible.
  • 11. The vector of any preceding paragraph, wherein the first sequence is under the control of a weak promoter.
  • 12. The vector of any one of paragraphs 1 to 7, wherein the first sequence is under the control of a medium strength promoter.
  • 13. The vector of any one of paragraphs 1 to 7, wherein the first sequence is under the control of a strong promoter.


In an example, the promoter is in combination with a Shine-Dalgarno sequence comprising the sequence 5′-aaagaggagaaa-3′ (SEQ ID NO: 5) or a ribosome binding site homologue thereof.

  • 14. The vector of any one of paragraphs 1 to 7, wherein the first sequence is under the control of a promoter that has an Anderson Score (AS) of AS>0.5.


See Table 2 for more information on Anderson Scores in relation to promoters.

  • 15. The vector of any one of paragraphs 1 to 7, wherein the first sequence is under the control of a promoter that has an Anderson Score (AS) of 0.5>AS>0.1.
  • 16. The vector of any one of paragraphs 1 to 7, wherein the first sequence is under the control of a promoter that has an Anderson Score (AS) of <0.1.
  • 17. The vector of any one of paragraphs 1 to 7, wherein the first sequence (and optionally the second sequence) is under the control of a promoter and translation initiation site (TIS) combination that is capable of producing expression of green fluorescent protein (GFP) from a first expression operating unit (EOU) in E. coli strain BW25113 cells with a fluorescence of from 0.5 to 4 times the fluorescence produced in E. coli strain BW25113 cells using a second EOU comprising a P10 promoter (SEQ ID NO: 1) combined with a BCD14 TIS (SEQ ID NO: 2), wherein the EOUs differ only in their promoter and TIS combinations, wherein each EOU comprises (in 5′ to 3′ direction) an upstream initiator, the respective promoter, the respective TIS, a nucleotide sequence encoding GFP, a 3′ UTR, a transcription terminator and a downstream insulator.
  • 18. The vector of paragraph 17, wherein fluorescence using the first EOU is 0.5 to 2 times the fluorescence using the second EOU.


For example, fluorescence using the first EOU is 0.5 to X times the fluorescence using the second EOU, wherein X is from 3.0 to 1.0, eg, 3, 2.5, 2, 1.5 or 1, wherein fluorescence is determined using excitation at 481 nm and emission at 507 nm. Optionally, E coli cultures at OD600 of 0.3-0.5 in the exponential growth phase are used.


For example, the upstream insulator, the nucleotide sequence encoding GFP, 3′ UTR, transcription terminator and downstream insulator of each EOU are as disclosed in Mutalik et al (2013). For example, the upstream insulator, the nucleotide sequence encoding GFP, 3′ UTR, transcription terminator and downstream insulator of each EOU are corresponding sequences of SEQ ID NO: 4. For example, the E coli is E. coli BW25113 is grown in MOPS EZ Rich Medium (Teknova) supplemented with 50 μg/ml kanamycin (kan) at 37° C., shaken at 900 r.p.m. For example, each EOUs is comprised by a medium copy plasmid, eg, a plasmid derived from pFAB217 comprising a p15A replication origin and a kan resistance gene.

  • 19. The vector of any preceding paragraph, wherein the vector comprises an origin of replication that is operable in the host cell.
  • 20. The vector of any preceding paragraph, wherein the vector comprises an origin of replication that is operable in a bacterial cell of a vector production strain, wherein the Cas3 is not operable in the production strain cell to target and cut a chromosomal sequence thereof.


An example of a production strain cell is an E coli cell. A production strain cell is a cell that is used to amplify DNA encoding Cas (and optionally other components of a CRISPR/Cas system). Usefully, the strain may package the amplified DNA into transduction particles that are may be isolated to produce a composition that can be contacted with a population of target host cells (eg, bacterial, archaeal, prokaryotic, eukaryotic, human, animal, mammal, rodent, mouse, rat, rabbit, Xenopus, fish, bird, amphibian, insect, plant, amoeba or algae cells) wherein the DNA is introduced into the cells for expression of the Cas (and optional other CRISPR/Cas system components), wherein the Cas is guided to a protospacer target sequence in the host cells and modifies (eg, cuts) the sequence. In another example, the amplified DNA isolated from a population of production strain cells and is combined with a delivery vehicle (eg, a carrier bacterium, nanoparticle or liposome), wherein the delivery vehicle can be contacted with a population of target host cells (eg, bacterial, archaeal, prokaryotic, eukaryotic, human, animal, mammal, rodent, mouse, rat, rabbit, Xenopus, fish, bird, amphibian, insect, plant, amoeba or algae cells) wherein the DNA is introduced into the cells for expression of the Cas (and optional other CRISPR/Cas system components), wherein the Cas is guided to a protospacer target sequence in the host cells and modifies (eg, cuts) the sequence.

  • 21. The vector of paragraph 20, wherein the first sequence is under the control of a promoter that is capable of controlling expression of the Cas3 at a level that is not toxic to the production strain cell.


In an example, substantially no production strain cells are killed when the Cas3-encoding sequence is amplified therein. In another example, no more than 40, 30, 20, 10, 5, 4, 3, 2, or 1% of production strain cells are killed when the Cas3-encoding sequence is amplified therein. For example this is in a 1, 2, 3, 4, 5, 6, 7, 8 9 10, 12 or 24 hour period of culturing the cells.

  • 22. The vector of paragraph 20, wherein the first sequence is under the control of a promoter that controls expression of the Cas3 in the production strain cell such that the cell is capable of growth and propagation sufficient to produce at least 1000 copies of the vector.


For example this is in a 1, 2, 3, 4, 5, 6, 7, 8 9 10, 12 or 24 hour period of culturing the cells. For example, at least 104, 105, 106, 107, 108, 109, 1010, 1011, 1012, 1013, 1014, 1015, 1016, 1017 or 1018 copies of the vector are produced per 103, 104, 105, 106, 107, 108, 109, 1010, 1011, 1012, 1013, 1014, 1015, 1016, 1017 production strain cells respectively.

  • 23. The vector of any one of paragraphs 20 to 22, wherein the cell is capable of at least 2 or 3 logs of expansion when the vector is comprised therein.


For example, this is in a 1, 2, 3, 4, 5, 6, 7, 8 9 10, 12 or 24 hour period of culturing the cells.

  • 24. The vector of any preceding paragraph, wherein the vector is a high copy number vector.
  • 25. The vector of any preceding paragraph, wherein the first nucleotide sequence or operon is comprised by a mobile genetic element.


Suitable mobile genetic elements, eg, transposons, are disclosed in WO2016177682 and US20170246221, the disclosures of which are explicitly incorporated herein for possible use in the invention and for providing one or more features for the claims herein.

  • 26. The vector of any preceding paragraph, wherein the vector is devoid of a Cas adaption module. For example, the vector is devoid of nucleotide sequences encoding a Cas1, Cas2 and/or Cas4.
  • 27. The vector of any preceding paragraph, wherein the vector is devoid of nucleotide sequence encoding one, more or all of a Cas1, Cas2, Cas4, Cas6 (optionally Cas6f), Cas7 and Cas 8 (optionally Cas8f).
  • 28. The vector of any preceding paragraph, wherein the vector is devoid of a sequence encoding a Cas6 (optionally a Cas6f).
  • 29. The vector of any one of paragraphs 1 to 27, wherein the module encodes a Cas6 (optionally a Cas6f).
  • 30. The vector of any preceding paragraph, wherein the vector comprises (optionally in 5′ to 3′ direction) nucleotide sequence encoding one, more or all of Cas11, Cas7 and Cas8a1.
  • 31. The vector of paragraph 30, wherein the vector comprises nucleotide sequence encoding Cas3′ and/or Cas3″ (optionally wherein the nucleotide sequences encoding the Cas3′ and/or Cas3″ are between the promoter and the sequence(s) recited in paragraph 30).


In one embodiment, the vector comprises nucleotide sequences (in 5′ to 3′ direction) that encode a Cas3 (eg, Cas3′ and/or Cas3″), Cas11, Cas7 and Cas8a1. Optionally, a nucleotide sequence encoding Cas6 is between the Cas3 sequence(s) and the Cas11 sequence. Optionally, the vector comprises a Type IA CRISPR array or one or more nucleotide sequences encoding single guide RNA(s) (gRNA(s)), wherein the array and each gRNA comprises repeat sequence that is cognate with the Cas3. Thus, the array is operable in a host cell when the vector has been introduced into the cell for production of guide RNAs, wherein the guide RNAs are operable with the Cas and Cascade proteins to target and modify (eg, cut) a target nucleotide sequence in the host cell, optionally thereby killing the host cell. Similarly, the single guide RNAs encoded by the vector in one embodiment are operable with the Cas and Cascade proteins to target and modify (eg, cut) a target nucleotide sequence in the host cell, optionally thereby killing the host cell.

  • 32. The vector of paragraph 30 or 31, wherein the host cell comprises a Type IA CRISPR array that is cognate with the Cas3.
  • 33. The vector of paragraph 30 or 31, wherein the host cell comprises an endogenous Type IB, C, U, D, E or F CRISPR/Cas system.
  • 34. The vector of any one of paragraphs 1 to 29, wherein the vector comprises (optionally in 5′ to 3′ direction) nucleotide sequence encoding one, more or all of Cas8b1, Cas7 and Cas5.
  • 35. The vector of paragraph 34, wherein the vector comprises a nucleotide sequence encoding Cas3 between the promoter and the sequence(s) recited in paragraph 34.


In one embodiment, the vector comprises nucleotide sequences (in 5′ to 3′ direction) that encode a Cas3, Cas8b1, Cas7 and Cas5. Optionally, a nucleotide sequence encoding Cas6 is between the Cas3 sequence(s) and the Cas8b1 sequence. Optionally, the vector comprises a Type IB CRISPR array or one or more nucleotide sequences encoding single guide RNA(s) (gRNA(s)), wherein the array and each gRNA comprises repeat sequence that is cognate with the Cas3. Thus, the array is operable in a host cell when the vector has been introduced into the cell for production of guide RNAs, wherein the guide RNAs are operable with the Cas and Cascade proteins to target and modify (eg, cut) a target nucleotide sequence in the host cell, optionally thereby killing the host cell. Similarly, the single guide RNAs encoded by the vector in one embodiment are operable with the Cas and Cascade proteins to target and modify (eg, cut) a target nucleotide sequence in the host cell, optionally thereby killing the host cell.

  • 36. The vector of paragraph 34 or 35, wherein the host cell comprises a Type IB CRISPR array that is cognate with the Cas3.
  • 37. The vector of paragraph 34 or 35, wherein the host cell comprises an endogenous Type IA, C, U, D, E or F CRISPR/Cas system.
  • 38. The vector of any one of paragraphs 1 to 29, wherein the vector comprises (optionally in 5′ to 3′ direction) nucleotide sequence encoding one, more or all of Cas5, Cas8c and Cas7.
  • 39. The vector of paragraph 38, wherein the vector comprises a nucleotide sequence encoding Cas3 between the promoter and the sequence(s) recited in paragraph 38.


In one embodiment, the vector comprises nucleotide sequences (in 5′ to 3′ direction) that encode a Cas3, Cas5, Cas8c and Cas7. Optionally, a nucleotide sequence encoding Cas6 is between the Cas3 sequence(s) and the Cas5 sequence. Optionally, the vector comprises a Type IC CRISPR array or one or more nucleotide sequences encoding single guide RNA(s) (gRNA(s)), wherein the array and each gRNA comprises repeat sequence that is cognate with the Cas3. Thus, the array is operable in a host cell when the vector has been introduced into the cell for production of guide RNAs, wherein the guide RNAs are operable with the Cas and Cascade proteins to target and modify (eg, cut) a target nucleotide sequence in the host cell, optionally thereby killing the host cell. Similarly, the single guide RNAs encoded by the vector in one embodiment are operable with the Cas and Cascade proteins to target and modify (eg, cut) a target nucleotide sequence in the host cell, optionally thereby killing the host cell.

  • 40. The vector of paragraph 38 or 39, wherein the host cell comprises a Type IC CRISPR array that is cognate with the Cas3.
  • 41. The vector of paragraph 38 or 39, wherein the host cell comprises an endogenous Type IA, B, U, D, E or F CRISPR/Cas system.
  • 42. The vector of any one of paragraphs 1 to 29, wherein the vector comprises (optionally in 5′ to 3′ direction) nucleotide sequence encoding one, more or all of Cas8U2, Cas7, Cas5 and Cas6.
  • 43. The vector of paragraph 42, wherein the vector comprises a nucleotide sequence encoding Cas3 between the promoter and the sequence(s) recited in paragraph 42.


In one embodiment, the vector comprises nucleotide sequences (in 5′ to 3′ direction) that encode a Cas3, Cas8U2, Cas7, Cas5 and Cas6. Optionally, a nucleotide sequence encoding Cas6 is between the Cas3 sequence(s) and the Cas8U2 sequence. Optionally, the vector comprises a Type IU CRISPR array or one or more nucleotide sequences encoding single guide RNA(s) (gRNA(s)), wherein the array and each gRNA comprises repeat sequence that is cognate with the Cas3. Thus, the array is operable in a host cell when the vector has been introduced into the cell for production of guide RNAs, wherein the guide RNAs are operable with the Cas and Cascade proteins to target and modify (eg, cut) a target nucleotide sequence in the host cell, optionally thereby killing the host cell. Similarly, the single guide RNAs encoded by the vector in one embodiment are operable with the Cas and Cascade proteins to target and modify (eg, cut) a target nucleotide sequence in the host cell, optionally thereby killing the host cell.

  • 44. The vector of paragraph 42 or 43, wherein the host cell comprises a Type IU CRISPR array that is cognate with the Cas3.
  • 45. The vector of paragraph 42 or 43, wherein the host cell comprises an endogenous Type IA, B, C, D, E or F CRISPR/Cas system.
  • 46. The vector of any one of paragraphs 1 to 29, wherein the vector comprises (optionally in 5′ to 3′ direction) nucleotide sequence encoding one, more or all of Cas10d, Cas7 and Cas5.
  • 47. The vector of paragraph 46, wherein the vector comprises a nucleotide sequence encoding Cas3′ and/or Cas3″ (optionally wherein the nucleotide sequences encoding the Cas3′ and/or Cas3″ are between the promoter and the sequence(s) recited in paragraph 46).


In one embodiment, the vector comprises nucleotide sequences (in 5′ to 3′ direction) that encode a Cas3, Cas10d, Cas7 and Cas5. Optionally, a nucleotide sequence encoding Cas6 is between the Cas3 sequence(s) and the Cas10d sequence. Optionally, the vector comprises a Type ID CRISPR array or one or more nucleotide sequences encoding single guide RNA(s) (gRNA(s)), wherein the array and each gRNA comprises repeat sequence that is cognate with the Cas3. Thus, the array is operable in a host cell when the vector has been introduced into the cell for production of guide RNAs, wherein the guide RNAs are operable with the Cas and Cascade proteins to target and modify (eg, cut) a target nucleotide sequence in the host cell, optionally thereby killing the host cell. Similarly, the single guide RNAs encoded by the vector in one embodiment are operable with the Cas and Cascade proteins to target and modify (eg, cut) a target nucleotide sequence in the host cell, optionally thereby killing the host cell.

  • 48. The vector of paragraph 46 or 47, wherein the host cell comprises a Type ID CRISPR array that is cognate with the Cas3.
  • 49. The vector of paragraph 46 or 47, wherein the host cell comprises an endogenous Type IA, B, C, U, E or F CRISPR/Cas system.
  • 50. The vector of any one of paragraphs 1 to 29, wherein the vector comprises (optionally in 5′ to 3′ direction) nucleotide sequence encoding one, more or all of Cas8e, Cas11, Cas7, Cas5 and Cas6.
  • 51. The vector of paragraph 50, wherein the vector comprises a nucleotide sequence encoding Cas3 between the promoter and the sequence(s) recited in paragraph 50.


In one embodiment, the vector comprises nucleotide sequences (in 5′ to 3′ direction) that encode a Cas3, Cas8e, Cas11, Cas7, Cas5 and Cas6. Optionally, a nucleotide sequence encoding Cas6 is between the Cas3 sequence(s) and the Cas11 sequence. Optionally, the vector comprises a Type IE CRISPR array or one or more nucleotide sequences encoding single guide RNA(s) (gRNA(s)), wherein the array and each gRNA comprises repeat sequence that is cognate with the Cas3. Thus, the array is operable in a host cell when the vector has been introduced into the cell for production of guide RNAs, wherein the guide RNAs are operable with the Cas and Cascade proteins to target and modify (eg, cut) a target nucleotide sequence in the host cell, optionally thereby killing the host cell. Similarly, the single guide RNAs encoded by the vector in one embodiment are operable with the Cas and Cascade proteins to target and modify (eg, cut) a target nucleotide sequence in the host cell, optionally thereby killing the host cell.

  • 52. The vector of paragraph 50 or 51, wherein the host cell comprises a Type IE CRISPR array that is cognate with the Cas3.
  • 53. The vector of paragraph 50 or 51, wherein the host cell comprises an endogenous Type IA, B, C, D, U or F CRISPR/Cas system.
  • 54. The vector of any one of paragraphs 1 to 29, wherein the vector comprises (optionally in 5′ to 3′ direction) nucleotide sequence encoding one, more or all of Cas8f, Cas5, Cas7 and Cas6f.
  • 55. The vector of paragraph 54, wherein the vector comprises a nucleotide sequence encoding Cas3 between the promoter and the sequence(s) recited in paragraph 54, wherein the vector is devoid of nucleotide sequence encoding further Cas between the promoter and the sequence encoding the Cas3.


In one embodiment, the vector comprises nucleotide sequences (in 5′ to 3′ direction) that encode a Cas3, Cas8f, Cas5, Cas7 and Cas6f. Optionally, a nucleotide sequence encoding Cas6 is between the Cas3 sequence(s) and the Cas8f sequence. Optionally, the vector comprises a Type IF CRISPR array or one or more nucleotide sequences encoding single guide RNA(s) (gRNA(s)), wherein the array and each gRNA comprises repeat sequence that is cognate with the Cas3. Thus, the array is operable in a host cell when the vector has been introduced into the cell for production of guide RNAs, wherein the guide RNAs are operable with the Cas and Cascade proteins to target and modify (eg, cut) a target nucleotide sequence in the host cell, optionally thereby killing the host cell. Similarly, the single guide RNAs encoded by the vector in one embodiment are operable with the Cas and Cascade proteins to target and modify (eg, cut) a target nucleotide sequence in the host cell, optionally thereby killing the host cell.

  • 56. The vector of paragraph 54 or 55, wherein the host cell comprises a Type IF CRISPR array that is cognate with the Cas3.
  • 57. The vector of paragraph 54 or 55, wherein the host cell comprises an endogenous Type IA, B, C, D, U or E CRISPR/Cas system.
  • 58. The vector of any one of paragraphs 1 to 29, wherein the Cas and Cascade are Type IA Cas and Cascade proteins.
  • 59. The vector of any one of paragraphs 1 to 29, wherein the Cas and Cascade are Type IB Cas and Cascade proteins.
  • 60. The vector of any one of paragraphs 1 to 29, wherein the Cas and Cascade are Type IC Cas and Cascade proteins.
  • 61. The vector of any one of paragraphs 1 to 29, wherein the Cas and Cascade are Type ID Cas and Cascade proteins.
  • 62. The vector of any one of paragraphs 1 to 29, wherein the Cas and Cascade are Type IE Cas and Cascade proteins.
  • 63. The vector of any one of paragraphs 1 to 29, wherein the Cas and Cascade are Type IF Cas and Cascade proteins.
  • 64. The vector of any one of paragraphs 1 to 29, wherein the Cas and Cascade are Type IU Cas and Cascade proteins.
  • 65. The vector of any one of paragraphs 1 to 29, wherein the Cas and Cascade are E coli (optionally Type IE or IF) Cas and Cascade proteins, optionally wherein the E coli is ESBL-producing E. coli or E. coli ST131-025b:H4.
  • 66. The vector of any one of paragraphs 1 to 29, wherein the Cas and Cascade are Clostridium (eg, C dificile) Cas and Cascade proteins, optionally C dificile resistant to one or more antibiotics selected from aminoglycosides, lincomycin, tetracyclines, erythromycin, clindamycin, penicillins, cephalosporins and fluoroquinolones.
  • 67. The vector of any one of paragraphs 1 to 29, wherein the Cas and Cascade are Pseudomonas aeruginosa Cas and Cascade proteins, optionally P aeruginosa resistant to one or more antibiotics selected from carbapenems, aminoglycosides, cefepime, ceftazidime, fluoroquinolones, piperacillin and tazobactam.
  • 68. The vector of any one of paragraphs 1 to 29, wherein the Cas and Cascade are Klebsiella pneumoniae (eg, carbapenem-resistant Klebsiella pneumoniae or Extended-Spectrum Beta-Lactamase (ESBL)-producing K pneumoniae) Cas and Cascade proteins.
  • 69. The vector of any one of paragraphs 1 to 29, wherein the Cas and Cascade are E coli, C difficile, P aeruginosa, K pneumoniae, P furiosus or B halodurans Cas and Cascade proteins.
  • 70. The vector of any preceding paragraph, wherein the Cas3 is a Cas3 of a CRISPR/Cas locus of a first bacterial or archaeal species, wherein the distance between the Cas3-encoding sequence of the locus and its cognate promoter is further than the distance between the Cas3-encoding sequence and the respective promoter comprised by the vector.


The cognate promoter here is the one that controls expression of Cas3 in the wild-type locus.

  • 71. The vector of any preceding paragraph, wherein the distance between the promoter and the Cas3-encoding sequence and/or Cascade protein-encoding sequence(s) is shorter than in a corresponding wild-type Type I locus.


A corresponding locus is a wild-type locus of a bacterial or archaeal species or strain that comprises an endogenous CRISPR/Cas system encoding the Cas3 and/or Cascade proteins of the type that are also encoded by the vector. Thus, when the vector comprises an operon, the operon may comprise Cas3- and Cascade-encoding nucleotide sequences that are not in a natural configuration.

  • 72. The vector of any preceding paragraph, wherein the vector comprises (i) a CRISPR array for producing crRNAs in the host cell and/or (ii) one or more nucleotide sequences encoding one or more single guide RNAs (gRNAs), wherein the crRNAs or gRNAs are cognate to the Cas3 (and optionally cognate to the Cascade proteins).
  • 73. The vector of paragraph 72 when dependent from paragraph 4, wherein the array or gRNA-encoding sequence(s) are comprised by the operon and under the control of the promoter.
  • 74. The vector of paragraph 72, wherein the array or gRNA-encoding sequence(s) are under the control of a promoter that is different from the promoter that controls the expression of the Cas3.
  • 75. The vector of any one of paragraphs 72 to 74, wherein one or more of the crRNAs or gRNAs comprises a spacer sequence that is capable of hybridising to a target nucleotide sequence of the host cell, wherein the target sequence is adjacent a PAM, the PAM being cognate to the Cas3.


Thus, the spacer hybridises to the protospacer to guide the Cas3 to the protospacer. Optionally, the Cas3 cuts the protospacer, eg, using exo- and/or endonuclease activity of the Cas3. Optionally, the Cas3 removes a plurality (eg, at least 2, 3,4, 5, 6, 7, 8, 9 or 10) nucleotides from the protospacer.

  • 76. The vector of paragraph 75, wherein the target sequence is a chromosomal sequence of the host cell.
  • 77. The vector of paragraph 75 or 76, wherein the Cas3 is operable to cut the target sequence.
  • 78. The vector of any preceding paragraph, wherein the vector is a plasmid or phagemid.
  • 79. A delivery vehicle comprising the vector of any preceding paragraph, wherein the delivery vehicle is capable of delivering the vector into the host cell.
  • 80. The vehicle of paragraph 79, wherein the delivery vehicle is a phage, non-replicative transduction particle, nanoparticle carrier, bacterium or liposome.


The phage or particles comprise phage coat proteins encapsidating DNA, wherein the DNA comprises the vector. Suitable examples of phage and particles are disclosed in U.S. Ser. No. 15/985,658 (and its equivalent publication by USPTO) the disclosures of which are incorporated herein by reference for possible use in the invention and for providing one or more features that may be included in the claims herein. Phage or particle is capable of infecting the cell, thereby introducing the vector into the cell.

  • 81. The vector or vehicle of any preceding paragraph, wherein the host cell is a bacterial or archaeal cell, optionally, the host cell is a C dificile, P aeruginosa, K pneumoniae (eg, carbapenem-resistant Klebsiella pneumoniae or Extended-Spectrum Beta-Lactamase (ESBL)-producing K pneumoniae), E coli (eg, ESBL-producing E. coli, or E. coli ST131-025b:H4), H pylori, S pneumoniae or S aureus cell.
  • 82. The vector or vehicle of any preceding paragraph for administration to a human or animal subject for treating or reducing the risk of a disease or condition in the subject.
  • 83. The vector or vehicle of paragraph 82, wherein the disease or condition is an infection of the subject with host cells (eg, bacterial cells), or wherein the disease or condition is mediated by host cells (eg, bacterial cells).
  • 84. A pharmaceutical composition comprising the vector or vehicle of any preceding paragraph and a pharmaceutically acceptable diluent, excipient or carrier.
  • 85. A method of amplifying copies of a DNA encoding a functional Cas protein (optionally a Cas nuclease) in a bacterial or archaeal production strain of cells, the method comprising
    • (a) Providing production strain cells, each cell comprising a copy of said DNA, wherein each DNA comprises a nucleotide sequence encoding said Cas, wherein the nucleotide sequence is under the control of a promoter for controlling the expression of the Cas in the production strain cell, the DNA comprising an origin of replication that is operable in the cell for replication of the DNA;
    • (b) Culturing the cells to allow replication of the DNA, whereby the DNA is amplified; and
    • (c) Optionally isolating copies of the DNA,
  • 86. The method of paragraph 85, wherein the promoter is a constitutive promoter.
  • 87. The method of paragraph 85, wherein the promoter is repressible (optionally repressible by a tetracycline repressor or a lac repressor).
  • 88. The method of paragraph 85, wherein the promoter is inducible.
  • 89. The method of any one of paragraphs 85 to 88, wherein the promoter is a medium strength promoter.
  • 90. The method of any one of paragraphs 85 to 89, wherein the promoter has an Anderson Score (AS) of 0.5>AS>0.1.
  • 91. The method of any one of paragraphs 85 to 90, wherein the nucleotide sequence encoding said Cas is under the control of a promoter and translation initiation site (TIS) combination that is capable of producing expression of green fluorescent protein (GFP) from a first expression operating unit (EOU) in E. coli strain BW25113 cells with a fluorescence of from 0.5 to 4 times the fluorescence produced in E. coli strain BW25113 cells using a second EOU comprising a P10 promoter (SEQ ID NO: 1) combined with a BCD14 TIS (SEQ ID NO: 2), wherein the EOUs differ only in their promoter and TIS combinations, wherein each EOU comprises (in 5′ to 3′ direction) an upstream initiator, the respective promoter, the respective TIS, a nucleotide sequence encoding GFP, a 3′ UTR, a transcription terminator and a downstream insulator.
  • 92. The method of paragraph 91, wherein fluorescence using the first EOU is 0.5 to 2 times the fluorescence using the second EOU.
  • 93. The method of any one of paragraphs 85 to 92, wherein the nuclease is Cas3 and optionally the DNA or cell encodes cognate Cascade proteins and/or one or more crRNAs that are operable for Cas nuclease targeting.


For example, the targeting is targeting of the Cas to a protospacer sequence comprised by a host cell chromosome or an episome thereof. In another example the targeting is in a recombineering method and the Cas is targeted to a protospacer sequence of a DNA that has been introduced into or amplified in the host cell. In an example of such recombineering, the host cell is an E coli cell.

  • 94. The method of any one of paragraphs 85 to 92, wherein the Cas is a Cas9.
  • 95. The method of any one of paragraphs 85 to 92, wherein the Cas is a Type IIIA csm protein or a Type IIIB cmr protein.
  • 96. The method of any one of paragraphs 85 to 92, wherein the Cas is a Csf1.
  • 97. The method of any one of paragraphs 85 to 92, wherein the Cas is a Cpf1.
  • 98. The method of any one of paragraphs 85 to 92, wherein the Cas is a Cas13 (optionally Cas13a or Cas13b).
  • 99. The method of any one of paragraphs 85 to 92, wherein the Cas is selected from a Cas3, Cas8a, Cas5, Cas8b, Cas8c, Cas10d, Cse1, Cse2, Csy1, Csy2, Csy3, GSU0054, Cas10, Csm2, Cmr5, Cas10, Csx11, Csx10, Csf1, Cas9, Csn2, Cas4, Cpf1, C2c1, C2c3, Cas13a, Cas13b and Cas13c.
  • 100. The method of any one of paragraphs 85 to 99, wherein the production strain cells comprise a helper phage genome that is inducible to produce phage coat proteins in the cells, wherein the method further comprises inducing production of the phage proteins and causing packaging of the amplified DNA into phage particles or non-self-replicative transduction particles, and further isolating the phage or transduction particles and optionally formulating the particles into a pharmaceutical composition for administration to a human or animal subject for treating or reducing the risk of a disease or condition in the subject.
  • 101. The method of paragraph 100, wherein the particles are capable of infecting target host cells in the subject and transducing the cells with the DNA, wherein the Cas and crRNAs (or gRNAs) encoded by the DNA are expressed in the cells, the crRNAs or (gRNAs) being operable to guide the Cas to a target nucleotide sequence (optionally a chromosomal sequence) comprised by the cells, wherein the Cas cuts the target sequences in the cells, thereby killing host cells and treating or reducing the risk of the disease or condition.
  • 102. The method of paragraph 101, wherein the host cells are bacterial or archaeal cells, optionally, the host cells are C dificile, P aeruginosa, K pneumoniae (eg, carbapenem-resistant Klebsiella pneumoniae or Extended-Spectrum Beta-Lactamase (ESBL)-producing K pneumoniae), E coli (eg, ESBL-producing E. coli, or E. coli ST131-025b:H4), H pylori, S pneumoniae or S aureus cells.
  • 103. The method of any one of paragraphs 85 to 102, wherein each DNA is comprised by a high copy number vector, optionally a high copy number plasmid (an optionally the promoter is a constitutive promoter).
  • 104. The method of any one of paragraphs 85 to 103, wherein each DNA is comprised by a vector or vehicle according to any one of paragraphs 1 to 83.
  • 105. Use of an attenuated strength promoter in a DNA construct comprising a nucleotide sequence encoding a functional Cas protein (optionally a Cas nuclease) that is under the control of the promoter, in a method of amplifying copies of the DNA in a population of bacterial or archaeal production strain cells, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, for enhancing the yield of amplified DNA produced by the production host cells.


Thus, said enhancing may be relative to the yield produced using a strong promoter, eg, a strong constitutive promoter (for example a promoter having an Anderson Score (AS) of AS>0.5). In another example, the strong promoter is a promoter comprised by a promoter and translation initiation site (TIS) combination that is capable of producing expression of green fluorescent protein (GFP) from a first expression operating unit (EOU) in E. coli strain BW25113 cells with a fluorescence of >4 times the fluorescence produced in E. coli strain BW25113 cells using a second EOU comprising a P10 promoter (SEQ ID NO: 1) combined with a BCD14 TIS (SEQ ID NO: 2), wherein the EOUs differ only in their promoter and TIS combinations, wherein each EOU comprises (in 5′ to 3′ direction) an upstream initiator, the respective promoter, the respective TIS, a nucleotide sequence encoding GFP, a 3′ UTR, a transcription terminator and a downstream insulator.

  • 106. The use of paragraph 105, wherein the use is for enhancing said yield by
    • (d) reducing toxicity of the Cas in the production strain;
    • (e) reducing mutation of the DNA (optionally the Cas-encoding sequence) in the production strain;
    • (f) promoting production cell viability during the amplification of the DNA; and/or
    • (g) reducing the occurrence of Cas cutting of DNA (optionally cutting of production host cell chromosomal DNA or said DNA construct).
  • 107. Use of an attenuated strength promoter in a DNA construct comprising a nucleotide sequence encoding a functional Cas protein (optionally a Cas nuclease) that is under the control of the promoter, in a method of amplifying copies of the DNA in a population of bacterial or archaeal production strain cells, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, for reducing toxicity of the Cas in the production strain.
  • 108. Use of an attenuated strength promoter in a DNA construct comprising a nucleotide sequence encoding a functional Cas protein (optionally a Cas nuclease) that is under the control of the promoter, in a method of amplifying copies of the DNA in a population of bacterial or archaeal production strain cells, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, for reducing mutation of the DNA (optionally the Cas-encoding sequence) in the production strain.
  • 109. Use of an attenuated strength promoter in a DNA construct comprising a nucleotide sequence encoding a functional Cas protein (optionally a Cas nuclease) that is under the control of the promoter, in a method of amplifying copies of the DNA in a population of bacterial or archaeal production strain cells, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, for promoting production cell viability during the amplification of the DNA.
  • 110. Use of an attenuated strength promoter in a DNA construct comprising a nucleotide sequence encoding a functional Cas protein (optionally a Cas nuclease) that is under the control of the promoter, in a method of amplifying copies of the DNA in a population of bacterial or archaeal production strain cells, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, for reducing the occurrence of Cas cutting of DNA.
  • 111. A method for enhancing the yield of amplified copies of a DNA construct in a population of bacterial or archaeal production strain cells, wherein the construct comprises a nucleotide sequence encoding a functional Cas protein (optionally a Cas nuclease) that is under the control of a promoter, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, wherein the promoter is an attenuated strength promoter.
  • 112. A method for reducing toxicity of a functional Cas protein (optionally a Cas nuclease) in a population of bacterial or archaeal production strain cells in a process of amplifying copies of a DNA construct, wherein the construct comprises a nucleotide sequence encoding the Cas and the sequence is under the control of a promoter, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, wherein the promoter is an attenuated strength promoter.
  • 113. A method for reducing mutation of a DNA construct encoding a functional Cas protein (optionally a Cas nuclease) in a population of bacterial or archaeal production strain cells in a process of amplifying copies of the construct, wherein the construct comprises a nucleotide sequence encoding the Cas and the sequence is under the control of a promoter, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, wherein the promoter is an attenuated strength promoter.
  • 114. A method for promoting production cell viability of a population of bacterial or archaeal production strain cells in a process of amplifying copies of a DNA construct comprised by the cells, wherein the construct comprises a nucleotide sequence encoding a functional Cas protein (optionally a Cas nuclease) and the sequence is under the control of a promoter, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, wherein the promoter is an attenuated strength promoter.
  • 115. A method for reducing the occurrence of Cas nuclease cutting of a DNA construct in a population of bacterial or archaeal production strain cells in a process of amplifying copies of the construct, wherein the construct comprises a nucleotide sequence encoding the Cas and the sequence is under the control of a promoter, the method comprising culturing the cells to allow replication of the DNA thereby amplifying the DNA in the cells, wherein the promoter is an attenuated strength promoter.
  • 116. The use of paragraph 108 or 110, or the method of paragraph 113 or 115, wherein the mutation or cutting is mutation or cutting of host cell chromosomal DNA or the construct DNA.
  • 117. The use or method of any one of paragraphs 105 to 116, wherein the promoter is a constitutive promoter.
  • 118. The use or method of any one of paragraphs 105 to 117, wherein the promoter is repressible (optionally repressible by a tetracycline repressor or a lac repressor).


In an example, the promoter is a constitutive promoter and optionally the DNA is comprised by a high copy number plasmid or phagemid.

  • 119. The use or method of any one of paragraphs 105 to 118, wherein the promoter is PLtetO-1, PLlacO-1 or a repressible homologue thereof.


PLlacO-1 is repressed by lac repressor (LacR). PLetO-1 is repressed by tet repressor (TetR).

  • 120. The use or method of any one of paragraphs 105 to 119, wherein the promoter is a medium strength promoter.
  • 121. The use or method of any one of paragraphs 105 to 120, wherein the promoter has an Anderson Score (AS) of 0.5>AS>0.1.
  • 122. The use or method of any one of paragraphs 105 to 121, wherein the nucleotide sequence encoding said Cas is under the control of a promoter and translation initiation site (TIS) combination that is capable of producing expression of green fluorescent protein (GFP) from a first expression operating unit (EOU) in E. coli strain BW25113 cells with a fluorescence of from 0.5 to 4 times the fluorescence produced in E. coli strain BW25113 cells using a second EOU comprising a P10 promoter (SEQ ID NO: 1) combined with a BCD14 TIS (SEQ ID NO: 2), wherein the EOUs differ only in their promoter and TIS combinations, wherein each EOU comprises (in 5′ to 3′ direction) an upstream initiator, the respective promoter, the respective TIS, a nucleotide sequence encoding GFP, a 3′ UTR, a transcription terminator and a downstream insulator.
  • 123. The use or method of paragraph 122, wherein fluorescence using the first EOU is 0.5 to 2 times the fluorescence using the second EOU.
  • 124. The use or method of any one of paragraphs 105 to 123, wherein the nuclease is Cas3 and optionally the DNA construct encodes cognate Cascade proteins.
  • 125. The use or method of any one of paragraphs 105 to 123, wherein the Cas is a Cas9.
  • 126. The use or method of any one of paragraphs 105 to 123, wherein the Cas is a Type IIIA csm protein or a Type IIIB cmr protein.
  • 127. The use or method of any one of paragraphs 105 to 123, wherein the Cas is a Csf1.
  • 128. The use or method of any one of paragraphs 105 to 123, wherein the Cas is a Cpf1.
  • 129. The use or method of any one of paragraphs 105 to 123, wherein the Cas is a Cas13 (optionally Cas13a or Cas13b).
  • 130. The use or method of any one of paragraphs 105 to 123, wherein the Cas is selected from a Cas3, Cas8a, Cas5, Cas8b, Cas8c, Cas10d, Cse1, Cse2, Csy1, Csy2, Csy3, GSU0054, Cas10, Csm2, Cmr5, Cas10, Csx11, Csx10, Csf1, Cas9, Csn2, Cas4, Cpf1, C2c1, C2c3, Cas13a, Cas13b and Cas13c.
  • 131. The use or method of any one of paragraphs 105 to 130, wherein the DNA construct comprises one or more nucleotide sequences for producing crRNAs or gRNAs that are operable for Cas nuclease targeting.
  • 132. The use or method of any one of paragraphs 105 to 131, wherein the production strain cells comprise a helper phage genome that is inducible to produce phage coat proteins in the cells, wherein the method further comprises inducing production of the phage proteins and causing packaging of the amplified DNA into phage particles or non-self-replicative transduction particles, and further isolating the phage or transduction particles and optionally formulating the particles into a pharmaceutical composition for administration to a human or animal subject for treating or reducing the risk of a disease or condition in the subject.
  • 133. The method of paragraph 132, wherein the particles are capable of infecting target host cells in the subject and transducing the cells with the DNA, wherein the Cas and crRNAs (or gRNAs) encoded by the DNA are expressed in the cells, the crRNAs or (gRNAs) being operable to guide the Cas to a target nucleotide sequence (optionally a chromosomal sequence) comprised by the cells, wherein the Cas cuts the target sequences in the cells, thereby killing host cells and treating or reducing the risk of the disease or condition.
  • 134. The method of paragraph 133, wherein the host cells are bacterial or archaeal cells, optionally, the host cells are C dificile, P aeruginosa, K pneumoniae (eg, carbapenem-resistant Klebsiella pneumoniae or Extended-Spectrum Beta-Lactamase (ESBL)-producing K pneumoniae), E coli (eg, ESBL-producing E. coli, or E. coli ST131-025b:H4), H pylori, S pneumoniae or S aureus cells.
  • 135. The use or method of any one of paragraphs 105 to 134, wherein each DNA is comprised by a high copy number vector, optionally a high copy number plasmid (an optionally the promoter is a constitutive promoter).
  • 136. The use or method of any one of paragraphs 105 to 135, wherein each DNA is comprised by a vector according to any one of paragraphs 1 to 78 and 81 to 83.


CLAUSES

The invention provides, by way of example, the following Clauses; the features of these are combinable with any other disclosure herein.

  • 1. A nucleic acid vector for introduction into a host cell, the vector comprising a first nucleotide sequence encoding a Type I Cas3 and a second nucleotide sequence encoding one or more Cascade proteins, wherein the first and second sequences are under the control of one or more promoters comprised by the vector for expression of the proteins in the cell.
  • 2. The vector of Clause 1, wherein the vector comprises an operon for expression in the cell of the Cas3 and Cascade proteins from a Cas module, the module comprising the nucleotide sequences encoding the Cas3 and Cascade proteins, and the operon comprising the Cas module under the control of a promoter for controlling the expression of both the Cas3 and Cascade proteins.
  • 3. The vector of Clause 2, wherein
    • (a) the first sequence is between the promoter and the second sequence in the operon;
    • (b) the operon comprises no Cas-encoding nucleotide sequences between the promoter and the first nucleotide sequence; and/or
    • (c) the operon comprises (in 5′ to 3′ direction) the promoter, the first sequence and the second sequence.
  • 4. The vector of any preceding Clause, wherein each promoter is a constitutive promoter.
  • 5. The vector of any one of Clauses 1 to 3, wherein the promoter is repressible (optionally repressible by a tetracycline repressor or lac repressor).
  • 6. The vector of any one of Clauses 1 to 3, wherein the promoter is inducible.
  • 7. The vector of any preceding Clause, wherein the first sequence is under the control of a medium strength promoter.
  • 8. The vector of any preceding Clause, wherein the first sequence is under the control of a promoter that has an Anderson Score (AS) of 0.5>AS>0.1.
  • 9. The vector of any preceding Clause, wherein the first sequence (and optionally the second sequence) is under the control of a promoter and translation initiation site (TIS) combination that is capable of producing expression of green fluorescent protein (GFP) from a first expression operating unit (EOU) in E. coli strain BW25113 cells with a fluorescence of from 0.5 to 4 times the fluorescence produced in E. coli strain BW25113 cells using a second EOU comprising a P10 promoter (SEQ ID NO: 1) combined with a BCD14 TIS (SEQ ID NO: 2), wherein the EOUs differ only in their promoter and TIS combinations, wherein each EOU comprises (in 5′ to 3′ direction) an upstream initiator, the respective promoter, the respective TIS, a nucleotide sequence encoding GFP, a 3′ UTR, a transcription terminator and a downstream insulator.
  • 10. The vector of Clause 9, wherein fluorescence using the first EOU is 0.5 to 2 times the fluorescence using the second EOU.
  • 11. The vector of any preceding Clause, wherein the vector comprises an origin of replication that is operable in the host cell.
  • 12. The vector of any preceding Clause, wherein the vector comprises an origin of replication that is operable in a bacterial cell of a vector production strain, wherein the Cas3 is not operable in the production strain cell to target and cut a chromosomal sequence thereof.
  • 13. The vector of Clause 12, wherein the first sequence is under the control of a promoter that is capable of controlling expression of the Cas3 at a level that is not toxic to the production strain cell.
  • 14. The vector of any preceding Clause, wherein the vector is a high copy number vector.
  • 15. The vector of any preceding Clause, wherein the first nucleotide sequence or operon is comprised by a mobile genetic element.
  • 16. The vector of any preceding Clause, wherein the vector is devoid of a Cas adaption module.
  • 17. The vector of any preceding Clause, wherein the vector is devoid of nucleotide sequence encoding one, more or all of a Cas1, Cast, Cas4, Cas6, Cas7 and Cas 8.
  • 18. The vector of any preceding Clause, wherein the vector comprises (optionally in 5′ to 3′ direction) nucleotide sequence encoding one, more or all of Cas11, Cas7 and Cas8a1.
  • 19. The vector of Clause 18, wherein the vector comprises nucleotide sequence encoding Cas3′ and/or Cas3″.
  • 20. The vector or Clause 19, wherein the nucleotide sequences encoding the Cas3′ and/or Cas3″ are between the promoter and the sequence(s) recited in Clause 18.
  • 21. The vector of any one of Clauses 18 to 20, wherein the host cell comprises a Type IA CRISPR array that is cognate with the Cas3.
  • 22. The vector of any one of Clauses 18 to 20, wherein the host cell comprises an endogenous Type 1B, C, U, D, E or F CRISPR/Cas system.
  • 23. The vector of any one of Clauses 1 to 17, wherein the vector comprises (optionally in 5′ to 3′ direction) nucleotide sequence encoding one, more or all of Cas8b1, Cas7 and Cas5.
  • 24. The vector of Clause 23, wherein the vector comprises a nucleotide sequence encoding Cas3 between the promoter and the sequence(s) recited in Clause 23.
  • 25. The vector of Clause 23 or 24, wherein the host cell comprises a Type IB CRISPR array that is cognate with the Cas3.
  • 26. The vector of Clause 23 or 24, wherein the host cell comprises an endogenous Type IA, C, U, D, E or F CRISPR/Cas system.
  • 27. The vector of any one of Clauses 1 to 17, wherein the vector comprises (optionally in 5′ to 3′ direction) nucleotide sequence encoding one, more or all of Cas5, Cas8c and Cas7.
  • 28. The vector of Clause 27, wherein the vector comprises a nucleotide sequence encoding Cas3 between the promoter and the sequence(s) recited in Clause 27.
  • 29. The vector of Clause 27 or 28, wherein the host cell comprises a Type IC CRISPR array that is cognate with the Cas3.
  • 30. The vector of Clause 27 or 28, wherein the host cell comprises an endogenous Type IA, B, U, D, E or F CRISPR/Cas system.
  • 31. The vector of any one of Clauses 1 to 17, wherein the vector comprises (optionally in 5′ to 3′ direction) nucleotide sequence encoding one, more or all of Cas8U2, Cas7, Cas5 and Cas6.
  • 32. The vector of Clause 31, wherein the vector comprises a nucleotide sequence encoding Cas3 between the promoter and the sequence(s) recited in Clause 31.
  • 33. The vector of Clause 31 or 32, wherein the host cell comprises a Type IU CRISPR array that is cognate with the Cas3.
  • 34. The vector of Clause 31 or 32, wherein the host cell comprises an endogenous Type IA, B, C, D, E or F CRISPR/Cas system.
  • 35. The vector of any one of Clauses 1 to 17, wherein the vector comprises (optionally in 5′ to 3′ direction) nucleotide sequence encoding one, more or all of Cas10d, Cas7 and Cas5.
  • 36. The vector of Clause 35, wherein the vector comprises a nucleotide sequence encoding Cas3′ and/or Cas3″.
  • 37. The vector of Clause 36, wherein the nucleotide sequences encoding the Cas3′ and/or Cas3″ are between the promoter and the sequence(s) recited in Clause 35.
  • 38. The vector of any one of Clauses 35 to 37, wherein the host cell comprises a Type ID CRISPR array that is cognate with the Cas3.
  • 39. The vector of any one of Clauses 35 to 37, wherein the host cell comprises an endogenous Type IA, B, C, U, E or F CRISPR/Cas system.
  • 40. The vector of any one of Clauses 1 to 17, wherein the vector comprises (optionally in 5′ to 3′ direction) nucleotide sequence encoding one, more or all of Cas8e, Cas11, Cas7, Cas5 and Cas6.
  • 41. The vector of Clause 40, wherein the vector comprises a nucleotide sequence encoding Cas3 between the promoter and the sequence(s) recited in Clause 40.
  • 42. The vector of Clause 40 or 41, wherein the host cell comprises a Type IE CRISPR array that is cognate with the Cas3.
  • 43. The vector of Clause 40 or 41, wherein the host cell comprises an endogenous Type IA, B, C, D, U or F CRISPR/Cas system.
  • 44. The vector of any one of Clauses 1 to 17, wherein the vector comprises (optionally in 5′ to 3′ direction) nucleotide sequence encoding one, more or all of Cas8f, Cas5, Cas7 and Cas6f.
  • 45. The vector of Clause 44, wherein the vector comprises a nucleotide sequence encoding Cas3 between the promoter and the sequence(s) recited in Clause 44, wherein the vector is devoid of nucleotide sequence encoding further Cas between the promoter and the sequence encoding the Cas3.
  • 46. The vector of Clause 44 or 45, wherein the host cell comprises a Type IF CRISPR array that is cognate with the Cas3.
  • 47. The vector of Clause 44 or 45, wherein the host cell comprises an endogenous Type IA, B, C, D, U or E CRISPR/Cas system.
  • 48. The vector of any one of Clauses 1 to 17, wherein the Cas and Cascade are
    • (a) Type IA Cas and Cascade proteins;
    • (b) Type IB Cas and Cascade proteins;
    • (c) Type IC Cas and Cascade proteins;
    • (d) Type ID Cas and Cascade proteins;
    • (e) Type IE Cas and Cascade proteins;
    • (f) Type IF Cas and Cascade proteins; or
    • (g) Type IU Cas and Cascade proteins.
  • 49. The vector of any preceding Clause, wherein the Cas and Cascade are E coli (optionally Type IE or IF) Cas and Cascade proteins.
  • 50. The vector of Clause 49, wherein the E coli is ESBL-producing E. coli or E. coli ST131-025b:H4.
  • 51. The vector of any preceding Clause, wherein the Cas and Cascade are
    • (a) Clostridium (eg, C dificile) Cas and Cascade proteins, optionally C dificile resistant to one or more antibiotics selected from aminoglycosides, lincomycin, tetracyclines, erythromycin, clindamycin, penicillins, cephalosporins and fluoroquinolones;
    • (b) Pseudomonas aeruginosa Cas and Cascade proteins, optionally P aeruginosa resistant to one or more antibiotics selected from carbapenems, aminoglycosides, cefepime, ceftazidime, fluoroquinolones, piperacillin and tazobactam; or
    • (c) Klebsiella pneumoniae (eg, carbapenem-resistant Klebsiella pneumoniae or Extended-Spectrum Beta-Lactamase (ESBL)-producing K pneumoniae) Cas and Cascade proteins.
  • 52. The vector of any preceding Clause, wherein the Cas and Cascade are E coli, C difficile, P aeruginosa, K pneumoniae, P furiosus or B halodurans Cas and Cascade proteins.
  • 53. The vector of any preceding Clause, wherein the Cas3 is a Cas3 of a CRISPR/Cas locus of a first bacterial or archaeal species, wherein the distance between the Cas3-encoding sequence of the locus and its cognate promoter is further than the distance between the Cas3-encoding sequence and the respective promoter comprised by the vector.
  • 54. The vector of any preceding Clause, wherein the distance between the promoter and the Cas3-encoding sequence and/or Cascade protein-encoding sequence(s) is shorter than in a corresponding wild-type Type I locus.
  • 55. The vector of any preceding Clause, wherein the vector comprises (i) a CRISPR array for producing crRNAs in the host cell and/or (ii) one or more nucleotide sequences encoding one or more guide RNAs (gRNAs or single gRNAs), wherein the crRNAs or gRNAs are cognate to the Cas3 (and optionally cognate to the Cascade proteins).
  • 56. The vector of Clause 55 when dependent from Clause 2, wherein the array or gRNA-encoding sequence(s) are comprised by the operon and under the control of the promoter.
  • 57. The vector of Clause 56, wherein the array or gRNA-encoding sequence(s) are under the control of a promoter that is different from the promoter that controls the expression of the Cas3.
  • 58. The vector of Clause 56 or 57, wherein one or more of the crRNAs or gRNAs comprises a spacer sequence that is capable of hybridising to a target nucleotide sequence of the host cell, wherein the target sequence is adjacent a PAM, the PAM being cognate to the Cas3.
  • 59. The vector of Clause 58, wherein the target sequence is a chromosomal sequence of the host cell.
  • 60. The vector of Clause 58 or 59, wherein the Cas3 is operable to cut the target sequence.
  • 61. The vector of any preceding Clause, wherein the vector is a plasmid or phagemid.
  • 62. A delivery vehicle comprising the vector of any preceding Clause, wherein the delivery vehicle is capable of delivering the vector into the host cell.
  • 63. The vehicle of Clause 62, wherein the delivery vehicle is a phage, non-replicative transduction particle, nanoparticle carrier, bacterium or liposome.
  • 64. The vector or vehicle of any preceding Clause, wherein the host cell is a bacterial or archaeal cell, optionally, the host cell is a C dificile, P aeruginosa, K pneumoniae (eg, carbapenem-resistant Klebsiella pneumoniae or Extended-Spectrum Beta-Lactamase (ESBL)-producing K pneumoniae), E coli (eg, ESBL-producing E. coli, or E. coli ST131-025b:H4), H pylori, S pneumoniae or S aureus cell.
  • 65. The vector or vehicle of any preceding Clause for administration to a human or animal subject for treating or reducing the risk of a disease or condition in the subject.
  • 66. The vector or vehicle of Clause 65, wherein the disease or condition is an infection of the subject with host cells (eg, bacterial cells), or wherein the disease or condition is mediated by host cells (eg, bacterial cells).
  • 67. A pharmaceutical composition comprising the vector or vehicle of any preceding Clause and a pharmaceutically acceptable diluent, excipient or carrier.


It will be understood that particular embodiments described herein are shown by way of illustration and not as limitations of the invention. The principal features of this invention can be employed in various embodiments without departing from the scope of the invention. Those skilled in the art will recognize, or be able to ascertain using no more than routine study, numerous equivalents to the specific procedures described herein. Such equivalents are considered to be within the scope of this invention and are covered by the claims. All publications and patent applications mentioned in the specification are indicative of the level of skill of those skilled in the art to which this invention pertains. All publications and patent applications and all US equivalent patent applications and patents are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference. Reference is made to WO2017/118598, US20180140698, US20170246221, US20180273940, US20160115488, US20180179547, US20170175142, US20160024510, US20150064138, US20170022499, US20160345578, US20180155729, US20180200342, WO2017112620, WO2018081502, PCT/EP2018/066954, PCT/EP2018/066980, PCT/EP2018/071454 and U.S. Ser. No. 15/985,658 and equivalent publications by the US Patent and Trademark Office (USPTO) or WIPO, the disclosures of which are incorporated herein by reference for providing disclosure that may be used in the present invention and/or to provide one or more features (eg, of a vector) that may be included in one or more claims herein.


The use of the word “a” or “an” when used in conjunction with the term “comprising” in the claims and/or the specification may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one,” and “one or more than one.” The use of the term “or” in the claims is used to mean “and/or” unless explicitly indicated to refer to alternatives only or the alternatives are mutually exclusive, although the disclosure supports a definition that refers to only alternatives and “and/or.” Throughout this application, the term “about” is used to indicate that a value includes the inherent variation of error for the device, the method being employed to determine the value, or the variation that exists among the study subjects.


As used in this specification and claim(s), the words “comprising” (and any form of comprising, such as “comprise” and “comprises”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “includes” and “include”) or “containing” (and any form of containing, such as “contains” and “contain”) are inclusive or open-ended and do not exclude additional, unrecited elements or method steps


The term “or combinations thereof” or similar as used herein refers to all permutations and combinations of the listed items preceding the term. For example, “A, B, C, or combinations thereof is intended to include at least one of: A, B, C, AB, AC, BC, or ABC, and if order is important in a particular context, also BA, CA, CB, CBA, BCA, ACB, BAC, or CAB. Continuing with this example, expressly included are combinations that contain repeats of one or more item or term, such as BB, AAA, MB, BBC, AAABCCCC, CBBAAA, CABABB, and so forth. The skilled artisan will understand that typically there is no limit on the number of items or terms in any combination, unless otherwise apparent from the context.


Any part of this disclosure may be read in combination with any other part of the disclosure, unless otherwise apparent from the context.


All of the compositions and/or methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and/or methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.


The present invention is described in more detail in the following non-limiting Examples.


EXAMPLES

The examples illustrate fast and precision killing of Escherichia coli strains. As a model programmable nuclease system, we used a CRISPR guided vector (CGV™) to specifically target Escherichia coli MG1655.


Example 1. Single-Vector Cas3 & Cascade: Type I CRISPR-Cas System Targeting E. coli

A plasmid (which we call a CRISPR Guided Vector™, CGV™) was constructed comprising an operon with nucleotide sequences encoding a Type I Cas3 and Cascade proteins under the control of a common promoter. C. dificile Type IB Cas3 and Cascade was used. A cognate CRISPR array comprising C. dificile repeat sequences and spacer sequence for targeting an E. coli host cell chromosome was also introduced into target cells. An adaptation module containing Cast, Cast and Cas4 was omitted in the vector (see FIG. 1A). In the wild-type C. dificile Type IB CRISPR/Cas locus, the cas3 gene is 3′ of the Cascade genes (cas8b1, cas7 and cas5) and thus spaced away from the promoter upstream of the Cascade genes. When we tried this arrangement, we found killing of E. coli cells, but surprisingly when we changed to a synthetic operon arrangement (in 5′ to 3′ orientation) of promoter, cas3, cas8b1, cas7 and cas5 we saw significantly higher killing of the target E. coli cells.


Results using this synthetic operon arrangement are shown in FIGS. 1A-1C. In FIG. 1B there is shown a dilution series (101-106) of drop spots (5 μl) of target E. coli MG1655 cells harboring the CGV on LB agar plates with and without inducers. CRISPR/Cas induction surprisingly killed 99.9% of the population (FIG. 1C, grey bar). Growth in absence of induction is shown in black. CGV™ refers to a CRISPR Guided Vector™, which is a nucleic acid vector comprising nucleotide sequences encoding CRISPR/Cas components.


We also managed to achieve desirable targeted killing of E coli cells using a similar set-up, except that E coli Type IE Cas and Cascade were used, together with a cognate array targeting host cell E coli chromosomal DNA (data not shown). In this case, a vector was used comprising (in 5′ to 3′ direction) a promoter controlling the expression of Cas3, Cas8e, Cas11, Cas7, Cas5 and Cas6 in an operon.


Materials and Methods



E. coli MG1655 was grown in lysogeny broth (LB) with shaking (250 rpm) at 37° C. When necessary, cultures were supplemented with tetracycline (10 μg/mL), and spectinomycin (400 μg/mL).


To construct a plasmid containing C. difficile CRISPR system under arabinose inducible pBAD promoter, cas3, cas6, cas8b, cas7 and cas5 genes from C. difficile were amplified and cloned in a low copy number plasmid (pSC101 ori). cas3 was located in the beginning of the operon followed by cas6, cas8b, cas7 and cas5. The adaptation module (consisting of cas1, cast, and cas4) was omitted in the vector (FIG. 1A). A second plasmid containing an IPTG inducible single-spacer array targeting a chromosomal intergenic region in E. coli MG1655 was constructed (FIG. 1A). The spacer was cloned under control of the IPTG-inducible Ptrc promoter, in a CloDF13 on backbone. It contains 37 nucleotides from the genome of E. coli MG1655 (ctttgccgcgcgcttcgtcacgtaattctcgtcgcaa) (SEQ ID NO: 26). Additionally, the 3′-CCT protospacer adjacent motif (PAM) is located adjacent to the selected target sequence in the genome of E. coli MG1655 (FIG. 1A).


To perform killing assays, both plasmids were transformed into E. coli MG1655 by electroporation. Transformants were grown in liquid LB with antibiotics to mid-log phase, and the killing efficiency was determined by serial dilution and spot plating onto LB, and LB+inducers (0.5 mM IPTG and 1 arabinose). Viability was calculated by counting colony forming units (CFUs) on the plates and data were calculated as viable cell concentration (CFU/ml).


Example 2. Single-Vector Cas3-Cascade & Array: Type I CRISPR-Cas System Targeting E. coli

A plasmid (which we call a CRISPR Guided Vector™, CGV™, which is a nucleic acid vector comprising nucleotide sequences encoding CRISPR/Cas components) was constructed comprising an operon with nucleotide sequences encoding a Type I Cas3 and Cascade proteins under the control of a common promoter. C. difficile Type IB Cas3 and Cascade was used. Adaptation module containing Cas1, Cas2 and Cas4 was omitted in the vector. A cognate CRISPR array comprising C. difficile repeat sequences and spacer sequence for targeting an E. coli host cell chromosome was also cloned in the vector (see FIG. 2A). Similarly we also constructed a plasmid comprising of an operon with nucleotide sequences encoding E. coli Type IE Cas3 and Cascade proteins under control of a common promoter. The E. coli adaption module containing Cas1 and Cas2 was omitted, in the vector. A cognate CRISPR array comprising E. coli repeat sequences and spacer sequence for targeting an E. coli host cell chromosome was also cloned in the vector.


The CGV containing the C. difficile CRISPR-Cas system was transformed into E. coli MG1655 which contains a pks sequence incorporated into the genome. Results using this synthetic operon arrangement are shown in FIGS. 2A-2C. In FIG. 2B there is shown a dilution series (101-105) of drop spots (5 μl) of target E. coli MG1655 cells harboring the CGV on synthetic medium (SM) agar plates with and without inducers. CRISPR/Cas induction resulted in more than 2-log10 reductions in viable cells of E. coli MG1655 (FIG. 2C, grey bar). Growth in absence of induction is shown in black. CGV™ refers to a CRISPR Guided Vector™.


The survival of E. coli MG1655 upon induction was followed over time by plating the cultures in serial dilutions every 60 minutes, for 2 h (FIG. 3A). Killing curves revealed that CRISPR/Cas induction mediated rapid killing of E. coli MG1655, generating a two-log10 reduction in E. coli by the first 60 minutes. FIG. 3B shows a dilution series (101-106) of drop spots (5 μI) of induced and non-induced cultures of target E. coli MG1655 on SM agar plates.


The CGV containing the E. coli CRISPR-Cas system was transformed into other E. coli MG1655 cells which contain a lambda sequence incorporated into the genome. Results using this synthetic operon arrangement are shown in FIGS. 6A-6B. In FIG. 6A there is shown a dilution series (101-105) of drop spots (5 μl) of target E. coli MG1655 cells harboring the CGV on synthetic medium (SM) agar plates with and without inducers. CRISPR/Cas induction resulted in more than 2-log10 reductions in viable cells of E. coli MG1655 (FIG. 6B, grey bar). Growth in absence of induction is shown in black. In a repeat experiment (not shown) we saw a 3-log10 reductions in viable cells of E. coli MG1655 with CRISPR/Cas induction.


Materials and Methods



E. coli MG1655 was grown in synthetic medium (SM) with shaking (250 rpm) at 37° C. Cultures were supplemented with 10 μg/mL tetracycline when required.


To construct a plasmid containing C. difficile CRISPR system under arabinose inducible pBAD promoter, cas3, cas6, cas8b, cas7 and cas5 genes from C. difficile were amplified and cloned in a low copy number plasmid (pSC101 ori). cas3 was located in the beginning of the operon followed by cas6, cas8b, cas7 and cas5. Additionally, an IPTG inducible single-spacer array targeting a chromosomal intergenic region in E. coli MG1655 was included in the vector under control of the IPTG-inducible Ptrc promoter (FIG. 2A). It contains 37 nucleotides from the PKS gene (previously integrated into the genome of E. coli MG1655) (gtttggcgatggcgcgggtgtggttgtgcttcggcgt) (SEQ ID NO: 27). Additionally, the 3′-CCT protospacer adjacent motif (PAM) is located adjacent to the selected target sequence in the genome of E. coli MG1655 (FIG. 2A).


To construct a plasmid containing E. coli CRISPR system under arabinose inducible pBAD promoter, cas3, cse1, cse2, cas7, cas5 and cas6 genes from E. coli were amplified and cloned in a low copy number plasmid (pSC101 ori). The operon comprised (in 5′ to 3′ direction) cas3 followed by cse1 cse2, cas7, cas5 and cas6. Additionally, an IPTG inducible single-spacer array targeting a chromosomal intergenic region in E. coli MG1655 was included in the vector under control of the IPTG-inducible Ptrc promoter. It contained 32 nucleotides from the lambda sequence (previously integrated into the genome of E. coli MG1655) (tgggatgcctaccgcaagcagcttggcctgaa) (SEQ ID NO: 28) and found to efficiently target in Brouns et al., 2008 (Science. 2008 Aug. 15; 321(5891):960-4. doi: 10.1126/science.1159689; “Small CRISPR RNAs guide antiviral defense in prokaryotes”). Additionally, the 3′-ATG protospacer adjacent motif (PAM) is located adjacent to the selected target sequence in the genome of E. coli MG1655.


The CGVs were transformed into E. coli MG1655 by electroporation. Transformants were grown in liquid SM with antibiotics to mid-log phase, and the killing efficiency was determined by serial dilution and spot plating onto LB, and LB+inducers (0.5 mM IPTG and 1% arabinose). Viability was calculated by counting colony forming units (CFUs) on the plates and data were calculated as viable cell concentration (CFU/ml).


To perform killing curves, E. coli MG1655 harboring the CGV was grown in liquid SM with antibiotics to mid-log phase. The culture was divided into two tubes and either inducers (0.5 mM IPTG and 1% arabinose) or PBS were added. Survival of the strain was followed over time by plating the cultures in serial dilutions (101-106) of drop spots (5 μl) every 60 minutes, for 2 h, on SM plates with antibiotics. Survival frequency was calculated by counting colony forming units (CFUs) on the plates and data were calculated as viable cell concentration (CFU/ml).


Example 3. Precision Killing of Target Strain E. coli MG1655 in a Microbiome

An artificial microbial consortium was constructed to study the efficiency of the CGV carrying the CRISPR-Cas system of C. difficile, to specifically target E. coli MG1655 in the presence of other microbes, mimicking the human microbiome.


The synthetic consortium consisted of three strains (two different species) with differential antibiotic resistance profiles: a streptomycin-resistant E. coli MG1655 (target strain), an ampicillin-resistant E. coli Top10, and a chloramphenicol-resistant Lactococcus lactis NZ9000. To create the consortium, bacterial cultures were grown separately in Brain Heart Infusion broth (BHI, optimal growth medium for L. lactis) to mid-log phase and mixed in fresh BHI broth with and without inducers. After 1 h induction at 30° C., the composition of the consortium was determined by counting viable colonies on selective plates. Induction of the CRISPR system in the mixed community, resulted in >10-fold killing of target E. coli MG1655, while leaving E. coli Top10 and L. lactis NZ9000 cell populations unharmed (FIG. 4A). In FIG. 4B there is shown a dilution series (101-105) of drop spots (5 μl) of the synthetic consortium after 1 h induction on BHI agar plates.


Additionally, CRISPR killing of target strain E. coli MG1655 in the synthetic microbial consortium was compared to a pure culture (ie, target strain E. coli MG1655 that is not mixed with another strain or species). Unexpectedly, in both conditions, killing of 3 logs was achieved when plated on BHI agar plates with inducers (FIG. 5A). Thus, surprisingly the killing in the microbiome setting was as efficient as the killing in pure culture. In FIG. 5B there is shown a dilution series (101-105) of drop spots (5 μl) of the synthetic consortium and E. coli MG1655 in pure culture on BHI agar plates with and without inducers.


Materials and Methods



E. coli MG1655, E. coli Top10, and Lactococcus lactis NZ9000 were grown in BHI broth with shaking (250 rpm) at 30° C. Cultures were supplemented with 1000 μg/mL streptomycin, 100 μg/mL ampicillin, or 10 μg/mL chloramphenicol, respectively.


To create the consortium, bacterial cultures were grown in BHI with appropriate antibiotics to mid-log phase. Cultures were washed twice in PBS to remove the antibiotics and mixed in fresh BHI broth. The mixed culture was spotted onto BHI plates with streptomycin, ampicillin or chloramphenicol to quantify the initial concentration of E. coli MG1655, E. coli Top10 and L. lactis NZ9000, respectively. The mixed culture was divided into two tubes and either inducers (0.5 mM IPTG and 1% arabinose) or PBS were added. After 1 h induction at 30° C., the composition of the consortium was calculated by counting colony forming units (CFUs) on selective plates and data were calculated as viable cell concentration (CFU/ml).


Example 4. Use of Promoter Repression in Vector Amplification Strains

We engineered an E coli Top10 production strain cell population comprising plasmid CGV DNA and an expressible sequence encoding a Tet repressor (TetR). The DNA comprised a Cas9-encoding nucleotide sequence under the control of a Tet promoter (pLtetO-1 promoter). The promoter is normally constitutively ON, but it was repressed by TetR in our cells. Thus, in this way we could successfully culture the cells and amplify the CGV without observing adverse toxicity due to Cas9 expression.


In an experiment in the absence of repression, we did not observe any colonies of production strain bacteria, and we surmise that this was due to Cas9 toxicity. We believe, in addition to providing a way of increasing CGV yield (eg, for subsequent packaging into phage or non-self-replicative transduction particles), our method using repression can minimize selection for mutations in the DNA that would otherwise be forced by higher Cas9 expression and cutting (eg, due to CGV cutting).


REFERENCES



  • Mutalik et al, Nat Methods. 2013 April; 10(4):354-60. doi: 10.1038/nmeth. 2404. Epub 2013 Mar. 10, “Precise and reliable gene expression via standard transcription and translation initiation elements”.










TABLE 1





Example Bacteria


Optionally, the target host cells are cells of a genus or species selected from this Table


and/or the production strain cells are cells of a genus or species selected from this Table




















Abiotrophia


Acidocella


Actinomyces


Alkalilimnicola


Aquaspirillum




Abiotrophia defectiva


Acidocella aminolytica


Actinomyces bovis


Alkalilimnicola ehrlichii


Aquaspirillum polymorphum




Acaricomes


Acidocella facilis


Actinomyces denticolens


Alkaliphilus


Aquaspirillum




Acaricomes phytoseiuli


Acidomonas


Actinomyces europaeus


Alkaliphilus oremlandii


putridiconchylium




Acetitomaculum


Acidomonas methanolica


Actinomyces georgiae


Alkaliphilus transvaalensis


Aquaspirillum serpens




Acetitomaculum ruminis


Acidothermus


Actinomyces gerencseriae


Allochromatium


Aquimarina




Acetivibrio


Acidothermus cellulolyticus


Actinomyces


Allochromatium vinosum


Aquimarina latercula




Acetivibrio cellulolyticus


Acidovorax


hordeovulneris


Alloiococcus


Arcanobacterium




Acetivibrio ethanolgignens


Acidovorax anthurii


Actinomyces howellii


Alloiococcus otitis


Arcanobacterium




Acetivibrio multivorans


Acidovorax caeni


Actinomyces hyovaginalis


Allokutzneria


haemolyticum




Acetoanaerobium


Acidovorax cattleyae


Actinomyces israelii


Allokutzneria albata


Arcanobacterium pyogenes




Acetoanaerobium noterae


Acidovorax citrulli


Actinomyces johnsonii


Altererythrobacter


Archangium




Acetobacter


Acidovorax defluvii


Actinomyces meyeri


Altererythrobacter


Archangium gephyra




Acetobacter aceti


Acidovorax delafieldii


Actinomyces naeslundii


ishigakiensis


Arcobacter




Acetobacter cerevisiae


Acidovorax facilis


Actinomyces neuii


Altermonas


Arcobacter butzleri




Acetobacter cibinongensis


Acidovorax konjaci


Actinomyces odontolyticus


Altermonas haloplanktis


Arcobacter cryaerophilus




Acetobacter estunensis


Acidovorax temperans


Actinomyces oris


Altermonas macleodii


Arcobacter halophilus




Acetobacter fabarum


Acidovorax valerianellae


Actinomyces radingae


Alysiella


Arcobacter nitrofigilis




Acetobacter ghanensis


Acinetobacter


Actinomyces slackii


Alysiella crassa


Arcobacter skirrowii




Acetobacter indonesiensis


Acinetobacter baumannii



Alysiella filifomis





Acetobacter lovaniensis


Acinetobacter baylyi


Actinomyces turicensis


Aminobacter


Arhodomonas




Acetobacter malorum


Acinetobacter bouvetii


Actinomyces viscosus


Aminobacter aganoensis


Arhodomonas aquaeolei




Acetobacter nitrogenifigens


Acinetobacter calcoaceticus


Actinoplanes


Aminobacter aminovorans


Arsenophonus




Acetobacter oeni


Acinetobacter gerneri


Actinoplanes auranticolor


Aminobacter niigataensis


Arsenophonus nasoniae




Acetobacter orientalis


Acinetobacter haemolyticus


Actinoplanes brasiliensis


Aminobacterium





Acetobacter orleanensis


Acinetobacter johnsonii


Actinoplanes consettensis


Aminobacterium mobile


Arthrobacter




Acetobacter pasteurianus


Acinetobacter junii


Actinoplanes deccanensis


Aminomonas


Arthrobacter agilis




Acetobacter pornorurn


Acinetobacter lwoffi


Actinoplanes derwentensis


Aminomonas paucivorans


Arthrobacter albus




Acetobacter senegalensis


Acinetobacter parvus


Actinoplanes digitatis


Ammoniphilus


Arthrobacter aurescens




Acetobacter xylinus


Acinetobacter radioresistens


Actinoplanes durhamensis


Ammoniphilus oxalaticus


Arthrobacter




Acetobacterium


Acinetobacter schindleri


Actinoplanes ferrugineus


Ammoniphilus oxalivorans


chlorophenolicus




Acetobacterium bakii


Acinetobacter soli


Actinoplanes globisporus


Amphibacillus


Arthrobacter citreus




Acetobacterium


Acinetobacter tandoii


Actinoplanes humidus


Amphibacillus xylanus


Arthrobacter clystallopoietes




carbinolicum








Acetobacterium


Acinetobacter tjernbergiae


Actinoplanes italicus


Amphritea


Arthrobacter cumminsii




dehalogenans








Acetobacterium fimetarium


Acinetobacter towneri


Actinoplanes liguriensis


Amphritea balenae


Arthrobacter globiformis




Acetobacterium malicum


Acinetobacter ursingii


Actinoplanes lobatus


Amphritea japonica


Arthrobacter




Acetobacterium paludosum


Acinetobacter venetianus


Actinoplanes missouriensis


Amycolatopsis


histidinolovorans




Acetobacterium tundrae


Acrocarpospora


Actinoplanes palleronii


Amycolatopsis alba


Arthrobacter ilicis




Acetobacterium wieringae


Acrocarpospora corrugata


Actinoplanes philippinensis


Amycolatopsis albidoflavus


Arthrobacter luteus




Acetobacterium woodii


Acrocarpospora


Actinoplanes rectilineatus


Amycolatopsis azurea


Arthrobacter methylotrophus




Acetofilamentum


macrocephala


Actinoplanes regularis


Amycolatopsis coloradensis


Arthrobacter mysorens




Acetofilamentum rigidum


Acrocarpospora


Actinoplanes


Amycolatopsis lurida


Arthrobacter nicotianae





pleiomorpha



Amycolatopsis mediterranei


Arthrobacter nicotinovorans




Acetohalobium


Actibacter


teichomyceticus


Amycolatopsis rifamycinica


Arthrobacter oxydans




Acetohalobium arabaticum


Actibacter sediminis


Actinoplanes utahensis


Amycolatopsis rubida


Arthrobacter pascens




Acetomicrobium


Actinoalloteichus


Actinopolyspora


Amycolatopsis sulphurea


Arthrobacter




Acetomicrobium faecale


Actinoalloteichus


Actinopolyspora halophila


Amycolatopsis tolypomycina


phenanthrenivorans




Acetomicrobium flavidum


cyanogriseus


Actinopolyspora


Anabaena


Arthrobacter




Acetonema


Actinoalloteichus


mortivallis


Anabaena cylindrica


polychromogenes




Acetonema longum


hymeniacidonis


Actinosynnema


Anabaena flos-aquae


Atrhrobacter protophomiae




Acetothermus


Actinoalloteichus spitiensis


Actinosynnema mirum


Anabaena variabilis


Arthrobacter




Acetothermus paucivorans


Actinobaccillus


Actinotalea


Anaeroarcus


psychrolactophilus




Acholeplasma


Actinobacillus capsulatus


Actinotalea fermentans


Anaeroarcus burkinensis


Arthrobacter ramosus




Acholeplasma axanthum


Actinobacillus delphinicola


Aerococcus


Anaerobaculum


Arthrobacter sulfonivorans




Acholeplasma brassicae


Actinobacillus hominis


Aerococcus sanguinicola


Anaerobaculum mobile


Arthrobacter sulfureus




Acholeplasma


Actinobacillus indolicus


Aerococcus urinae


Anaerobiospirillum


Arthrobacter uratoxydans




cavigenitalium








Acholeplasma equifetale


Actinobacillus lignieresii


Aerococcus urinaeequi


Anaerobiospirillum


Arthrobacter ureafaciens




Acholeplasma granularum


Actinobacillus minor


Aerococcus urinaehominis


succiniciproducens


Arthrobacter viscosus




Acholeplasma hippikon


Actinobacillus muris


Aerococcus viridans


Anaerobiospirillum thomasii


Arthrobacter woluwensis




Acholeplasma laidlawii


Actinobacillus


Aeromicrobium


Anaerococcus


Asaia




Acholeplasma modicum


pleuropneumoniae


Aeromicrobium elythreum


Anaerococcus hydrogenalis


Asaia bogorensis




Acholeplasma morum


Actinobacillus porcinus


Aeromonas


Anaerococcus lactolyticus


Asanoa




Acholeplasma multilocale


Actinobacillus rossii


Aeromonas


Anaerococcus prevotii


Asanoa ferruginea



Acholeplasma oculi

Actinobacillus scotiae


allosaccharophila


Anaerococcus tetradius


Asticcacaulis




Acholeplasma palmae


Actinobacillus seminis


Aeromonas bestiarum


Anaerococcus vaginalis


Asticcacaulis biprosthecium




Acholeplasma parvum


Actinobacillus succinogenes


Aeromonas caviae



Asticcacaulis excentricus




Acholeplasma pleciae


Actinobaccillus suis


Aeromonas encheleia


Anaerofustis


Atopobacter




Acholeplasma vituli


Actinobacillus ureae


Aeromonas


Anaerofustis stercorihominis


Atopobacter phocae




Achromobacter


Actinobaculum


enteropelogenes


Anaeromusa


Atopobium




Achromobacter denitrificans


Actinobaculum massiliense


Aeromonas eucrenophila


Anaeromusa acidaminophila


Atopobium fossor




Achromobacter insolitus


Actinobaculum schaalii


Aeromonas ichthiosmia


Anaeromyxobacter


Atopobium minutum




Achromobacter piechaudii


Actinobaculum suis


Aeromonas jandaei


Anaeromyxobacter


Atopobium parvulum




Achromobacter ruhlandii


Actinomyces urinale


Aeromonas media


dehalogenans


Atopobium rimae




Achromobacter spanius


Actinocatenispora


Aeromonas popoffii


Anaerorhabdus


Atopobium vaginae




Acidaminobacter


Actinocatenispora rupis


Aeromonas sobria


Anaerorhabdus furcosa


Aureobacterium




Acidaminobacter


Actinocatenispora


Aeromonas veronii


Anaerosinus


Aureobacterium barkeri




hydrogenoformans


thailandica


Agrobacterium


Anaerosinus glycerini


Aurobacterium




Acidaminococcus


Actinocatenispora sera


Agrobacterium


Anaerovirgula


Aurobacterium liquefaciens




Acidaminococcus fermentans


Actinocorallia


gelatinovorum


Anaerovirgula multivorans


Avibacterium




Acidaminococcus intestini


Actinocorallia aurantiaca


Agrococcus


Ancalomicrobium


Avibacterium avium




Acidicaldus


Actinocorallia aurea


Agrococcus citreus


Ancalomicrobium adetum


Avibacterium gallinarum




Acidicaldus organivorans


Actinocorallia cavernae


Agrococcus jenensis


Ancylobacter


Avibacterium paragallinarum




Acidimicrobium


Actinocorallia glomerata


Agromonas


Ancylobacter aquaticus


Avibacterium volantium




Acidimicrobium


Actinocorallia herbida


Agromonas oligotrophica


Aneurinibacillus


Azoarcus




ferrooxidans








Acidiphilium


Actinocorallia libanotica


Agromyces


Aneurinibacillus


Azoarcus indigens




Acidiphilium acidophilum


Actinocorallia longicatena


Agromyces fucosus


aneurinilyticus


Azoarcus tolulyticus




Acidiphilium angustum


Actinomadura


Agromyces hippuratus


Aneurinibacillus migulanus


Azoarcus toluvorans




Acidiphilium cryptum


Actinomadura alba


Agromyces luteolus


Aneurinibacillus





Acidiphilium multivorum


Actinomadura atramentaria


Agromyces mediolanus


themioaerophilus





Acidiphilium organovorum


Actinomadura


Agromyces ramosus


Angiococcus


Azohydromonas




Acidiphilium rubrum


bangladeshensis


Agromyces rhizospherae


Angiococcus disciformis


Azohydromonas australica




Acidisoma


Actinomadura catellatispora


Akkermansia


Angulomicrobium


Azohydromonas lata




Acidisoma sibiricum


Actinomadura chibensis


Akkermansia muciniphila


Angulomicrobium tetraedrale


Azomonas




Acidisoma tundrae


Actinomadura chokoriensis


Albidiferax


Anoxybacillus


Azomonas agilis




Acidisphaera


Actinomadura citrea


Albidiferax ferrireducens


Anoxybacillus pushchinoensis


Azomonas insignis




Acidisphaera rubrifaciens


Actinomadura coerulea


Albidovulum


Aquabacterium


Azomonas macrocytogenes




Acidithiobacillus


Actinomadura echinospora


Albidovulum inexpectatum


Aquabacterium commune


Azorhizobium




Acidithiobacillus albertensis


Actinomadura fibrosa


Alcaligenes


Aquabacterium parvum


Azorhizobium caulinodans




Acidithiobacillus caldus


Actinomadura formosensis


Alcaligenes denitrificans



Azorhizophilus




Acidithiobacillus


Actinomadura hibisca


Alcaligenes faecalis



Azorhizophilus paspali




ferrooxidans








Acidithiobacillus


Actinomadura kijaniata


Alcanivorax



Azospirillum




thiooxidans








Acidobacterium


Actinomadura latina


Alcanivorax borkumensis



Azospirillum brasilense




Acidobacterium capsulatum


Actinomadura livida


Alcanivorax jadensis



Azospirillum halopraeferens





Actinomadura


Algicola



Azospirillum irakense





luteofluorescens


Algicola bacteriolytica



Azotobacter





Actinomadura macra


Alicyclobacillus



Azotobacter beijerinckii





Actinomadura madurae


Alicyclobacillus



Azotobacter chroococcum





Actinomadura oligospora


disulfidooxidans



Azotobacter nigricans





Actinomadura pelletieri


Alicyclobacillus



Azotobacter salinestris





Actinomadura rubrobrunea


sendaiensis



Azotobacter vinelandii





Actinomadura


Alicyclobacillus vulcanalis







rugatobispora








Actinomadura umbrina








Actinomadura


Alishewanella







verrucosospora


Alishewanella fetalis







Actinomadura vinacea


Alkalibacillus







Actinomadura viridilutea


Alkalibacillus







Actinomadura viridis


haloalkaliphilus







Actinomadura yumaensis







Bacillus


Bacteroides


Bibersteinia


Borrelia


Brevinema



[see below]

Bacteroides caccae


Bibersteinia trehalosi


Borrelia afzelii


Brevinema andersonii





Bacteroides coagulans


Bifidobacterium


Borrelia americana


Brevundimonas




Bacteriovorax


Bacteroides eggerthii


Bifidobacterium adolescentis


Borrelia burgdorferi


Brevundimonas alba




Bacteriovorax stolpii


Bacteroides fragilis


Bifidobacterium angulatum


Borrelia carolinensis


Brevundimonas aurantiaca





Bacteroides galacturonicus


Bifidobacterium animalis


Borrelia coriaceae


Brevundimonas diminuta





Bacteroides helcogenes


Bifidobacterium asteroides


Borrelia garinii


Brevundimonas intermedia





Bacteroides ovatus


Bifidobacterium bifidum


Borrelia japonica


Brevundimonas subvibrioides





Bacteroides pectinophilus


Bifidobacterium bourn


Bosea


Brevundimonas vancanneytii





Bacteroides pyogenes


Bifidobacterium breve


Bosea minatitlanensis


Brevundimonas variabilis





Bacteroides salyersiae


Bifidobacterium catenulatum


Bosea thiooxidans


Brevundimonas vesicularis





Bacteroides stercoris


Bifidobacterium choerinum


Brachybacterium


Brochothrix





Bacteroides suis


Bifidobacterium colyneforme


Brachybacterium


Brochothrix campestris





Bacteroides tectus


Bifidobacterium cuniculi


alimentarium


Brochothrix thermosphacta





Bacteroides


Bifidobacterium dentium


Brachybacterium faecium






thetaiotaomicron








Bacteroides unifomiis


Bifidobacterium gallicum


Brachybacterium


Brucella





Bacteroides ureolyticus


Bifidobacterium gallinarum


paraconglomeratum


Brucella canis





Bacteroides vulgatus


Bifidobacterium indicum


Brachybacterium rhamnosum


Brucella neotomae





Balnearium


Bifidobacterium longum


Brachybacterium


Bryobacter





Balnearium lithotrophicum


Bifidobacterium


tyrofermentans


Biyobacter aggregatus





Balneatrix


magnumBifidobacterium


Brachyspira


Burkholderia





Balneatrix alpica


merycicum


Brachyspira alvinipulli


Burkholderia ambifaria





Balneola


Bifidobacterium minimum


Brachyspira hyodysenteriae


Burkholderia andropogonis





Balneola vulgaris


Bifidobacterium


Brachyspira innocens


Burkholderia anthina





Barnesiella


pseudocatenulatum


Brachyspira murdochii


Burkholderia caledonica





Barnesiella viscericola


Bifidobacterium


Brachyspira pilosicoli


Burkholderia caryophylli





Bartonella


pseudolongum



Burkholderia cenocepacia





Bartonella alsatica


Bifidobacterium pullorum


Bradyrhizobium


Burkholderia cepacia





Bartonella bacilliformis


Bifidobacterium ruminantium


Bradyrhizobium canariense


Burkholderia cocovenenans





Bartonella clarridgeiae


Bifidobacterium saeculare


Bradyrhizobium elkanii


Burkholderia dolosa





Bartonella doshiae


Bifidobacterium subtile


Bradyrhizobium japonicum


Burkholderia fungorum





Bartonella elizabethae


Bifidobacterium


Bradyrhizobium liaoningense


Burkholderia glathei





Bartonella grahamii


thermophilum


Brenneria


Burkholderia glumae





Bartonella henselae


Bilophila


Brenneria alni


Burkholderia graminis





Bartonella rochalimae


Bilophila wadsworthia


Brenneria nigrifluens


Burkholderia kururiensis





Bartonella vinsonii


Biostraticola


Brenneria quercina


Burkholderia multivorans





Bavariicoccus


Biostraticola tofi


Brenneria quercina


Burkholderia phenazinium





Bavariicoccus seileri



Brenneria salicis


Burkholderia plantarii





Bdellovibrio


Bizionia


Brevibacillus


Burkholderia pyrrocinia





Bdellovibrio bacteriovorus


Bizionia argentinensis


Brevibacillus agri


Burkholderia silvatlantica





Bdellovibrio exovorus


Blastobacter


Brevibacillus borstelensis


Burkholderia stabilis





Beggiatoa


Blastobacter capsulatus


Brevibacillus brevis


Burkholderia thailandensis





Beggiatoa alba


Blastobacter denitrificans


Brevibacillus centrosporus


Burkholderia tropica





Beijerinckia


Blastococcus


Brevibacillus choshinensis


Burkholderia unamae





Beijerinckia derxii


Blastococcus aggregatus


Brevibacillus invocatus


Burkholderia vietnamiensis





Beijerinckia fluminensis


Blastococcus saxobsidens


Brevibacillus laterosporus


Buttiauxella





Beijerinckia indica


Blastochloris


Brevibacillus parabrevis


Buttiauxella agrestis





Beijerinckia mobilis


Blastochloris viridis


Brevibacillus reuszeri


Buttiauxella brennerae





Belliella


Blastomonas


Brevibacterium


Buttiauxella ferragutiae





Belliella baltica


Blastomonas natatoria


Brevibacterium abidum


Buttiauxella gaviniae





Bellilinea


Blastopirellula


Brevibacterium album


Buttiauxella izardii





Bellilinea caldifistulae


Blastopirellula marina


Brevibacterium aurantiacum


Buttiauxella noackiae





Belnapia


Blautia


Brevibacterium celere


Buttiauxella wamiboldiae





Belnapia moabensis


Blautia coccoides


Brevibacterium epidermidis


Butyrivibrio





Bergeriella


Blautia hansenii


Brevibacterium


Butyrivibrio fibrisolvens





Bergeriella denitrificans


Blautia producta


frigoritolerans


Butyrivibrio hungatei





Beutenbergia


Blautia wexlerae


Brevibacterium halotolerans


Butyrivibrio proteoclasticus





Beutenbergia cavernae


Bogoriella


Brevibacterium iodinum







Bogoriella caseilytica


Brevibacterium linens







Bordetella


Brevibacterium lyticum







Bordetella avium


Brevibacterium mcbrellneri







Bordetella bronchiseptica


Brevibacterium otitidis







Bordetella hinzii


Brevibacterium oxydans







Bordetella holmesii


Brevibacterium paucivorans







Bordetella parapertussis


Brevibacterium stationis







Bordetella pertussis








Bordetella petrii








Bordetella trematum






Bacillus








B. acidiceler


B. aminovorans


B. glucanolyticus


B. taeanensis


B. lautus




B. acidicola


B. amylolyticus


B. gordonae


B. tequilensis


B. lehensis




B. acidiproducens


B. andreesenii


B. gottheilii


B. thermantarcticus


B. lentimorbus




B. acidocaldarius


B. aneurinilyticus


B. graminis


B. thermoaerophilus


B. lentus




B. acidoterrestris


B. anthracis


B. halmapalus


B. thermoamylovorans


B. lichenifomis




B. aeolius


B. aquimaris


B. haloalkaliphilus


B. thermocatenulatus


B. ligniniphilus




B. aerius


B. arenosi


B. halochares


B. thermocloacae


B. litoralis




B. aerophilus


B. arseniciselenatis


B. halodenitfificans


B. thermocopriae


B. locisalis




B. agaradhaerens


B. arsenicus


B. halodurans


B. thermodenitrificans


B. luciferensis




B. agri


B. aurantiacus


B. halophilus


B. thermoglucosidasius


B. luteolus




B. aidingensis


B. arvi


B. halosaccharovorans


B. thermolactis


B. luteus




B. akibai


B. aryabhattai


B. hemicellulosilyticus


B. thermoleovorans


B. macauensis




B. alcalophilus


B. asahii


B. hemicentroti


B. thermophilus


B. macerans




B. algicola


B. atrophaeus


B. herbersteinensis


B. thermoruber


B. macquariensis




B. alginolyticus


B. axarquiensis


B. horikoshii


B. thermosphaericus


B. macyae




B. alkalidiazotrophicus


B. azotofixans


B. horneckiae


B. thiaminolyticus


B. malacitensis




B. alkalinitrilicus


B. azotoformans


B. horti


B. thioparans


B. mannanilyticus




B. alkalisediminis


B. badius


B. huizhouensis


B. thuringiensis


B. marisflavi




B. alkalitelluris


B. barbaricus


B. humi


B. tianshenii


B. marismortui




B. altitudinis


B. bataviensis


B. hwajinpoensis


B. trypoxylicola


B. marmarensis




B. alveayuensis


B. beijingensis


B. idriensis


B. tusciae


B. massiliensis




B. alvei


B. benzoevorans


B. indicus


B. validus


B. megaterium



B. amyloliquefaciens

B. beringensis


B. infantis


B. vallismortis


B. mesonae




B.


B. berkeleyi


B. infernus


B. vedderi


B. methanolicus




a. subsp. amyloliquefaciens


B. beveridgei


B. insolitus


B. velezensis


B. methylotrophicus




B. a. subsp. plantarum


B. bogoriensis


B. invictae


B. vietnamensis


B. migulanus





B. boroniphilus


B. iranensis


B. vireti


B. mojavensis




B. dipsosauri


B. borstelensis


B. isabeliae


B. vulcani


B. mucilaginosus




B. drentensis


B. brevis Migula


B. isronensis


B. wakoensis


B. muralis




B. edaphicus


B. butanolivorans


B. jeotgali


B. weihenstephanensis


B. murimartini




B. ehimensis


B. canaveralius


B. kaustophilus


B. xiamenensis


B. mycoides




B. eiseniae


B. carboniphilus


B. kobensis


B. xiaoxiensis


B. naganoensis




B. enclensis


B. cecembensis


B. kochii


B. zhanjiangensis


B. nanhaiensis




B. endophyticus


B. cellulosilyticus


B. kokeshiifomiis


B. peoriae


B. nanhaiisediminis




B. endoradicis


B. centrosporus


B. koreensis


B. persepolensis


B. nealsonii




B. farraginis


B. cereus


B. korlensis


B. persicus


B. neidei




B. fastidiosus


B. chagannorensis


B. kribbensis


B. pervagus


B. neizhouensis




B. fengqiuensis


B. chitinolyticus


B. krulwichiae


B. plakortidis


B. niabensis




B. firmus


B. chondroitinus


B. laevolacticus


B. pocheonensis


B. niacini




B. flexus


B. choshinensis


B. larvae


B. polygoni


B. novalis




B. foraminis


B. chungangensis


B. laterosporus


B. polymyxa


B. oceanisediminis




B. fordii


B. cibi


B. salexigens


B. popilliae


B. odysseyi




B. formosus


B. circulans


B. saliphilus


B. pseudalcalophilus


B. okhensis




B. fortis


B. clarkii


B. schlegelii


B. pseudofirmus


B. okuhidensis




B. fumarioli


B. clausii


B. sediminis


B. pseudomycoides


B. oleronius




B. funiculus


B. coagulans


B. selenatarsenatis


B. psychrodurans


B. olyzaecorticis




B. fusiformis


B. coahuilensis


B. selenitireducens


B. psychrophilus


B. oshimensis




B. galactophilus


B. cohnii


B. seohaeanensis


B. psychrosaccharolyticus


B. pabuli




B. galactosidilyticus


B. composti


B. shacheensis


B. psychrotolerans


B. pakistanensis




B. galliciensis


B. curdlanolyticus


B. shackletonii


B. pulvifaciens


B. pallidus




B. gelatini


B. cycloheptanicus


B. siamensis


B. pumilus


B. pallidus




B. gibsonii


B. cytotoxicus


B. silvestris


B. purgationiresistens


B. panacisoli




B. ginsengi


B. daliensis


B. simplex


B. pycnus


B. panaciterrae




B. ginsengihumi


B. decisifrondis


B. siralis


B. qingdaonensis


B. pantothenticus




B. ginsengisoli


B. decolorationis


B. smithii


B. qingshengii


B. parabrevis




B. globisporus (eg, B.


B. deserti


B. soli


B. reuszeri


B. paraflexus




g. subsp. Globisporus; or B.



B. solimangrovi


B. rhizosphaerae


B. pasteurii




g. subsp. Marinus)



B. solisalsi


B. rigui


B. patagoniensis






B. songklensis


B. ruris







B. sonorensis


B. safensis







B. sphaericus


B. salarius







B. sporothermodurans








B. stearothermophilus








B. stratosphericus








B. subterraneus








B. subtilis (eg, B.








s. subsp. Inaquosorum; or B.








s. subsp. Spizizeni; or B.








s. subsp. Subtilis)






Caenimonas


Campylobacter


Cardiobacterium


Catenuloplanes


Curtobacterium




Caenimonas koreensis


Campylobacter coli


Cardiobacterium hominis


Catenuloplanes atrovinosus


Curtobacterium




Caldalkalibacillus


Campylobacter concisus


Carnimonas


Catenuloplanes castaneus


albidum




Caldalkalibacillus uzonensis


Campylobacter curvus


Carnimonas nigrificans


Catenuloplanes crispus


Curtobacterium citreus




Caldanaerobacter


Campylobacter fetus


Carnobacterium


Catenuloplanes indicus





Caldanaerobacter


Campylobacter gracilis


Carnobacterium


Catenuloplanes japonicus





subterraneus








Caldanaerobius


Campylobacter helveticus


alterfunditum


Catenuloplanes nepalensis





Caldanaerobius fijiensis


Campylobacter hominis


Carnobacterium divergens


Catenuloplanes niger





Caldanaerobius


Campylobacter


Carnobacterium funditum


Chryseobacterium






hyointestinalis







polysaccharolyticus


Campylobacter jejuni


Carnobacterium gallinarum


Chlyseobacterium





Caldanaerobius zeae


Campylobacter lari


Carnobacterium


balustinum






Campylobacter mucosalis


maltaromaticum






Caldanaerovirga


Campylobacter rectus


Carnobacterium mobile


Citrobacter





Caldanaerovirga


Campylobacter showae


Carnobacterium viridans


C. amalonaticus





acetigignens








Caldicellulosiruptor


Campylobacter sputorum


Caryophanon


C. braakii





Caldicellulosiruptor bescii


Campylobacter upsaliensis


Calyophanon latum


C. diversus





Caldicellulosiruptor


Capnocytophaga


Calyophanon tenue


C. farmeri





kristjanssonii








Caldicellulosiruptor


Capnocytophaga canimorsus


Catellatospora


C. freundii





owensensis


Capnocytophaga cynodegmi


Catellatospora citrea


C. gillenii






Capnocytophaga gingivalis


Catellatospora


C. koseri






Capnocytophaga granulosa


methionotrophica


C. murliniae






Capnocytophaga


Catenococcus


C. pasteurii
[1]






haemolytica








Capnocytophaga ochracea


Catenococcus thiocycli


C. rodentium






Capnocytophaga sputigena



C. sedlakii








C. werkmanii








C. youngae








Clostridium







(see below)







Coccochloris








Coccochloris elabens








Corynebacterium








Corynebacterium flavescens








Corynebacterium variabile










Clostridium




Clostridium absonum, Clostridium aceticum, Clostridium acetireducens, Clostridium acetobutylicum, Clostridium acidisoli, Clostridium aciditolerans,




Clostridium acidurici, Clostridium aerotolerans, Clostridium aestuarii, Clostridium akagii, Clostridium aldenense, Clostridium aldrichii, Clostridium




algidicarni, Clostridium algidixylanolyticum, Clostridium algifaecis, Clostridium algoriphilum, Clostridium alkalicellulosi, Clostridium aminophilum,




Clostridium aminovalericum, Clostridium amygdalinum, Clostridium amylolyticum, Clostridium arbusti, Clostridium arcticum, Clostridium




argentinense, Clostridium asparagifomie, Clostridium aurantibutyricum, Clostridium autoethanogenum, Clostridium baratii, Clostridium barkeri,




Clostridium bartlettii, Clostridium beijerinckii, Clostridium bifermentans, Clostridium bolteae, Clostridium bornimense, Clostridium botulinum,




Clostridium bowmanii, Clostridium bryantii, Clostridium butyricum, Clostridium cadaveris, Clostridium caenicola, Clostridium caminithermale,



Clostridium carboxidivorans, Clostridium carnis, Clostridium cavendishii, Clostridium celatum, Clostridium celerecrescens, Clostridium



cellobioparum, Clostridium cellulofermentans, Clostridium cellulolyticum, Clostridium cellulosi, Clostridium cellulovorans, Clostridium




chartatabidum, Clostridium chauvoei, Clostridium chromiireducens, Clostridium citroniae, Clostridium clariflavum, Clostridium clostridioforme,




Clostridium coccoides, Clostridium cochlearium, Clostridium colletant, Clostridium colicanis, Clostridium colinum, Clostridium collagenovorans,




Clostridium cylindrosporum, Clostridium difficile, Clostridium diolis, Clostridium disporicum, Clostridium drakei, Clostridium durum,




Clostridium estertheticum, Clostridium estertheticum estertheticum, Clostridium estertheticum laramiense, Clostridium fallax, Clostridium




felsineum, Clostridium fervidum, Clostridium fimetarium, Clostridium formicaceticum, Clostridium frigidicarnis, Clostridium frigoris,




Clostridium ganghwense, Clostridium gasigenes, Clostridium ghonii, Clostridium glycolicum, Clostridium glycyrrhizinilyticum, Clostridium




grantii, Clostridium haemolyticum, Clostridium halophilum, Clostridium hastiforme, Clostridium hathewayi, Clostridium herbivorans,




Clostridium hiranonis, Clostridium histolyticum, Clostridium homopropionicum, Clostridium huakuii, Clostridium hungatei, Clostridium




hydrogenifomians, Clostridiumhydroxybenzoicum, Clostridium hylemonae, Clostridium jejuense, Clostridium indolis, Clostridium




innocuum, Clostridium intestinale, Clostridium irregulare, Clostridium isatidis, Clostridium josui, Clostridium kluyveri, Clostridium




lactatifermentans, Clostridium lacusfryxellense, Clostridium laramiense, Clostridium lavalense, Clostridium lentocellum, Clostridium




lentoputrescens, Clostridium leptum, Clostridium limosum, Clostridium litorale, Clostridium lituseburense, Clostridium ljungdahlii, Clostridium




lortetii, Clostridium lundense, Clostridium magnum, Clostridium malenominatum, Clostridium mangenotii, Clostridium mayombei, Clostridium




methoxybenzovorans, Clostridium methylpentosum, Clostridium neopropionicum, Clostridium nexile, Clostridium nitrophenolicum,




Clostridium novyi, Clostridium oceanicum, Clostridium orbiscindens, Clostridium oroticum, Clostridium oxalicum, Clostridium papyrosolvens,




Clostridium
paradoxum, Clostridium paraperfringens (Alias: C. welchii), Clostridium paraputrificum, Clostridium pascui, Clostridium




pasteurianum, Clostridiumpeptidivorans, Clostridium perenne, Clostridium perfringens, Clostridium pfennigii, Clostridium phytofermentans,




Clostridium pilifomie, Clostridium polysaccharolyticum, Clostridium populeti, Clostridium propionicum, Clostridium proteoclasticum, Clostridium




proteolyticum, Clostridium psychrophilum, Clostridium puniceum, Clostridium purinilyticum, Clostridium putrefaciens, Clostridium




putrificum, Clostridium quercicolum, Clostridium quinii, Clostridium ramosum, Clostridium rectum, Clostridium roseum, Clostridium




saccharobutylicum, Clostridium saccharogumia, Clostridium saccharolyticum, Clostridium saccharoperbutylacetonicum, Clostridium




sardiniense, Clostridium sartagoforme, Clostridium scatologenes, Clostridium schirmacherense, Clostridium scindens, Clostridium septicum,




Clostridium sordellii, Clostridium sphenoides, Clostridium spiroforme, Clostridium sporogenes, Clostridium sporosphaeroides, Clostridium




stercorarium, Clostridium stercorarium leptospartum, Clostridium stercorarium stercorarium, Clostridium stercorarium thermolacticum,




Clostridium sticklandii, Clostridium straminisolvens, Clostridium subterminale, Clostridium sufflavum, Clostridium sulfidigenes, Clostridium




symbiosum, Clostridium tagluense, Clostridium tepidiprofundi, Clostridium termitidis, Clostridium tertium, Clostridium tetani, Clostridium




tetanomorphum, Clostridium thermaceticum, Clostridium thermautotrophicum, Clostridium thermoalcaliphilum, Clostridium thermobutyricum,




Clostridium thermocellum, Clostridium thermocopriae, Clostridium thermohydrosulfuricum, Clostridium thermolacticum, Clostridium




thermopalmarium, Clostridiumthermopapyrolyticum, Clostridium thermosaccharolyticum, Clostridium thermosuccinogenes, Clostridium




thermosulfurigenes, Clostridiumthiosulfatireducens, Clostridium tyrobutyricum, Clostridium uliginosum, Clostridium ultunense,




Clostridium villosum, Clostridium vincentii, Clostridium viride, Clostridium xylanolyticum, Clostridium xylanovorans













Dactylosporangium


Deinococcus


Delftia


Echinicola





Dactylosporangium


Deinococcus aerius


Delftia acidovorans


Echinicola pacifica





aurantiacum








Dactylosporangium fulvum


Deinococcus apachensis


Desulfovibrio


Echinicola vietnamensis





Dactylosporangium


Deinococcus aquaticus


Desulfovibrio desulfuricans






matsuzakiense








Dactylosporangium roseum


Deinococcus aquatilis


Diplococcus






Dactylosporangium


Deinococcus caeni


Diplococcus pneumoniae






thailandense








Dactylosporangium








vinaceum









Deinococcus radiodurans








Deinococcus radiophilus







Enterobacter


Enterobacter kobei


Faecalibacterium


Flavobacterium





E. aerogenes


E. ludwigii


Faecalibacterium prausnitzii


Flavobacterium antarcticum





E. amnigenus


E. mori


Fangia


Flavobacterium aquatile





E. agglomerans


E. nimipressuralis


Fangia hongkongensis


Flavobacterium





E. arachidis


E. olyzae


Fastidiosipila


aquidurense





E. asburiae


E. pulveris


Fastidiosipila sanguinis


Flavobacterium balustinum





E. cancerogenous


E. pyrinus


Fusobacterium


Flavobacterium croceum





E. cloacae


E. radicincitans


Fusobacterium nucleatum


Flavobacterium cucumis





E. cowanii


E. taylorae



Flavobacterium





E. dissolvens


E. turicensis



daejeonense





E. gergoviae


E. sakazakii



Flavobacterium defluvii






Enterobacter soli







E. helveticus


Enterococcus



Flavobacterium degerlachei





E. hormaechei


Enterococcus durans



Flavobacterium





E. intermedius


Enterococcus faecalis



denitrificans






Enterococcus faecium



Flavobacterium filum






Erwinia



Flavobacterium flevense






Erwinia hapontici



Flavobacterium frigidarium






Escherichia



Flavobacterium mizutaii






Escherichia coli










Flavobacterium








okeanokoites





Gaetbulibacter


Haemophilus


Ideonella


Janibacter





Gaetbulibacter


Haemophilus aegyptius


Ideonella azotifigens


Janibacter anophelis





saemankumensis








Gallibacterium


Haemophilus aphrophilus


Idiomarina


Janibacter corallicola





Gallibacterium anatis


Haemophilus felis


Idiomarina abyssalis


Janibacter limosus





Gallicola


Haemophilus gallinarum


Idiomarina baltica


Janibacter melonis





Gallicola barnesae


Haemophilus haemolyticus


Idiomarina fontislapidosi


Janibacter terrae





Garciella


Haemophilus influenzae


Idiomarina loihiensis


Jannaschia




Garciella nitratireducens

Haemophilus paracuniculus


Idiomarina ramblicola


Jannaschia cystaugens





Geobacillus


Haemophilus


Idiomarina seosinensis


Jannaschia helgolandensis






parahaemolyticus







Geobacillus


Haemophilus parainfluenzae


Idiomarina zobellii


Jannaschia pohangensis





thermoglucosidasius








Geobacillus


Haemophilus


Ignatzschineria


Jannaschia rubra





stearothermophilus








Geobacter


paraphrohaemolyticus


Ignatzschineria larvae






Geobacter bemidjiensis


Haemophilus parasuis



Janthinobacterium





Geobacter bremensis


Haemophilus pittmaniae


Ignavigranum


Janthinobacterium





Geobacter chapellei


Hafnia


Ignavigranum ruoffiae


agaricidamnosum





Geobacter grbiciae


Hafnia alvei


Ilumatobacter


Janthinobacterium lividum





Geobacter hydrogenophilus


Hahella


Ilumatobacter fluminis


Jejuia





Geobacter lovleyi


Hahella ganghwensis


Ilyobacter


Jejuia pallidilutea





Geobacter metallireducens



Ilyobacter delafieldii






Geobacter pelophilus


Halalkalibacillus


Ilyobacter insuetus


Jeotgalibacillus





Geobacter pickeringii


Halalkalibacillus halophilus


Ilyobacter polytropus


Jeotgalibacillus





Geobacter sulfurreducens


Helicobacter


Ilyobacter tartaricus


alimentarius





Geodermatophilus


Helicobacter pylori



Jeotgalicoccus





Geodermatophilus obscurus




Jeotgalicoccus halotolerans





Gluconacetobacter








Gluconacetobacter xylinus








Gordonia








Gordonia rubripertincta








Kaistia


Labedella


Listeria ivanovii


Micrococcus


Nesterenkonia




Kaistia adipata


Labedella gwakjiensis


L. marthii


Micrococcus luteus


Nesterenkonia holobia




Kaistia soli


Labrenzia


L. monocytogenes


Micrococcus lylae


Nocardia




Kangiella


Labrenzia aggregata


L. newyorkensis


Moraxella


Nocardia argentinensis




Kangiella aquimarina


Labrenzia alba


L. riparia


Moraxella bovis


Nocardia corallina




Kangiella koreensis


Labrenzia alexandrii


L. rocourtiae


Moraxella nonliquefaciens


Nocardia





Labrenzia marina


L. seeligeri


Moraxella osloensis


otitidiscaviarum




Kerstersia


Labrys


L. weihenstephanensis


Nakamurella





Kerstersia gyiorum


Labrys methylaminiphilus


L. welshimeri


Nakamurella multipartita





Kiloniella


Labrys miyagiensis


Listonella


Nannocystis





Kiloniella laminariae


Labrys monachus


Listonella anguillarum


Nannocystis pusilla





Klebsiella


Labrys okinawensis


Macrococcus


Natranaerobius





K. granulomatis


Labrys portucalensis


Macrococcus bovicus


Natranaerobius





K. oxytoca



Marinobacter


themophilus





K. pneumoniae


Lactobacillus


Marinobacter algicola


Natranaerobius trueperi





K. terrigena

[see below]

Marinobacter bryozoorum


Naxibacter





K. variicola


Laceyella


Marinobacter flavimaris


Naxibacter alkalitolerans





Kluyvera


Laceyella putida


Meiothermus


Neisseria





Kluyvera ascorbata


Lechevalieria


Meiothermus ruber


Neisseria cinerea





Kocuria


Lechevalieria


Methylophilus


Neisseria denitrificans






aerocolonigenes







Kocuria roasea


Legionella


Methylophilus


Neisseria gonorrhoeae





Kocuria varians

[see below]

methylotrophus


Neisseria lactamica





Kurthia


Listeria


Microbacterium


Neisseria mucosa





Kurthia zopfii


L. aquatica


Microbacterium


Neisseria sicca






L. booriae


ammoniaphilum


Neisseria subflava






L. cornellensis


Microbacterium arborescens


Neptunomonas






L. fleischmannii


Microbacterium liquefaciens


Neptunomonas japonica






L. floridensis


Microbacterium oxydans







L. grandensis








L. grayi








L. innocua







Lactobacillus








L. acetotolerans


L. catenaformis


L. mali


L. parakefiri


L. sakei




L. acidifarinae


L. ceti


L. manihotivorans


L. paralimentarius


L. salivarius




L. acidipiscis


L. coleohominis


L. mindensis


L. paraplantarum


L. sanfranciscensis




L. acidophilus


L. collinoides


L. mucosae


L. pentosus


L. satsumensis




Lactobacillus agilis


L. composti


L. murinus


L. perolens


L. secaliphilus




L. algidus


L. concavus


L. nagelii


L. plantarum


L. sharpeae




L. alimentarius


L. colyniformis


L. namurensis


L. pontis


L. siliginis




L. amylolyticus


L. crispatus


L. nantensis


L. protectus


L. spicheri




L. amylophilus


L. crustorum


L. oligofermentans


L. psittaci


L. suebicus




L. amylotrophicus


L. curvatus


L. oris


L. rennini


L. thailandensis




L. amylovorus


L. delbrueckii subsp.


L. panis


L. reuteri


L. ultunensis




L. animalis


bulgaricus


L. pantheris


L. rhamnosus


L. vaccinostercus




L. antri


L. delbrueckii subsp.


L. parabrevis


L. rimae


L. vaginalis




L. apodemi


delbrueckii


L. parabuchneri


L. rogosae


L. versmoldensis




L. aviarius


L. delbrueckii subsp. lactis


L. paracasei


L. rossiae


L. vini




L. bifementans


L. dextrinicus


L. paracollinoides


L. ruminis


L. vitulinus




L. brevis


L. diolivorans


L. parafarraginis


L. saerimneri


L. zeae




L. buchneri


L. equi


L. homohiochii


L. jensenii


L. zymae




L. camelliae


L. equigenerosi


L. iners


L. johnsonii


L. gastricus




L. casei


L. farraginis


L. ingluviei


L. kalixensis


L. ghanensis




L. kitasatonis


L. farciminis


L. intestinalis


L. kefiranofaciens


L. graminis




L. kunkeei


L. fermentum


L. fuchuensis


L. kefiri


L. hammesii




L. leichmannii


L. fomicalis


L. gallinarum


L. kimchii


L. hamsteri




L. lindneri


L. fructivorans


L. gasseri


L. helveticus


L. harbinensis




L. malefermentans


L. frumenti



L. hilgardii


L. hayakitensis




Legionella








Legionella adelaidensis


Legionella drancourtii


Candidatus Legionella jeonii


Legionella quinlivanii





Legionella anisa


Legionella dresdenensis


Legionella jordanis


Legionella rowbothamii





Legionella beliardensis


Legionella drozanskii


Legionella lansingensis


Legionella rubrilucens





Legionella birminghamensis


Legionella dumoffii


Legionella londiniensis


Legionella sainthelensi





Legionella bozemanae


Legionella erythra


Legionella longbeachae


Legionella santicrucis





Legionella brunensis


Legionella fairfieldensis


Legionella lytica


Legionella shakespearei





Legionella busanensis


Legionella fallonii


Legionella maceachernii


Legionella spiritensis





Legionella cardiaca


Legionella feeleii


Legionella massiliensis


Legionella steelei





Legionella cherrii


Legionella geestiana


Legionella micdadei


Legionella steigerwaltii





Legionella cincinnatiensis


Legionella genomospecies


Legionella monrovica


Legionella taurinensis




Legionella clemsonensis

Legionella gormanii


Legionella moravica


Legionella tucsonensis





Legionella donaldsonii


Legionella gratiana


Legionella nagasakiensis


Legionella tunisiensis






Legionella gresilensis


Legionella nautarum


Legionella wadsworthii






Legionella hackeliae


Legionella norrlandica


Legionella waltersii






Legionella impletisoli


Legionella oakridgensis


Legionella worsleiensis






Legionella israelensis


Legionella parisiensis


Legionella yabuuchiae






Legionella jamestowniensis


Legionella pittsburghensis








Legionella pneumophila








Legionella quateirensis






Oceanibulbus


Paenibacillus


Prevotella


Quadrisphaera





Oceanibulbus indolifex


Paenibacillus


Prevotella albensis


Quadrisphaera granulorum






thiaminolyticus







Oceanicaulis


Pantoea


Prevotella amnii


Quatrionicoccus





Oceanicaulis alexandrii


Pantoea agglomerans


Prevotella bergensis


Quatrionicoccus





Oceanicola



Prevotella bivia


australiensis





Oceanicola batsensis


Paracoccus


Prevotella brevis






Oceanicola granulosus


Paracoccus alcaliphilus


Prevotella bryantii


Quinella





Oceanicola nanhaiensis


Paucimonas


Prevotella buccae


Quinella ovalis





Oceanimonas


Paucimonas lemoignei


Prevotella buccalis






Oceanimonas baumannii


Pectobacterium


Prevotella copri


Ralstonia





Oceaniserpentilla


Pectobacterium aroidearum


Prevotella dentalis


Ralstonia eutropha





Oceaniserpentilla haliotis


Pectobacterium


Prevotella denticola


Ralstonia insidiosa






atrosepticum







Oceanisphaera


Pectobacterium


Prevotella disiens


Ralstonia mannitolilytica





Oceanisphaera donghaensis


betavasculorum


Prevotella histicola


Ralstonia pickettii





Oceanisphaera litoralis


Pectobacterium cacticida


Prevotella intermedia


Ralstonia





Oceanithermus


Pectobacterium carnegieana


Prevotella maculosa


pseudosolanacearum





Oceanithermus desulfurans


Pectobacterium


Prevotella marshii


Ralstonia syzygii






carotovorum







Oceanithermus profundus


Pectobacterium


Prevotella melaninogenica


Ralstonia solanacearum






chrysanthemi








Pectobacterium cypripedii


Prevotella micans






Oceanobacillus


Pectobacterium rhapontici


Prevotella multiformis


Ramlibacter





Oceanobacillus caeni


Pectobacterium wasabiae


Prevotella nigrescens


Ramlibacter henchirensis





Oceanospirillum


Planococcus


Prevotella oralis


Ramlibacter tataouinensis





Oceanospirillum linum


Planococcus citreus


Prevotella oris







Planomicrobium


Prevotella oulorum


Raoultella






Planomicrobium


Prevotella pallens


Raoultella ornithinolytica






okeanokoites








Plesiomonas


Prevotella salivae


Raoultella planticola






Plesiomonas shigelloides


Prevotella stercorea


Raoultella terrigena






Proteus


Prevotella tannerae


Rathayibacter






Proteus vulgaris


Prevotella timonensis


Rathayibacter caricis







Prevotella veroralis


Rathayibacter festucae







Providencia


Rathayibacter iranicus







Providencia stuartii


Rathayibacter rathayi







Pseudomonas


Rathayibacter toxicus







Pseudomonas aeruginosa


Rathayibacter tritici







Pseudomonas alcaligenes


Rhodobacter







Pseudomonas anguillispetica


Rhodobacter sphaeroides







Pseudomonas fluorescens


Ruegeria







Pseudoalteromonas


Ruegeria gelatinovorans







haloplanktis








Pseudomonas mendocina








Pseudomonas








pseudoalcaligenes








Pseudomonas putida








Pseudomonas tutzeri








Pseudomonas syringae








Psychrobacter








Psychrobacter faecalis








Psychrobacter








phenylpyruvicus






Saccharococcus


Sagittula


Sanguibacter


Stenotrophomonas


Tatlockia




Saccharococcus


Sagittula stellata


Sanguibacter keddieii


Stenotrophomonas


Tatlockia maceachernii




thermophilus








Saccharomonospora


Salegentibacter


Sanguibacter suarezii


maltophilia


Tatlockia micdadei




Saccharomonospora azurea


Salegentibacter salegens


Saprospira


Streptococcus


Tenacibaculum




Saccharomonospora cyanea


Salimicrobium


Saprospira grandis



Tenacibaculum




Saccharomonospora viridis


Salimicrobium album


Sarcina

[also see below]

amylolyticum




Saccharophagus


Salinibacter


Sarcina maxima


Streptomyces


Tenacibaculum discolor




Saccharophagus degradans


Salinibacter ruber


Sarcina ventriculi


Streptomyces


Tenacibaculum




Saccharopolyspora


Salinicoccus


Sebaldella


achromogenes


gallaicum




Saccharopolyspora elythraea


Salinicoccus alkaliphilus


Sebaldella termitidis


Streptomyces cesalbus


Tenacibaculum




Saccharopolyspora gregorii


Salinicoccus hispanicus



Streptomyces cescaepitosus


lutimaris




Saccharopolyspora hirsuta


Salinicoccus roseus


Serratia


Streptomyces cesdiastaticus


Tenacibaculum




Saccharopolyspora hordei



Serratia fonticola


Streptomyces cesexfoliatus


mesophilum




Saccharopolyspora



Serratia marcescens


Streptomyces fimbriatus





rectivirgula








Saccharopolyspora spinosa


Salinispora


Sphaerotilus


Streptomyces fradiae


Tenacibaculum




Saccharopolyspora taberi


Salinispora arenicola


Sphaerotilus natans


Streptomyces fulvissimus


skagerrakense




Saccharothrix


Salinispora tropica


Sphingobacterium


Streptomyces griseoruber


Tepidanaerobacter




Saccharothrix australiensis


Salinivibrio


Sphingobacterium


Streptomyces griseus


Tepidanaerobacter






multivorum






Saccharothrix coeruleofusca


Salinivibrio costicola


Staphylococcus


Streptomyces lavendulae


syntrophicus




Saccharothrix espanaensis


Salmonella

[see below]

Streptomyces


Tepidibacter




Saccharothrix longispora


Salmonella bongori



phaeochromogenes


Tepidibacter




Saccharothrix mutabilis


Salmonella enterica



Streptomyces


fomicigenes




Saccharothrix syringae


Salmonella subterranea



themodiastaticus


Tepidibacter




Saccharothrix tangerinus


Salmonella typhi



Streptomyces tubercidicus


thalassicus




Saccharothrix texasensis





Thermus








Thermus aquaticus








Thermus filiformis








Thermus thermophilus




Staphylococcus








S. arlettae


S. equorum


S. microti


S. schleiferi





S. agnetis


S. felis


S. muscae


S. sciuri





S. aureus


S. fleurettii


S. nepalensis


S. simiae





S. auricularis


S. gallinarum


S. pasteuri


S. simulans





S. capitis


S. haemolyticus


S. petrasii


S. stepanovicii





S. caprae


S. hominis


S. pettenkoferi


S. succinus





S. carnosus


S. hyicus


S. piscifermentans


S. vitulinus





S. caseolyticus


S. intermedius


S. pseudintermedius


S. warneri





S. chromogenes


S. kloosii


S. pseudolugdunensis


S. xylosus





S. cohnii


S. leei


S. pulvereri






S. condimenti


S. lentus


S. rostri






S. delphini


S. lugdunensis


S. saccharolyticus






S. devriesei


S. lutrae


S. saprophyticus






S. epidermidis


S. lyticans








S. massiliensis







Streptococcus








Streptococcus agalactiae


Streptococcus infantarius


Streptococcus orisratti


Streptococcus themophilus





Streptococcus anginosus


Streptococcus iniae


Streptococcus parasanguinis


Streptococcus sanguinis





Streptococcus bovis


Streptococcus intermedius


Streptococcus peroris


Streptococcus sobrinus





Streptococcus canis


Streptococcus lactarius


Streptococcus pneumoniae


Streptococcus suis





Streptococcus constellatus


Streptococcus milleri


Streptococcus


Streptococcus uberis





Streptococcus downei


Streptococcus mitis


pseudopneumoniae


Streptococcus vestibularis





Streptococcus dysgalactiae


Streptococcus mutans


Streptococcus pyogenes


Streptococcus viridans





Streptococcus equines


Streptococcus oralis


Streptococcus ratti


Streptococcus





Streptococcus faecalis


Streptococcus tigurinus


Streptococcus salivariu


zooepidemicus





Streptococcus ferus








Uliginosibacterium


Vagococcus


Vibrio


Virgibacillus


Xanthobacter





Vagococcus carniphilus


Vibrio aerogenes


Virgibacillus


Xanthobacter agilis




Uliginosibacterium


Vagococcus elongatus


Vibrio aestuarianus


halodenitrificans


Xanthobacter




gangwonense








Ulvibacter


Vagococcus fessus


Vibrio albensis


Virgibacillus


aminoxidans




Ulvibacter litoralis


Vagococcus fluvialis


Vibrio alginolyticus


pantothenticus


Xanthobacter




Umezawaea


Vagococcus
lutrae


Vibrio campbellii


Weissella


autotrophicus




Umezawaea tangerina


Vagococcus salmoninarum


Vibrio cholerae


Weissella cibaria


Xanthobacter flavus




Undibacterium


Variovorax


Vibrio cincinnatiensis


Weissella confusa


Xanthobacter tagetidis




Undibacterium pigrum


Variovorax boronicumulans


Vibrio coralliilyticus


Weissella halotolerans


Xanthobacter viscosus




Ureaplasma


Variovorax dokdonensis


Vibrio cyclitrophicus


Weissella hellenica


Xanthomonas




Ureaplasma urealyticum


Variovorax paradoxus


Vibrio diazotrophicus


Weissella kandleri


Xanthomonas





Variovorax soli


Vibrio fluvialis


Weissella koreensis


albilineans




Ureibacillus


Veillonella


Vibrio furnissii


Weissella minor


Xanthomonas alfalfae




Ureibacillus composti


Veillonella atypica


Vibrio gazogenes


Weissella


Xanthomonas




Ureibacillus suwonensis


Veillonella caviae


Vibrio halioticoli


paramesenteroides


arboricola




Ureibacillus terrenus


Veillonella criceti


Vibrio harveyi


Weissella soli


Xanthomonas




Ureibacillus thermophilus


Veillonella dispar


Vibrio ichthyoenteri


Weissella thailandensis


axonopodis




Ureibacillus


Veillonella montpellierensis


Vibrio mediterranei


Weissella viridescens


Xanthomonas




thermosphaericus









Veillonella parvula


Vibrio metschnikovii


Williamsia


campestris





Veillonella ratti


Vibrio mytili


Williamsia marianensis


Xanthomonas citri





Veillonella rodentium


Vibrio natriegens


Williamsia maris


Xanthomonas codiaei





Venenivibrio


Vibrio navarrensis


Williamsia serinedens


Xanthomonas





Venenivibrio


Vibrio nereis



cucurbitae





stagnispumantis









Vibrio nigripulchritudo


Winogradskyella


Xanthomonas





Verminephrobacter


Vibrio ordalii


Winogradskyella


euvesicatoria





Verminephrobacter eiseniae


Vibrio orientalis


thalassocola


Xanthomonas fragariae






Vibrio parahaemolyticus


Wolbachia


Xanthomonas fuscans





Verrucomicrobium


Vibrio pectenicida


Wolbachia persica


Xanthomonas gardneri





Verrucomicrobium


Vibrio penaeicida



Xanthomonas hortorum





spinosum









Vibrio proteolyticus


Wolinella


Xanthomonas hyacinthi






Vibrio shilonii


Wolinella succinogenes


Xanthomonas perforans






Vibrio splendidus



Xanthomonas phaseoli






Vibrio tubiashii


Zobellia


Xanthomonas pisi






Vibrio vulnificus


Zobellia galactanivorans


Xanthomonas populi







Zobellia uliginosa


Xanthomonas theicola







Zoogloea


Xanthomonas







Zoogloea ramigera


translucens







Zoogloea resiniphila









Xanthomonas








vesicatoria








Xylella








Xylella fastidiosa








Xylophilus








Xylophilus ampelinus




Xenophilus


Yangia


Yersinia mollaretii


Zooshikella


Zobellella




Xenophilus azovorans


Yangia pacifica


Yersinia philomiragia


Zooshikella ganghwensis


Zobellella denitrificans




Xenorhabdus


Yaniella


Yersinia pestis


Zunongwangia


Zobellella taiwanensis




Xenorhabdus beddingii


Yaniella flava


Yersinia pseudotuberculosis


Zunongwangia profunda





Xenorhabdus bovienii


Yaniella halotolerans


Yersinia rohdei


Zymobacter


Zeaxanthinibacter




Xenorhabdus cabanillasii


Yeosuana


Yersinia ruckeri


Zymobacter palmae


Zeaxanthinibacter




Xenorhabdus doucetiae


Yeosuana aromativorans


Yokenella


Zymomonas


enoshimensis




Xenorhabdus griffiniae


Yersinia


Yokenella regensburgei


Zymomonas mobilis


Zhihengliuella




Xenorhabdus hominickii


Yersinia aldovae


Yonghaparkia


Zymophilus


Zhihengliuella




Xenorhabdus koppenhoeferi


Yersinia bercovieri


Yonghaparkia alkaliphila


Zymophilus paucivorans


halotolerans




Xenorhabdus nematophila


Yersinia enterocolitica


Zavarzinia


Zymophilus raffinosivorans


Xylanibacterium




Xenorhabdus poinarii


Yersinia entomophaga


Zavarzinia compransoris



Xylanibacterium ulmi




Xylanibacter


Yersinia frederiksenii







Xylanibacter olyzae


Yersinia intermedia








Yersinia kristensenii

















TABLE 2





Sequences


Nucleic acid sequences herein are written in 5′


to 3′ direction; amino acid sequences are


written in N- to C-terminal direction.















SEQ ID NO: 1 (P10)


TTTCAATTTAATCATCCGGCTCGTATAATGTGTGGA





SEQ ID NO: 2 (BCD14)


GGGCCCAAGTTCACTTAAAAAGGAGATCAACAATGAAAGCAATTTTCGTA


CTGAAACATCTTAATCATGCGGTGGAGGGTTTCTAATG





SEQ ID NO: 3 (gfp)


ATGAGCAAAGGAGAAGAACTTTTCACTGGAGTTGTC





SEQ IDs NO: 4 & 29 (example Expression Operating


Unit, EOU)


The EOU is (in 5′ to 3′ direction):-


[SEQ ID NO: 4]-[promoter]-[TIS]-[GFP-encoding


nucleotide sequence]-[SEQ ID NO: 29]


Where


SEQ ID NO: 4 is


GAATTCAAAAGATCTTAAGTAAGTAAGAGTATACGTATATCGGCTAATAA


CGTATTAAGGCGCTTCGGCGCCTTTTTTTATGGGGGTATTTTCATCCCAA


TCCACACGTCCAACGCACAGCAAACACCACGTCGACCCTATCAGCTGCGT


GCTTTCTATGAGTCGTTGCTGCATAACTTGACAATTAATCATCCGGCTCG


TATAATGTGTGGAA





SEQ ID NO: 29 is


GGATCCAAACTCGAGTAAGGATCTCCAGGCATCAAATAAAACGAAAGGCT


CAGTCGAAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGC


TCTCTACTAGAGTCACACTGGCTCACCTTCGGGTGGGCCTTTCTGCGTTT


ATA





SEQ ID NO: 5 (Example Shine Dalgarno Sequence)


AAAGAGGAGAAA





SEQ ID NO: 26 (Spacer sequence)


CTTTGCCGCGCGCTTCGTCACGTAATTCTCGTCGCAA





SEQ ID NO: 27 (Spacer sequence)


GTTTGGCGATGGCGCGGGTGTGGTTGTGCTTCGGCGT





SEQ ID NO: 28 (Spacer sequence)


TGGGATGCCTACCGCAAGCAGCTTGGCCTGAA
















TABLE 3







Anderson Promoter Collection










SEQ





ID
Identi-

Measured


NO:
fier
Sequencea
Strengthb





 6
BBa 
TTGACAGCTAGCTCAGTCCTAGGTA
n/a



J23119
TAATGCTAGC






 7
BBa 
TTGACGGCTAGCTCAGTCCTAGGTA
1



J23100
CAGTGCTAGC






 8
BBa 
TTTACAGCTAGCTCAGTCCTAGGTA
0.7



J23101
TTATGCTAGC






 9
BBa 
TTGACAGCTAGCTCAGTCCTAGGTA
0.86



J23102
CTGTGCTAGC






10
BBa 
CTGATAGCTAGCTCAGTCCTAGGGA
0.01



J23103
TTATGCTAGC






11
BBa 
TTGACAGCTAGCTCAGTCCTAGGTA
0.72



J23104
TTGTGCTAGC






12
BBa 
TTTACGGCTAGCTCAGTCCTAGGTA
0.24



J23105
CTATGCTAGC






13
BBa 
TTTACGGCTAGCTCAGTCCTAGGTA
0.47



J23106
TAGTGCTAGC






14
BBa 
TTTACGGCTAGCTCAGCCCTAGGTA
0.36



J23107
TTATGCTAGC






15
BBa 
CTGACAGCTAGCTCAGTCCTAGGTA
0.51



J23108
TAATGCTAGC






16
BBa 
TTTACAGCTAGCTCAGTCCTAGGGA
0.04



J23109
CTGTGCTAGC






17
BB3 
TTTACGGCTAGCTCAGTCCTAGGTA
0.33



J23110
CAATGCTAGC






18
BBa 
TTGACGGCTAGCTCAGTCCTAGGTA
0.58



J23111
TAGTGCTAGC






19
BBa 
CTGATAGCTAGCTCAGTCCTAGGGA
0



J23112
TTATGCTAGC






20
BBa 
CTGATGGCTAGCTCAGTCCTAGGGA
0.01



J23113
TTATGCTAGC






21
BBa 
TTTATGGCTAGCTCAGTCCTAGGTA
0.1



J23114
CAATGCTAGC






22
BBa 
TTTATAGCTAGCTCAGCCCTTGGTA
0.15



J23115
CAATGCTAGC






23
BBa 
TTGACAGCTAGCTCAGTCCTAGGGA
0.16



J23116
CTATGCTAGC






24
BBa 
TTGACAGCTAGCTCAGTCCTAGGGA
0.06



J23117
TTGTGCTAGC






25
BBa 
TTGACGGCTAGCTCAGTCCTAGGTA
0.56



J23118
TTGTGCTAGC






aalso shown in the Anderson Catalog, see parts.igem.org/Promoters/Catalog/Anderson




bStrength is the Anderson Score (AS), e.g., a strength of 1 is a AS of 1. Reported activities of the promoters are given as the relative fluorescence of plasmids in strain TG1 grown in LB media to saturation. A suitable plasmid is EX-Ptet-S-rbsRFP-P /RFP reporter/ as described at parts.igem.org/Part:BBa_J61002; insertion of a promoter element between XbaI and SpeI sites results in a RFP reporter.






Claims
  • 1. A cell of a production strain of bacterial or archaeal cells, comprising a first DNA construct wherein: the first DNA construct comprises a nucleotide sequence encoding a Cas nuclease, wherein the nucleotide sequence is under the control of a promoter for controlling the expression of the Cas nuclease in the production strain cell, whereinthe first DNA construct comprises an origin of replication that is operable in the cell for replication of the construct;the promoter comprises a nucleotide sequence that is capable of binding to a repressor;wherein the production strain cell comprises a nucleic acid encoding the repressor;wherein the nucleic acid encoding the repressor is a chromosomally-integrated sequence or comprised by a second DNA construct;wherein the promoter is repressible by the repressor in the production strain;wherein the Cas nuclease is operable with one or more crRNAs or gRNAs to cut target nucleotide sequences in a target host cell.
  • 2. The cell of claim 1, wherein the nucleotide sequence that is capable of binding to the repressor is a tetO or lacO.
  • 3. The cell of claim 2, wherein the promoter is PLtetO-1, PLlacO-1, or a repressible homologue thereof.
  • 4. The cell of claim 1, wherein the repressor is a tetracycline repressor (TetR) or a lac repressor (LacR).
  • 5. The cell of claim 1, wherein the nucleic acid encoding the repressor is a chromosomally-integrated sequence.
  • 6. The cell of claim 1, wherein the nucleic acid encoding the repressor is a sequence comprised by an episome.
  • 7. The cell of claim 1, wherein the first DNA construct is a plasmid or phagemid.
  • 8. The cell of claim 1, wherein the first DNA construct is capable of being amplified in the cell of the production strain.
  • 9. The cell of claim 8, wherein the repressor is expressible while the first DNA construct is amplified.
  • 10. The cell of claim 1, wherein the promoter for controlling the expression of the Cas nuclease in the production strain cell combined with a translation initiation site (TIS) is capable of producing expression of green fluorescent protein (GFP) from a first expression operating unit (EOU) in E. coli strain BW25113 cells with a fluorescence of from 0.5 to 4 times the fluorescence produced in E. coli strain BW25113 cells using a second EOU comprising a P10 promoter (SEQ ID NO: 1) combined with a BCD14 TIS (SEQ ID NO: 2), wherein the EOUs differ only in their promoter and TIS combinations, wherein each EOU comprises (in 5′ to 3′ direction) an upstream initiator, the respective promoter, the respective TIS, a nucleotide sequence encoding GFP, a 3′ UTR, a transcription terminator and a downstream insulator.
  • 11. The cell of claim 10, wherein fluorescence using the first EOU is 0.5 to 2 times the fluorescence using the second EOU.
  • 12. The cell of claim 7, wherein the first DNA construct is a high copy number plasmid or phagemid.
  • 13. The cell of claim 1, wherein the cell is capable of growth and propagation sufficient to produce at least 1000 copies of the first DNA construct.
  • 14. The cell of claim 1, wherein at least 105 copies of the first DNA construct can be produced per 103 cells of the production strain.
  • 15. The cell of claim 1, wherein a cell of the production strain is capable of at least 2 or 3 logs of expansion when the first DNA construct is comprised therein.
  • 16. The cell of claim 1, wherein the Cas is a Type I Cas.
  • 17. The cell of claim 1, wherein the Cas is a Cas3.
  • 18. The cell of claim 17, wherein the first DNA construct or the cell encodes Cascade proteins that are cognate with the Cas3.
  • 19. The cell of claim 1, wherein the Cas is a Cas9.
  • 20. The cell of claim 1, wherein the Cas is a Cpf1.
  • 21. The cell claim 1, wherein the cell of a production strain comprises a helper phage genome that is inducible to produce phage coat proteins in the cell.
  • 22. The cell of claim 21, wherein the cell of a production strain is capable of producing phage coat proteins in the cell, wherein the first DNA construct is packaged into phage particles or non-self-replicative transduction particles for introducing the first DNA into the target host cell.
  • 23. The cell of claim 22, wherein the phage particles or non-self-replicative transduction particles are devoid of an expressible nucleotide sequence encoding the repressor, whereby the promoter is functional when the first DNA construct is introduced into the target host cell.
  • 24. The cell of claim 1, wherein the first DNA construct comprises one or more nucleotide sequences for producing crRNAs or gRNAs that are operable with the Cas nuclease to cut target nucleotide sequences in the target host cell.
  • 25. The cell of claim 1, wherein the cell of the production strain is an E. coli cell.
  • 26. The cell of claim 23, wherein the target host cell is comprised by a gut microbiota.
  • 27. The cell of claim 23, wherein the target host cell is selected from the group consisting of a C. dificile, P. aeruginosa, K. pneumoniae (eg, carbapenem-resistant Klebsiella pneumoniae or Extended-Spectrum Beta-Lactamase (ESBL)-producing K. pneumoniae), E. coli (eg, ESBL-producing E. coli, or E. coli ST131-025b:H4), H. pylori, S. pneumoniae and S. aureus cell.
  • 28. The cell of claim 1, wherein the first DNA construct comprises an origin of replication that is operable in the cell of the production strain, wherein the Cas is not operable in the production strain cell to target and cut a chromosomal sequence thereof.
Priority Claims (2)
Number Date Country Kind
1816700.7 Oct 2018 GB national
1817509.1 Oct 2018 GB national
Continuations (1)
Number Date Country
Parent 16201736 Nov 2018 US
Child 17166941 US