Patent Application
20100184181
The invention relates to a genetic cluster of strains of Streptococcus thermophilus (S. thermophilus) having appropriate acidifying and texturizing properties for dairy fermentations.
Bacteriophages are viruses capable of attacking bacteria. During se viral attacks, the bacteriophages infect the bacterial culture, and multiply in order to finally destroy this culture. The technological impact on the milk processing industry (production of cheese, yoghurt, fermented milk) of these bacteriophages is significant since they can cause a complete cessation of fermentation and therefore prevent the production of these milk-derived products.
One way of combating the problems linked to the infection of the fermentations by bacteriophages is the use of strains having appropriate sensitivity spectra to the phages. In particular, producers of dairy ferments have developed strategies to combat the bacteriophages by constructing ferments constituted by several strains having distinct lysotypes, and using several of these ferments in rotation. It is clear that in order to be able to adopt this strategy it is important to possess a diversity of strains having the same functionalities (such as for example acidification, thickening power, flavouring etc.) but distinct lysotypes.
S. thermophilus are used extensively alone or in combination with other bacteria for the production of fermented food products. They are included in particular in the formulation of the ferments used for producing yoghurts. Strains of S. thermophilus are expected to participate in the formation of lactic curd by acidification of milk and in the development of the texture of the fermented product. A distinction generally drawn between 4 groups of S. thermophilus based on these functional properties: 1) non-texturizing and non-acidifying strains, 2) the non-texturizing and acidifying strains, 3) the texturizing and non-acidifying strains, and 4) the texturizing and acidify strains. A texturizing strain is a strain making, it possible to obtain fermented milks the gels of which can be described by their rheological properties.
Hitherto only four strains of S. thermophilus corresponding criteria of acidifying and texturizing strains have been described in the literature: Sfi39, CNCM I-2423, CNCM I-2426 and the strain CNCM I-2980 described in the Application WO2004/085607.
The rarity of such strains (rapid acidification and texturizing) makes it difficult to combat the bacteriophages during the fermentation of the milk. In fact, ideally, the fight against the bacteriophages would involve the combination in the same ferment of strains having similar technological properties but distinct lysotypes, then the use of ferments of this type in rotation. The ferments used in rotation should also have distinct lysotypes but similar technological properties. In the case of the texturizing and rapidly acidifying ferments, this approach is difficult in view of the small number of strains having these functional qualities.
Thus one of the problems which the invention proposes to resolve is to provide novel strains of S. thermophilus which have a lysotype distinct from the strains currently used, in particular strains which are acidifying and texturizing.
For this purpose, the invention relates to the strains of S. thermophilus in a genetic cluster which have a lysotype distinct from that of the acidifying and texturizing strains of S. thermophilus currently used. Within this cluster novel acidifying and texturizing strains have been identified.
The invention also describes a method making it possible to predict a strain's membership of a family of strains having identical or related lysotypes. This method analyzes the restriction polymorphism of the epsA-B-C-D region of the genome of S. thermophilus.
By the epsA-B-C-D region is meant the region of the chromosome of S. thermophilus overlapping the cpsA to epsD genes of the cps locus. The DNA fragment corresponding to this region, called the cpsAD fragment, can be obtained by PCR reaction on the chromosomic DNA or S. thermophilus oligonucleotides of SEQ ID No1 and SEQ ID No2 as primers.
A subject of the present invention is a strain of Streptococcus thermophilus the epsAD fragment of which, after digestion by the restriction enzymes Mn/I, FokI and HindIII, has a restriction profile characterized by DNA fragments of 344±2 base pairs (bp), 341±2 bp, 305±2 bp, 299±2 bp, 277±2 bp, 210±2 bp, 160±2 bp, 142±2 bp, 100±2 bp, 79±2 bp, 75±2 bp, 66±2 bp, 42±2 bp, 23±2 by and 9±2 bp. The restriction profile of the epsAD fragment is determined by standard sequencing of the epsAD fragment followed by in silico determination of the restriction profile.
Typically the sequencing can be carried out with the CEQ8000 equipment (Beckman) and the in silico determination of the restriction profile can be carried out starting from the sequence of the epsAD fragment using the NEBcutter V2.0 tool accessible on the internet via the website http://tools.neb.com/.
Typically a strain according to the invention comprises a nucleotide sequence having at least 80%, preferentially at least 90%, at least 95% or at least 97% and still more preferentially 100% identity with the nucleotide sequence of SEQ ID No4.
Typically a strain according to the invention comprises a nucleotide sequence having at least 80%, preferentially at least 90%, at least 95% or at least 97% and still more preferentially 100% identity with the nucleotide sequence of SEQ ID No5.
In order to calculate the percentage identity, a person skilled in the art will example use the “BLAST 2 Sequences” tool (Tatusova & Madden, 1999; http://www.ncbi.nlm.nih.gov/BLAST/) with the default parameters of the “blastn” program (for alignment of nucleotide sequences) or of the “blastp” program (for alignment of protein sequences). The percentage similarity between two protein sequences is calculated using the BLOSUM62 matrix.
Preferentially the strain according to the invention is texturizing. Preferentially the strain according to the invention acidifies rapidly. Still more preferentially the strain according to the invention is texturizing and acidifies rapidly.
By texturizing strain of Streptococcus thermophilus is meant a strain which produces fermented milks having, under the conditions described in the example, a viscosity greater than approximately 35 Pa·s, a thixotropic area of less than approximately 2000 Pa/s and/or a yield point of less than approximately 14 Pa.
By rapidly acidifying strain is meant a strain which under the conditions described in the example, a Vm of less than −0.0100 upH/min.
Preferentially, a strain according to the invention is the strain of Streptococcus thermophilus deposited on 14 Jun. 2006 at the Collection Nationale de Cultures de Microorganismes under no. CNCM I-3617 or a mutant strain which can be obtained from the latter.
Typically in order to obtain such mutant strains, a person skilled in the art can use the usual mutagenesis techniques such as UV irradiation or exposure to mutagenic chemical products (ethyl-methane-sulphonate, nitrosoguanidine, nitrous acid etc.).
Preferentially, a subject of the invention is the strain of Streptococcus thermophilus deposited on 14 Jun. 2006 in the name of Danisco France SAS, 20 rue de Brunel, 75017 Paris at the Collection Nationale de Cultures de Microorganismes under no. CNCM I-3617.
A person skilled in the art, starting from the restriction profiles described previously and/or from the sequences of SEQ ID No4 and/or No5, can identify the strains which belong to the same genetic cluster the strain CNCM I-3617. Typically in order to do this, he can use PCR and/or hybridization and/or DNA sequencing techniques.
A subject of the invention is also a bacterial composition comprising at least one strain according to the invention. By bacterial composition is meant a mixture of different strains, in particular a ferment, or a leaven.
The mixtures of preferred strains according to the invention are mixtures of Streptococcus thermophilus with other Streptococcus thermophilus, or mixtures of Streptococcus thermophilus with Lactobacillus delbrueckii subsp. bulgaricus, or mixtures of Streptococcus thermophilus with other Lactobacillus and/or with Bifidobacterium, or mixtures of Streptococcus thermophilus with Lactococcus, or mixtures of Streptococcus thermophilus with other strains of lactic bacteria and/or yeasts.
A subject of the invention is also a manufacturing process for a food product, a food complement, a dietary supplement or a product with probiotic properties, comprising a stage in which a strain according to the invention is used.
Typically the food product, the food complement, the dietary supplement or the product with probiotic properties is a dairy product, a meat product, a cereal product, a drink, a foam or a powder.
Preferentially the food product, the food complement, the dietary supplement or the product with probiotic properties is a dairy product. It is for example a fermented milk, a yoghurt, a matured cream, a cheese, a fromage frais, a milk drink, a dairy product retentate, a processed cheese, a cream dessert, a cottage cheese or an infant milk. Typically the dairy product comprises milk of animal and/or plant origin.
A subject of the invention is also a food product, a food complement, a dietary supplement or a product with probiotic properties comprising at least one strain according to the invention or the bacterial composition described previously.
The invention also describes a method for predicting the lysotype of a strain of S. thermophilus starting from analysis of the restriction polymorphism of the epsA-B-C-D region of its genome, comprising the following stages:
a) amplification of the epsAD fragment by PCR reaction on the chromosomic DNA of S. thermophilus using the oligonucleotides of SEQ ID No1 and SEQ ID No2 as primers;
b) sequencing of the epsAD fragment;
c) in silico determination of the restriction profile of the epsAD fragment after digestion by the restriction enzymes Mn/I, FokI and HindIII; and
d) comparison of the restriction profile obtained in Stage c) with the restriction profiles of the epsAD region of strains of S. thermophilus the lysotype which is known.
Examples of strains of Streptococcus thermophilus the lysotype of which is known are listed in Table 3.
The present invention is better illustrated below using the examples which follow. These examples are given only by way of illustration of the subject-matter of the invention, of which they in no way constitute a limitation.
Table 1 and Table 3 show some of the strains used for the study. Some of these strains are obtained from the Danisco collection of strains and phages (DGCC: Danisco Global Culture Collection). The preparation of cultures of these strains was carried out according to the standard methods of microbiology.
aon the basis of industrial use and the present study.
bon the basis of published sequence results of the eps locus and/or the structure of the polysaccharide and data internal to Danisco.
con the strain studied and/or on related strains.
The recent determination of the complete sequence of the chromosome of two strains of S. thermophilus CNRZ1066 and LMG18311 shows a high level of conservation of the genetic content and the organization of the genes in this species) Bolotin et al., 2004). One of the rare regions exhibiting major genetic differences between these two strains corresponds to the cps locus which codes for the genes involved in the biosynthesis of exopolysaccharides. Moreover, a great diversity has already been described at the level of this genetic locus (cf.
epsAD method: The tool developed is based on the specific amplification (PCR) of the epsA-B-C-D region followed by the analysis of its restriction polymorphism (RFLP). For this purpose primers have been determined which allow the PCR amplification of this region for the great majority of the strains of S. thermophilus. They have been determined by the alignment of the sequences of the epsAD region (cf.
Composition of the reaction mixture (50 μL): buffer for the DNA polymerase ×1, MgCl2 2 mM, dNTP 200 μM each, genomic DNA 100 to 500 ng, primer EPSA632 (5′-AAATgAATTCAgAgCAAgCACTTg-3′ (SEQ ID No1)) 200 nM, primer EPSD1064 (5′-gTCATgTCAACTTTATTAAggACg-3′ (SEQ ID No2)) 200 nM, DNA polymerase 1.25 units, H2O qsf 50 μL.
predenaturation at 94° C. for 1 min
35 cycles alternating denaturation at 94° C. for 30 s, hybridization at 56° C. for 30 s, elongation at 72° C. for 3 min
post-elongation at 72° C. for 6 min.
After amplification, the PCR product is checked by electrophoresis on 1.5% agarose gel. The size of the amplified product is approximately 2480 bp.
The sequence of the PCR fragment is determined (according to a method derived from Sanger et al., 1977) with CEQ8000 equipment (Beckman). The sequence is processed by the NEBcutter tool (for example, http://tools.neb.com/) by selecting the restriction enzymes Mn/I, FokI and HindIII in order to establish its restriction profile in silico, and in particular in order to define the size of the restriction fragments.
For the strains of S. thermophilus the sequence of the eps locus of which is partially or completely available in the public databases (GENBANK for example), the in silico analysis of the theoretical restriction products of the PCR fragment of approximately 2480 by with the restriction enzymes Mn/I, FokI and HindIII produces the restriction profiles shown in
S. thermophilus
Alternatively, the PCR product can be digested by the restriction enzymes Mn/I, FokI and HindIII under the following conditions: PCR product 15 to 30 μL, buffer 2 (New England Biolabs)×1, bovine serum albumin (New England Biolabs)×1, enzyme Mn/I (New England Biolabs) 1 unit, enzyme FokI (New England Biolabs) 1 unit, enzyme HindIII (New England Biolabs) 1 unit, H2O qsf 50 μL. Incubation at 37° C. for 1 hour.
The restriction fragments are then analyzed by electrophoresis. Electrophoresis on agarose gel can be used. However, in order to remedy the low resolution power of this type of electrophoresis (precision +/−10%) and the difficulty of visualizing fragments smaller than 100 bp, methods with a higher resolution (+/−0.1 to 1%) such as micro-fluidic electrophoresis (Agilent) or capillary electrophoresis may be preferred.
These methods (in silico analysis of the restriction profile or electrophoresis analysis of the restriction fragments) were applied to several hundreds of strains from the Danisco collection of S. thermophilus strains and the reference strains described in the literature.
The strains which have the same restriction profile have been grouped together genetic clusters (or genetic groups) denoted CL-1 to CL-12. Comparison of the restriction profiles was carried out by means of Bionumerics software version 3.5. Table 3 summarizes some of the results obtained.
Method for determining the sensitivity of a strain to a bacteriophage: The sensitivity of a strain to a bacteriophage is established by the lysis plaque method. 100 μl of a culture of the strain to be tested and 100 μl of an appropriate dilution of a serum containing the bacteriophage to be studied are used in order to seed 5 ml of an agar medium under suffusion (0.6% agar weight/volume) M17+glucose supplemented at 10 mM with CaCl2. The mixture is poured onto the surface of a solidified attar medium (1.5% agar weight/volume) M17+glucose supplemented at 10 mM with CaCl2. After incubation overnight at 42° C., the strain's sensitivity to the bacteriophage is evaluated by the presence of lysis plaques. The absence of lysis plaque signifies this strain's resistance to the bacteriophages tested. The spectrum of a strain's sensitivity to the bacteriophages, also called lysotype, is constituted by all of the sensitivities and resistances to the bacteriophages studied. A reference system with approximately sixty phages has been implemented in order to establish the lysotype of the strains of S. thermophilus in the Danisco collection. The strains which have the same lysotype have been grouped together in different groups denoted LT-n.
Some of the results are given in Table 3. It demonstrates in particular that the strains of the same genetic cluster virtually always have the same lysotype. The strain CNCM I-3617 belongs to a novel genetic group called CL-1 which has the very particular lysotype of being resistant to all the bacteriophages tested.
The genetic knowledge acquired with regard to S. thermophilus has shown that the eps locus is one of the major sites of heterogeneity between strains. This characteristic has already been exploited in part in order to develop the abovementioned genotyping method which uses the diversity in the epsA-B-C-D region which is the proximal region of the eps locus. An even greater diversity appears in the distal region of the eps locus (region encoding the glycosyl-transferases, see
The sequences SEQ ID No4 and SEQ ID No5 (cf.
The structural analysis of the eps locus of the strain CNCM I-3617 shows that it possesses an overall organization similar to that of the eps loci already known (cf.
The results of sequence comparison between the potential proteins deduced from the ORFs of the eps locus of CNCM I-3617 and those available in the public of databases (GENBANK) are summarized in Table 4. The eps locus of the strain CNCM I-3617 codes for proteins potentially involved in the synthesis of polysaccharide such as for example glycosyltransferases.
On the basis of these data, 6 regions can be distinguished (region 1 to region 6, from the 5′ end to the 3′ end of the eps locus; see
Overall, the distal part of the eps locus resembles a hybrid assembly of genes certain of which had never previously been described.
gasseri ATCC 33323
delbrueckii subsp. bulgaricus Lfi5
delbrueckii subsp. bulgaricus ATCC
johnsonii NCC 533
The fermentation support is obtained by supplementing 100 ml of semi-skimmed UHT milk (Le Petit Vendéen®) with 3% (weight/volume) of skimmed milk powder (SUP'R TOP®, Eurial Poitouraine). The sterility of the solution is obtained by pasteurization for 10 min at 90° C. (at the core). The fermentation support thus obtained is inoculated with the strain to be tested at a rate of 106 cfu/ml, then incubated at 43° C. (in a water bath). The pH is continuously monitored using a CINAC apparatus (Ysebaert).
The acidifying properties of the strains of S. thermophilus can be described by the maximum rate of acidification, Vm (pH unit/min (pHu/min)), calculated by the maximum value of the first derivative of the pH curve as a function of time. Under these operating conditions, it is estimated that this variable is characteristic of the strain. Its value is constant whatever the physiological state of the micro-upon inoculation of the milk and the level of seeding. Two groups of strains are distinguished, the strains with so-called slow acidification, the Vm of which is greater than −0.0100 pHu/min, and the strains with so-called rapid acidification the Vm of which is less than −0.0100 pHu/min. The strain CNCM I-3617 clearly belongs to the group of the so-called rapid acidification strains (Table 5). This property is very often linked to the presence in the genome of the strains of a gene encoding the wall protease PrtS which could be detected in the genome of CNCM I-3617.
Streptococcus thermophilus evaluated under the
The fermentation support obtained by supplementing 100 ml of semi-skimmed UHT milk (Le Petit Vendéen®) with 3% (weight/volume) of skimmed milk powder (SUP'R TOP®, Eurial Poitouraine). The sterility of the solution is obtained by pasteurization for 10 min at 90° C. (at the core). The fermentation support thus obtained is inoculated with the strain to be tested at a rate of 106 cfu/ml, then incubated at 43° C. (in a water bath) until a pH of 4.6 is obtained. The pH is continuously monitored using a CINAC apparatus (Ysebaert). The fermented milks thus obtained are placed in a ventilated oven at 6° C., until they are analyzed. Two types of rheological measurements are carried out: viscosity and flow. The viscosity measurements are carried out at a temperature of 2° C. on fermented milks after storage for 1, 7, 14 and 28 days at 6° C. The equipment used is a RVF-type Brookfield® viscosimeter (Brookfield Engineering Laboratories, Inc.) mounted on a Helipath stand Brookfield Engineering Laboratories, Inc.). The viscosimeter is equipped with a type C needle and the oscillation speed applied to the needle is 10 rpm. The flow measurements are carried out at a temperature of 8° C. on previously-stirred fermented milks, after storage for 14 days at 6° C. The equipment used is an AR1000-N rheometer (TA Instrument) equipped with co-axial cylinders (Radius 1=15 mm, Radius 2=13.83 mm, Height=32 mm, Air gap=2 mm). For the ascending segment, the stress applied in a continuous sweep varies from 0 to 60 Pa for a duration of 1 min according to a linear mode. For the descending segment, the stress applied in a continuous sweep varies from 60 to 0 Pa for a duration of 1 min according to a linear mode. The values taken into account are the thixotropic area and the yield point; the latter is calculated according to the Casson model.
The texturizing ability of a strain can be evaluated in a first phase by a viscosity measurement of the curd obtained under the operating conditions described above. The recognized non-texturizing strains provide viscosity values close to 30 Pa·s while the texturizing strains exceed 40 Pa·s. This texturizing ability can be more or less pronounced (Table 6). For example the strain CNCM I-2979 produces a curd the viscosity of which reaches 42 Pa·s, and the strain DGCC7966 makes it possible to obtain a clearly higher viscosity, of 70 Pa·s. The strain CNCM I-3611 provides curds the viscosity of which amounts to 54 Pa·s (Table 6). This value places this strain among the group of strains with a texturizing ability fully comparable to the industrial strains currently used to devise lactic ferments for the production of yoghurts and fermented milks.
The rheological analyses using the AR1000-N rheometer made it possible to measure two rheological descriptors relevant for qualifying fermented milks: the yield point of the product (Pa) and the thixotropic area (Pa/s). These measurements are reported in Table 7 for each of the strains. For the fermented milk with the strain CNCM I-3617, the average values are 11.25 Pa and 352 Pa/s respectively. These values are significantly different from those measured on curds obtained with strains deemed non-texturizing (DGCC7766 or DGCC7919).
The strain CNCM I-3617 has several characteristics of interest for the construction of ferments and in particular for ferments used during the production of yoghurts or fermented milks. It exhibits a rare combination of functional properties (acidifying and thickening strain) and its lysotype is distinct from that of the other strains used in a standard manner for these applications.
| Number | Date | Country | Kind |
|---|---|---|---|
| 0608657 | Oct 2006 | FR | national |
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/EP07/60463 | 10/2/2007 | WO | 00 | 4/1/2009 |
