PHARMACEUTICAL COMPOSITION CONTAINING BACTERIA

SUMMARY

In certain aspects, provided herein are pharmaceutical agents (e.g., powders) comprising bacteria (e.g., freeze dried bacteria), wherein the bacteria in the pharmaceutical agent are present at a total cell count (TCC) of at least 1×10¹¹cells/gram of the pharmaceutical agent. In some embodiments, the bacteria are present in the pharmaceutical agent at a total cell count (TCC) of at least 3.3×10¹¹cells/gram of the pharmaceutical agent. In some embodiments, the bacteria are present in the pharmaceutical agent at a total cell count (TCC) of at least 5×10¹¹cells/gram of the pharmaceutical agent. In some embodiments, the bacteria are present in the pharmaceutical agent at a total cell count (TCC) of at least 7×10¹¹cells/gram of the pharmaceutical agent. In some embodiments, the bacteria are present in the pharmaceutical agent at a total cell count (TCC) of at least 1×10¹²cells/gram of the pharmaceutical agent. In some embodiments, the bacteria are present in the pharmaceutical agent at a total cell count (TCC) of at least 2×10¹²cells/gram of the pharmaceutical agent. In some embodiments, the bacteria are present in the pharmaceutical agent at a total cell count (TCC) of between about 1×10¹¹cells/gram to about 2.5×10¹²cells/gram of the pharmaceutical agent. In some embodiments, the bacteria are present in the pharmaceutical agent at a total cell count (TCC) of between about 3.3×10¹¹cells/gram to about 2.5×10¹²cells/gram of the pharmaceutical agent. In some embodiments, the bacteria are present in the pharmaceutical agent at a total cell count (TCC) of between about 5×10¹¹cells/gram to about 2.5×10¹²cells/gram of the pharmaceutical agent. In some embodiments, the bacteria are present in the pharmaceutical agent at a total cell count (TCC) of between about 7×10¹¹cells/gram to about 2.4×10¹²cells/gram of the pharmaceutical agent. In some embodiments, the bacteria are present in the pharmaceutical agent at a total cell count (TCC) of about 2×10¹²cells/gram of the pharmaceutical agent. In some embodiments, the bacteria are present in the pharmaceutical agent at a total cell count (TCC) of between about 1×10¹²cells/gram to about 2×10¹²cells/gram of the pharmaceutical agent. In some embodiments, the bacteria are present in the pharmaceutical agent at a total cell count (TCC) of between about 1.3×10¹²cells/gram to about 2.4×10¹²cells/gram of the pharmaceutical agent. In some embodiments, the bacteria are present in the pharmaceutical agent at a total cell count (TCC) of about 2.5×10¹²cells/gram of the pharmaceutical agent. In some embodiments, the bacteria are present in the pharmaceutical agent at a total cell count (TCC) of about 1.2×10¹²cells/gram of the pharmaceutical agent. In some embodiments, the bacteria are present in the pharmaceutical agent at a total cell count (TCC) of about 1.5×10¹²cells/gram of the pharmaceutical agent. In some embodiments, the bacteria are present in the pharmaceutical agent at a total cell count (TCC) of about 6×10¹¹cells/gram of the pharmaceutical agent.

In certain aspects, provided herein are pharmaceutical agents (e.g., powders) comprising bacteria (e.g., freeze dried bacteria) and a cryoprotectant.

In some embodiments, the cryoprotectant comprises sucrose. In some embodiments, the cryoprotectant comprises dextran. In some embodiments, the cryoprotectant comprises sucrose and dextran. In some embodiments, the cryoprotectant comprises sucrose and dextran in equivalent amounts (e.g., on a percent weight by weight basis). In some embodiments, the cryoprotectant comprises sucrose, and dextran. In some embodiments, the cryoprotectant comprises sucrose, dextran, and L-cysteine HCl (e.g., a form of L-cysteine). In some embodiments, the cryoprotectant does not comprise L-cysteine HCl.

In some embodiments, the pharmaceutical agent comprises about 6% to about 12% (weight/weight) sucrose. In some embodiments, the pharmaceutical agent comprises about 8% to about 12% (weight/weight) sucrose. In some embodiments, the pharmaceutical agent comprises about 11% (weight/weight) sucrose. In some embodiments, the pharmaceutical agent comprises about 6% to about 12% (weight/weight) dextran. In some embodiments, the pharmaceutical agent comprises about 8% to about 12% (weight/weight) dextran. In some embodiments, the pharmaceutical agent comprises about 11% (weight/weight) dextran. In some embodiments, the pharmaceutical agent comprises about 6% to about 12% (weight/weight) sucrose and about 6% to about 12% (weight/weight) dextran. In some embodiments, the pharmaceutical agent comprises about 8% to about 12% (weight/weight) sucrose and about 8% to about 12% (weight/weight) dextran. In some embodiments, the pharmaceutical agent comprises about 11% (weight/weight) sucrose and about 11% (weight/weight) dextran. In some embodiments, the pharmaceutical agent comprises about 0.1% (weight/weight) L-cysteine HCl. In some embodiments, the pharmaceutical agent comprises about 0.1% to about 0.3% (weight/weight) L-cysteine HCl. In some embodiments, the pharmaceutical agent comprises about 0.15% to about 0.25% (weight/weight) L-cysteine HCl. In some embodiments, the pharmaceutical agent comprises about 10% to about 0.25% or about 0.15% to about 0.35% (weight/weight) L-cysteine HCl.

In some embodiments, the pharmaceutical agent comprises about 7% to about 21% (weight/weight) sucrose. In some embodiments, the pharmaceutical agent comprises about 10% to about 19% (weight/weight) sucrose. In some embodiments, the pharmaceutical agent comprises about 15% (weight/weight) sucrose. In some embodiments, the pharmaceutical agent comprises about 7% to about 21% (weight/weight) dextran. In some embodiments, the pharmaceutical agent comprises about 10% to about 19% (weight/weight) dextran. In some embodiments, the pharmaceutical agent comprises about 15% (weight/weight) dextran. In some embodiments, the pharmaceutical agent comprises about 7% to about 21% (weight/weight) sucrose and about 7% to about 21% (weight/weight) dextran. In some embodiments, the pharmaceutical agent comprises about 10% to about 19% (weight/weight) sucrose and about 10% to about 19% (weight/weight) dextran. In some embodiments, the pharmaceutical agent comprises about 15% (weight/weight) sucrose and about 15% (weight/weight) dextran. In some embodiments, the pharmaceutical agent comprises about 0.01% (weight/weight) L-cysteine HCl. In some embodiments, the pharmaceutical agent comprises about 0.1% to about 0.4% (weight/weight) L-cysteine HCl. In some embodiments, the pharmaceutical agent comprises about 0.15% to about 0.35% (weight/weight) L-cysteine HCl.

In some embodiments, the cryoprotectant comprises a dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21). In some embodiments, the cryoprotectant comprises sucrose. In some embodiments, the cryoprotectant comprises dextrose (also referred to as glucose). In some embodiments, the cryoprotectant comprises monosodium glutamate. In some embodiments, the cryoprotectant comprises dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21) and sucrose. In some embodiments, the cryoprotectant comprises dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21) and sucrose in equivalent amounts (e.g., on a percent weight by weight basis). In some embodiments, the cryoprotectant comprises dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21), sucrose, and dextrose. In some embodiments, the cryoprotectant comprises dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21), sucrose, and monosodium glutamate. In some embodiments, the cryoprotectant comprises dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21), sucrose, dextrose, and monosodium glutamate. In some embodiments, the cryoprotectant comprises dextrose and monosodium glutamate in equivalent amounts (e.g., on a percent weight by weight basis). In some embodiments, the cryoprotectant comprises dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21), sucrose, dextrose, monosodium glutamate, and L-cysteine HCl (e.g., a form of L-cysteine). In some embodiments, the cryoprotectant does not comprise L-cysteine HCl.

In some embodiments, the pharmaceutical agent comprises about 23% to about 30% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21); about 21% to about 29% (weight/weight) sucrose; and about 6% to about 11% (weight/weight) dextrose. In some embodiments, the pharmaceutical agent comprises about 23% to about 30% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21); about 21% to about 29% (weight/weight) sucrose; and about 4% to about 10% (weight/weight) glutamate. In some embodiments, the pharmaceutical agent comprises about 23% to about 30% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21); about 21% to about 29% (weight/weight) sucrose; about 6% to about 11% (weight/weight) dextrose; and about 4% to about 10% (weight/weight) glutamate. In some embodiments, the pharmaceutical agent comprises about 24% to about 28% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21); about 23% to about 27% (weight/weight) sucrose; and about 7% to about 10% (weight/weight) dextrose. In some embodiments, the pharmaceutical agent comprises about 24% to about 28% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21); 23% to about 27% (weight/weight) sucrose; and about 5% to about 9% (weight/weight) glutamate. In some embodiments, the pharmaceutical agent comprises about 24% to about 28% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21); 23% to about 27% (weight/weight) sucrose; about 7% to about 1% (weight/weight) dextrose; and about 5% to about 9% (weight/weight) glutamate. In some embodiments, the pharmaceutical agent comprises about 0.05% to about 0.6% (weight/weight) L-cysteine HCl. In some embodiments, the pharmaceutical agent comprises about 0.1% to about 0.5% (weight/weight) L-cysteine HCl.

In certain embodiments, the pharmaceutical agent comprises about 40% to about 75% (weight/weight) bacteria (e.g., freeze dried bacteria). In certain embodiments, the pharmaceutical agent comprises about 35% to about 70% (weight/weight) bacteria (e.g., freeze dried bacteria). In certain embodiments, the pharmaceutical agent comprises about 64% (weight/weight) bacteria (e.g., freeze dried bacteria).

In certain embodiments, the pharmaceutical agent comprises about 15% to about 35% (weight/weight) bacteria (e.g., freeze dried bacteria). In certain embodiments, the pharmaceutical agent comprises about 18% to about 30% (weight/weight) bacteria (e.g., freeze dried bacteria). In certain embodiments, the pharmaceutical agent comprises about 25% (weight/weight) bacteria (e.g., freeze dried bacteria).

In certain embodiments, the pharmaceutical agent comprises Prevotella bacteria.

In certain embodiments, the pharmaceutical agent comprises Veillonella bacteria.

In some embodiments, the pharmaceutical agent has a fine and smooth granulated powder appearance.

In some embodiments, the pharmaceutical agent has an off-white to brown, fine powder appearance.

In some aspects, the disclosure provides a pharmaceutical composition that comprises a pharmaceutical agent (e.g., powder) described herein and one or more excipients.

In some aspects, the disclosure provides a method comprising combining bacteria (e.g., a pellet comprising bacteria) with a cryoprotectant solution, thereby preparing a formulated paste. In some embodiments, the disclosure provides a formulated paste prepared by this method.

In some embodiments, the method further comprises freeze drying the formulated paste, to thereby prepare a freeze-dried product. In some embodiments, the freeze drying comprises primary drying. In some embodiments, the freeze drying comprises primary drying and secondary drying. In some embodiments, the disclosure provides a freeze-dried product prepared by this method.

In some embodiments, the method further comprises milling the freeze-dried product, to thereby prepare a freeze-dried powder (e.g., powder, e.g., pharmaceutical agent). In some embodiments, the disclosure provides a pharmaceutical agent prepared by this method.

In some embodiments, the method further comprises combining the freeze-dried powder with one or more excipients to thereby prepare a pharmaceutical composition. In some embodiments, the disclosure provides a pharmaceutical composition prepared by this method.

In some embodiments, the cryoprotectant solution is mixed with the pellet in a ratio of about 0.2 to about 0.5 gram (g) cryoprotectant solution per gram of pellet; about 0.05 to about 0.25 gram (g) cryoprotectant solution per gram of pellet; about 0.06 to about 0.1 gram (g) cryoprotectant solution per gram of pellet; or about 0.15 to about 0.2 gram (g) cryoprotectant solution per gram of pellet. In some embodiments, the cryoprotectant solution is mixed with the pellet in a ratio of about 0.4 gram (g) cryoprotectant solution per gram of pellet. In some embodiments, the cryoprotectant solution is mixed with the pellet in a ratio of about 0.18 gram (g) cryoprotectant solution per gram of pellet. In some embodiments, the cryoprotectant solution is mixed with the pellet in a ratio of about 0.1 (e.g., 0.08) gram (g) of cryoprotectant solution per gram of pellet.

In some embodiments, the cryoprotectant solution is mixed with the pellet at a ratio of 4% to 10% (volume/volume), e.g., 5% to 8% (volume/volume). In some embodiments, the cryoprotectant solution is mixed with the pellet at a ratio of about 6.5% (volume/volume).

In some embodiments, the cryoprotectant solution comprises sucrose. In some embodiments, the cryoprotectant solution comprises dextran. In some embodiments, the cryoprotectant solution comprises sucrose and dextran. In some embodiments, the cryoprotectant solution comprises sucrose and dextran in equivalent amounts (e.g., on a percent weight by weight basis). In some embodiments, the cryoprotectant solution comprises sucrose, dextran, and L-cysteine HCl (e.g., a form of L-cysteine). In some embodiments, the cryoprotectant solution does not comprise L-cysteine HCl.

In some embodiments, the cryoprotectant solution comprises about 10% to about 30% (weight/weight) sucrose. In some embodiments, the cryoprotectant solution comprises about 15% to about 35% (weight/weight) sucrose. In some embodiments, the cryoprotectant solution comprises about 20% (weight/weight) sucrose.

In some embodiments, the cryoprotectant solution comprises about 10% to about 30% (weight/weight) dextran. In some embodiments, the cryoprotectant solution comprises about 15% to about 35% (weight/weight) dextran. In some embodiments, the cryoprotectant solution comprises about 20% (weight/weight) dextran.

In some embodiments, the cryoprotectant solution comprises about 10% to about 30% (weight/weight) sucrose and about 10% to about 30% (weight/weight) dextran. In some embodiments, the cryoprotectant solution comprises about 15% to about 35% (weight/weight) sucrose and about 15% to about 35% (weight/weight) dextran. In some embodiments, the cryoprotectant solution comprises about 20% (weight/weight) sucrose and about 20% (weight/weight) dextran.

In some embodiments, the cryoprotectant solution comprises about 40% to about 80% (weight/weight) water. In some embodiments, the cryoprotectant solution comprises about 50% to about 70% (weight/weight) water. In some embodiments, the cryoprotectant solution comprises about 55% to about 65% (weight/weight) water. In some embodiments, the cryoprotectant solution comprises about 60% (weight/weight) water.

In some embodiments, the cryoprotectant solution comprises about 0.05% to about 0.6% (weight/weight) L-cysteine HCl (e.g., a form of L-cysteine). In some embodiments, the cryoprotectant solution comprises about 0.1% to about 0.5% (weight/weight) L-cysteine HCl. In some embodiments, the cryoprotectant solution comprises about 0.15% to about 0.45% (weight/weight) L-cysteine HCl. In some embodiments, the pharmaceutical agent comprises about 0.1% to about 0.25% or about 0.15% to about 0.35% (weight/weight) L-cysteine HCl.

In some embodiments, the cryoprotectant solution comprises about 0.2% (weight/weight) L-cysteine HCl.

In some embodiments, the cryoprotectant solution comprises about 59.8% (weight/weight) water.

In some embodiments, the cryoprotectant solution comprises about 0.4% (weight/weight) L-cysteine HCl.

In some embodiments, the cryoprotectant solution comprises about 59.6% (weight/weight) water.

In certain embodiments, the cryoprotectant solution provided herein comprises: (i) about 20% (weight/weight) sucrose; (ii) about 20% (weight/weight) dextran; (iii) about 0.4% (weight/weight) L-cysteine HCl; and (iv) about 59.6% (weight/weight) water.

In certain embodiments, the cryoprotectant solution provided herein comprises: (i) about 20% (weight/weight) sucrose; (ii) about 20% (weight/weight) dextran; (iii) about 0.2% (weight/weight) L-cysteine HCl; and (iv) about 59.8% (weight/weight) water.

In certain embodiments, the cryoprotectant solution provided herein comprises: (i) about 20% (weight/weight) sucrose; (ii) about 20% (weight/weight) dextran; and (iii) about 60% (weight/weight) water.

In some embodiments, the cryoprotectant (e.g., dry composition not containing water) comprises about 40% to about 60% (weight/weight) sucrose. In some embodiments, the cryoprotectant comprises about 45% to about 55% (weight/weight) sucrose. In some embodiments, the cryoprotectant comprises about 50% (weight/weight) sucrose.

In some embodiments, the cryoprotectant comprises about 40% to about 60% (weight/weight) dextran. In some embodiments, the cryoprotectant comprises about 45% to about 55% (weight/weight) dextran. In some embodiments, the cryoprotectant comprises about 50% (weight/weight) dextran.

In some embodiments, the cryoprotectant comprises about 40% to about 60% (weight/weight) sucrose and 40% to about 60% (weight/weight) dextran. In some embodiments, the cryoprotectant comprises about 45% to about 55% (weight/weight) sucrose and about 45% to about 55% (weight/weight) dextran. In some embodiments, the cryoprotectant comprises about 50% (weight/weight) sucrose and about 50% (weight/weight) dextran.

In some embodiments, the cryoprotectant comprises about 0.25% to about 5% (weight/weight) L-cysteine HCl (e.g., a form of L-cysteine). In some embodiments, the cryoprotectant comprises about 0.5% to about 2.5% (weight/weight) L-cysteine HCl. In some embodiments, the cryoprotectant comprises about 0.75% to about 1.5% (weight/weight) L-cysteine HCl. In some embodiments, the cryoprotectant comprises about 1% (weight/weight) L-cysteine HCl.

In certain embodiments, the cryoprotectant provided herein comprises: (i) about 50% (weight/weight) sucrose; (ii) about 50% (weight/weight) dextran; and (iii) about 1% (weight/weight) L-cysteine HCl.

In certain embodiments, the cryoprotectant provided herein comprises: (i) about 50% (weight/weight) sucrose; and (ii) about 50% (weight/weight) dextran.

In some embodiments, the cryoprotectant (e.g., dry composition not containing water) comprises about 27% to about 47% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21). In some embodiments, the cryoprotectant comprises about 32% to about 42% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21). In some embodiments, the cryoprotectant comprises about 37% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21).

In some embodiments, the cryoprotectant (e.g., dry composition not containing water) comprises about 27% to about 47% (weight/weight) sucrose. In some embodiments, the cryoprotectant comprises about 32% to about 42% (weight/weight) sucrose. In some embodiments, the cryoprotectant comprises about 37% (weight/weight) sucrose.

In some embodiments, the cryoprotectant comprises about 8% to about 18% (weight/weight) dextrose. In some embodiments, the cryoprotectant comprises about 11% to about 15% (weight/weight) dextrose. In some embodiments, the cryoprotectant comprises about 13% (weight/weight) dextrose.

In some embodiments, the cryoprotectant comprises about 8% to about 18% (weight/weight) monosodium glutamate. In some embodiments, the cryoprotectant comprises about 11% to about 15% (weight/weight) monosodium glutamate. In some embodiments, the cryoprotectant comprises about 13% (weight/weight) monosodium glutamate.

In some embodiments, the cryoprotectant comprises about 27% to about 47% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21) and about 27% to about 47% (weight/weight) sucrose. In some embodiments, the cryoprotectant comprises about 32% to about 42% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21) and about 32% to about 42% (weight/weight) sucrose. In some embodiments, the cryoprotectant comprises about 37% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21) and about 37% (weight/weight) sucrose.

In some embodiments, the cryoprotectant comprises about 27% to about 47% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21); about 27% to about 47% (weight/weight) sucrose; and about 8% to about 18% (weight/weight) dextrose. In some embodiments, the cryoprotectant comprises about 27% to about 47% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21); about 27% to about 47% (weight/weight) sucrose; and about 8% to about 18% (weight/weight) monosodium glutamate. In some embodiments, the cryoprotectant comprises about 27% to about 47% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21); about 27% to about 47% (weight/weight) sucrose; about 8% to about 18% (weight/weight) dextrose; and about 8% to about 18% (weight/weight) monosodium glutamate.

In some embodiments, the cryoprotectant comprises about 32% to about 42% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21); about 32% to about 42% (weight/weight) sucrose; and about 11% to about 15% (weight/weight) dextrose. In some embodiments, the cryoprotectant comprises about 32% to about 42% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21); about 32% to about 42% (weight/weight) sucrose; and about 11% to about 15% (weight/weight) monosodium glutamate. In some embodiments, the cryoprotectant comprises about 32% to about 42% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21); about 32% to about 42% (weight/weight) sucrose; about 11% to about 15% (weight/weight) dextrose; and about 11% to about 15% (weight/weight) monosodium glutamate.

In some embodiments, the cryoprotectant comprises about 37% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21); about 37% (weight/weight) sucrose; and about 13% (weight/weight) dextrose. In some embodiments, the cryoprotectant comprises about 37% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21); about 37% (weight/weight) sucrose; and about 13% (weight/weight) monosodium glutamate. In some embodiments, the cryoprotectant comprises about 37% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21); about 37% (weight/weight) sucrose; about 13% (weight/weight) dextrose; and about 13% (weight/weight) monosodium glutamate.

In some embodiments, the cryoprotectant comprises about 0.05% to about 0.6% (weight/weight) L-cysteine HCl (e.g., a form of L-cysteine). In some embodiments, the cryoprotectant comprises about 0.1% to about 0.5% (weight/weight) L-cysteine HCl. In some embodiments, the cryoprotectant comprises about 0.1% to about 0.25% (weight/weight) L-cysteine HCl. In some embodiments, the cryoprotectant comprises about 0.2% (weight/weight) L-cysteine HCl.

In certain embodiments, the cryoprotectant provided herein comprises: (i) about 37% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21); (ii) about 37% (weight/weight) sucrose; (iii) about 13% (weight/weight) dextrose; (iv) about 13% (weight/weight) monosodium glutamate; and (v) about 0.2% (weight/weight) L-cysteine HCl.

In certain embodiments, the cryoprotectant provided herein comprises: (i) about 37% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21); (ii) about 37% (weight/weight) sucrose; (iii) about 13% (weight/weight) dextrose; and (iv) about 13% (weight/weight) monosodium glutamate.

In certain aspects provided herein are pharmaceutical agents that comprise bacteria. In certain embodiments, the pharmaceutical agents maintain their stability, e.g., for three, six, twelve, eighteen and/or twenty-four months under long-term (2-8° C.) and/or accelerated (23-27° C. (optionally at 60% relative humidity (RH))) storage conditions, e.g., as determined by total cell count (TCC), e.g., as determined by Coulter counter and described herein. In certain embodiments, the pharmaceutical agents maintain their stability, e.g., for three, six, twelve, eighteen and/or twenty-four months under long-term (−20° C.) and/or accelerated (2-8° C.) storage conditions, e.g., as determined by total cell count (TCC), e.g., as determined by Coulter counter and described herein.

In certain aspects provided herein are pharmaceutical agents that comprise bacteria. In some embodiments, the water content of the pharmaceutical agents is between about 0.5% and about 9/6, between about 1% and about 8%, between about 1% and about 6%, (e.g., about 1.7%, e.g., 1.8%, e.g., about 2%, e.g., about 2.2%, e.g., about 2.3%, e.g., about 2.4%, e.g., about 2.8%, e.g., about 2.9%, e.g., about 3%, e.g., about 3.1%, e.g., about 3.2%, e.g., about 3.3%, e.g., about 3.5%, e.g., about 3.6%, e.g., about 4%, e.g., about 4.5%, e.g., about 5%, e.g., about 5.3%, e.g., about 5.4%, or e.g., about 7.8%), e.g., as determined by the Karl-Fischer method for water content analysis provided in Ph. Eur. method 2.5.12, and as described herein. In some embodiments, the pharmaceutical agents maintain their water content, e.g., for three, six, twelve, eighteen and/or twenty-four months under long-term (2-8° C.) and/or accelerated (25° C. (optionally at 60% RH)) storage conditions. In some embodiments, the pharmaceutical agents maintain their water content, e.g., for three, six, twelve, eighteen and/or twenty-four months under long-term (−20° C.) and/or accelerated (2-8° C.) storage conditions.

The pharmaceutical agent can be of bacterial origin (e.g., mixture of selected strains or agents (e.g., components) thereof. The pharmaceutical agent can be of bacterial origin (e.g., a single selected strain and/or agents (e.g., components) thereof. The pharmaceutical agent can be a powder that comprises the bacteria and/or components thereof, and can comprise additional agents such as, e.g., cryoprotectant. For example, in some embodiments, the pharmaceutical agent is a freeze dried (e.g., lyophilized) powder of bacteria and/or components thereof that optionally, further comprise additional agents, such as a cryoprotectant.

In some aspects, the disclosure provides a solid dosage form (e.g., capsule, tablet, or minitablet) that comprises a pharmaceutical agent (e.g., powder) described herein. The solid dosage form can be enteric coated.

In some embodiments, the solid dosage form comprises a tablet. In some embodiments, the tablet (e.g., enterically coated tablet) is a 5 mm, 6 mm, 7 mm, 8 mm, 9 mm, 10 mm, 11 mm, 12 mm, 13 mm, 14 mm, 15 mm, 16 mm, 17 mm, or 18 mm tablet.

In some embodiments, the solid dosage form comprises a minitablet. In some embodiments, the minitablet (e.g., enterically coated minitablet) is a 1 mm minitablet, 1.5 mm minitablet, 2 mm minitablet, 3 mm minitablet, or 4 mm minitablet. In some embodiments, a plurality of enterically coated minitablets are contained in a capsule (e.g., a size 0 capsule can contain about 31 to about 35 (e.g., 33) minitablets, wherein the minitablets are 3 mm in size). In some embodiments, the capsule is a size 00, size 0, size 1, size 2, size 3, size 4, or size 5 capsule. In some embodiments, the capsule comprises HPMC (hydroxyl propyl methyl cellulose) or gelatin.

In some embodiments, the enteric coating comprises one enteric coating.

In some embodiments, the enteric coating comprises an inner enteric coating and an outer enteric coating. In some embodiments, the enteric coating comprises an inner enteric coating and an outer enteric coating, and wherein the inner and outer enteric coatings are not identical (e.g., the inner and outer enteric coatings do not contain identical components in identical amounts).

In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises a polymethacrylate-based copolymer.

In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises a methacrylic acid ethyl acrylate (MAE) copolymer (1:1).

In some embodiments, the one enteric coating comprises methacrylic acid ethyl acrylate (MAE) copolymer (1:1) (such as Kollicoat MAE 100P).

In some embodiments, the one enteric coating comprises a Eudragit copolymer, e.g., a Eudragit L (e.g., Eudragit L 100-55; Eudragit L 30 D-55), a Eudragit S, a Eudragit RL, a Eudragit RS, a Eudragit E, or a Eudragit FS (e.g., Eudragit FS 30 D).

In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises cellulose acetate phthalate (CAP), cellulose acetate trimellitate (CAT), poly(vinyl acetate phthalate) (PVAP), hydroxypropyl methylcellulose phthalate (HPMCP), a fatty acid, a wax, shellac (esters of aleurtic acid), a plastic, a plant fiber, zein, Aqua-Zein (an aqueous zein formulation containing no alcohol), amylose starch, a starch derivative, a dextrin, a methyl acrylate-methacrylic acid copolymer, cellulose acetate succinate, hydroxypropyl methyl cellulose acetate succinate (hypromellose acetate succinate), a methyl methacrylate-methacrylic acid copolymer, or sodium alginate.

In some embodiments, the enteric coating (e.g., the one enteric coating or the inner enteric coating and/or the outer enteric coating) comprises an anionic polymeric material.

In some embodiments, the pharmaceutical agent comprises bacteria.

In some embodiments, the pharmaceutical agent has one or more beneficial immune effects outside the gastrointestinal tract, e.g., when the solid dosage form is orally administered.

In some embodiments, the pharmaceutical agent modulates immune effects outside the gastrointestinal tract in the subject, e.g., when the solid dosage form is orally administered.

In some embodiments, the pharmaceutical agent causes a systemic effect (e.g., an effect outside of the gastrointestinal tract), e.g., when the solid dosage form is orally administered.

In some embodiments, the pharmaceutical agent acts on immune cells and/or epithelial cells in the small intestine (e.g., causing a systemic effect (e.g., an effect outside of the gastrointestinal tract), e.g., when the solid dosage form is orally administered.

In some embodiments, the pharmaceutical agent comprises isolated bacteria (e.g., from one or more strains of bacteria (e.g., bacteria of interest) (e.g., a therapeutically effective amount thereof)). E.g., wherein at least 5%, at least 10%, at least 25%, at least 50%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% of the content of the pharmaceutical agent is the isolated bacteria (e.g., bacteria of interest).

In some embodiments, the pharmaceutical agent comprises bacteria that have been gamma irradiated, UV irradiated, heat inactivated, acid treated, or oxygen sparged.

In some embodiments, the pharmaceutical agent comprises live bacteria.

In some embodiments, the pharmaceutical agent comprises dead bacteria.

In some embodiments, the pharmaceutical agent comprises non-replicating bacteria.

In some embodiments, the pharmaceutical agent comprises bacteria from one strain of bacteria.

In some embodiments, the bacteria are lyophilized (e.g., the lyophilized product further comprises a pharmaceutically acceptable excipient) (e.g., a powder form).

In some embodiments, the bacteria are gamma irradiated.

In some embodiments, the bacteria are UV irradiated.

In some embodiments, the bacteria are heat inactivated (e.g., at 50° C. for two hours or at 90° C. for two hours).

In some embodiments, the bacteria are acid treated.

In some embodiments, the bacteria are oxygen sparged (e.g., at 0.1 vvm for two hours).

In some embodiments, the bacteria are Gram positive bacteria.

In some embodiments, the bacteria are Gram negative bacteria.

In some embodiments, the bacteria are aerobic bacteria.

In some embodiments, the bacteria are anaerobic bacteria. In some embodiments, the anaerobic bacteria comprise obligate anaerobes. In some embodiments, the anaerobic bacteria comprise facultative anaerobes. In some embodiments, the bacteria are acidophile bacteria.

In some embodiments, the bacteria are alkaliphile bacteria.

In some embodiments, the bacteria are neutralophile bacteria.

In some embodiments, the bacteria are fastidious bacteria.

In some embodiments, the bacteria are nonfastidious bacteria.

In some embodiments, the bacteria are of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table 1, Table 2, Table 3, or Table 4.

In some embodiments, the bacteria are a bacterial strain listed in Table 1, Table 2, Table 3, or Table 4.

In some embodiments, the bacteria are of a taxonomic group (e.g., class, order, family, genus, species or strain) listed in Table J.

In some embodiments, the bacteria are a bacterial strain listed in Table J.

In some embodiments, the Gram negative bacteria belong to class Negativicutes.

In some embodiments, the Gram negative bacteria belong to family Veillonellaceae, Selenomonadaceae, Acidaminococcaceae, or Sporomusaceae.

In some embodiments, the bacteria of the genus Megasphaera, Selenomonas, Propionospora, or Acidaminococcus.

In some embodiments, the bacteria are Megasphaera sp., Selenomonas felix, Acidaminococcus intestini, or Propionospora sp. bacteria.

In some embodiments, the bacteria are of the genus Lactococcus, Prevotella, Bifidobacterium, or Veillonella.

In some embodiments, the bacteria are Lactococcus lactis cremoris bacteria.

In some embodiments, the bacteria are Prevotella histicola bacteria.

In some embodiments, the bacteria are Bifidobacterium animalis bacteria.

In some embodiments, the bacteria are Veillonella parvula bacteria.

In some embodiments, the bacteria are Lactococcus lactis cremoris bacteria. In some embodiments, the Lactococcus lactis cremoris bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are a strain comprising at least 99/6 genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368). In some embodiments, the Lactococcus bacteria are Lactococcus lactis cremoris Strain A (ATCC designation number PTA-125368).

In some embodiments, the bacteria are Prevotella bacteria. In some embodiments, the Prevotella bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Prevotella Strain B 50329 (NRRL accession number B 50329). In some embodiments, the Prevotella bacteria are Prevotella Strain B 50329 (NRRL accession number B 50329).

In some embodiments, the bacteria are Bifidobacterium bacteria. In some embodiments, the Bifidobacterium bacteria are from a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Bifidobacterium bacteria deposited as ATCC designation number PTA-125097. In some embodiments, the Bifidobacterium bacteria are Bifidobacterium bacteria deposited as ATCC designation number PTA-125097.

In some embodiments, the bacteria are Veillonella bacteria. In some embodiments, the Veillonella bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Veillonella bacteria deposited as ATCC designation number PTA-125691. In some embodiments, the Veillonella bacteria are Veillonella bacteria deposited as ATCC designation number PTA-125691.

In some embodiments, the bacteria are from Ruminococcus gnavus bacteria. In some embodiments, the Ruminococcus gnavus bacteria are a strain comprising at least 90/a (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are a strain comprising at least 99/a genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695. In some embodiments, the Ruminococcus gnavus bacteria are Ruminococcus gnavus bacteria deposited as ATCC designation number PTA-126695.

In some embodiments, the bacteria are Megasphaera sp. bacteria. In some embodiments, the Megasphaera sp. bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770. In some embodiments, the Megasphaera sp. bacteria are Megasphaera sp. bacteria deposited as ATCC designation number PTA-126770.

In some embodiments, the bacteria are Fournierella massiliensis bacteria. In some embodiments, the Fournierella massiliensis bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are a strain comprising at least 99% genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696. In some embodiments, the Fournierella massiliensis bacteria are Fournierella massiliensis bacteria deposited as ATCC designation number PTA-126696.

In some embodiments, the bacteria are Harryflintia acetispora bacteria. In some embodiments, the Harryflintia acetispora bacteria are a strain comprising at least 90% (or at least 97%) genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are a strain comprising at least 99/a genomic, 16S and/or CRISPR sequence identity to the nucleotide sequence of the Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694. In some embodiments, the Harryflintia acetispora bacteria are Harryflintia acetispora bacteria deposited as ATCC designation number PTA-126694.

In some embodiments, the bacteria are of the family Acidaminococcaceae, Alcaligenaceae, Akkermansiaceae, Bacteriodaceae, Bifidobacteriaceae, Burkholderiaceae, Catabacteriaceae, Clostridiaceae, Coriobacteriaceae, Enterobacteriaceae, Enterococcaceae, Fusobacteriaceae, Lachnospiraceae, Listeraceae, Mycobacteriaceae, Neisseriaceae, Odoribacteraceae, Oscillospiraceae, Peptococcaceae, Peptostreptococcaceae, Porphyromonadaceae, Prevotellaceae, Propionibacteraceae, Rikenellaceae, Ruminococcaceae, Selenomonadaceae, Sporomusaceae, Streptococcaceae, Streptomycetaceae, Sutterellaceae, Synergistaceae, or Veillonellaceae.

In some embodiments, the bacteria are of the genus Akkermansia, Christensenella, Blautia, Enterococcus, Eubacterium, Roseburia, Bacteroides, Parabacteroides, or Erysipelatoclostridium.

In some embodiments, the bacteria are Blautia hydrogenotrophica, Blautia stercoris, Blautia wexlerae, Eubacterium faecium, Eubacterium contortum, Eubacterium rectale, Enterococcus faecalis, Enterococcus durans, Enterococcus villorum, Enterococcus gallinarum; Bifidobacterium lactis, Bifidobacterium bifidium, Bifidobacterium longum, Bifidobacterium animalis, or Bfidobacterium breve bacteria.

In some embodiments, the bacteria are BCG (bacillus Calmette-Guerin). Parabacteroides, Blautia, Veillonella, Lactobacillus salivarius, Agathobaculum, Ruminococcus gnavus, Paraclostridium benzoelyticum, Turicibacter sanguinus, Burkholderia, Klebsiella quasipneumoniae ssp similpneumoniae, Klebsiella oxytoca, Tyzzerela nexilis, or Neisseria bacteria.

In some embodiments, the bacteria are Blautia hydrogenotrophica bacteria.

In some embodiments, the bacteria are Blautia stercoris bacteria.

In some embodiments, the bacteria are Blautia wexlerae bacteria.

In some embodiments, the bacteria are Enterococcus gallinarum bacteria.

In some embodiments, the bacteria are Enterococcus faecium bacteria.

In some embodiments, the bacteria are Bfidobacterium bifidium bacteria.

In some embodiments, the bacteria are Bfidobacterium breve bacteria.

In some embodiments, the bacteria are Bfidobacterium longum bacteria.

In some embodiments, the bacteria are Roseburia hominis bacteria.

In some embodiments, the bacteria are Bacteroides thetaiotaomicron bacteria.

In some embodiments, the bacteria are Bacteroides coprocola bacteria.

In some embodiments, the bacteria are Erysipelatoclostridium ramosum bacteria.

In some embodiments, the bacteria are Megasphera massiliensis bacteria.

In some embodiments, the bacteria are Eubacterium bacteria.

In some embodiments, the bacteria are Parabacteroides distasonis bacteria.

In some embodiments, the bacteria are Lactobacillus plantarum bacteria.

In some embodiments, the bacteria are bacteria of the Negativicutes class.

In some embodiments, the bacteria are of the Veillonellaceae family.

In some embodiments, the bacteria are of the Selenomonadaceae family.

In some embodiments, the bacteria are of the Acidaminococcaceae family.

In some embodiments, the bacteria are of the Sporomusaceae family.

In some embodiments, the bacteria are of the Megasphaera genus.

In some embodiments, the bacteria are of the Selenomonas genus.

In some embodiments, the bacteria are of the Propionospora genus.

In some embodiments, the bacteria are of the Acidaminococcus genus.

In some embodiments, the bacteria are Megasphaera sp. bacteria.

In some embodiments, the bacteria are Selenomonas felix bacteria.

In some embodiments, the bacteria are Acidaminococcus intestini bacteria.

In some embodiments, the bacteria are Propionospora sp. bacteria.

In some embodiments, the bacteria are bacteria of the Clostridia class.

In some embodiments, the bacteria are of the Oscillospriraceae family.

In some embodiments, the bacteria are of the Faecalibacterium genus.

In some embodiments, the bacteria are of the Fournierella genus.

In some embodiments, the bacteria are of the Harryflintia genus.

In some embodiments, the bacteria are of the Agathobaculum genus.

In some embodiments, the bacteria are Faecalibacterium prausnitzii (e.g., Faecalibacterium prausnitzii Strain A) bacteria.

In some embodiments, the bacteria are Fournierella massiliensis (e.g., Fournierella massiliensis Strain A) bacteria.

In some embodiments, the bacteria are Harryflintia acetispora (e.g., Harryflintia acetispora Strain A) bacteria.

In some embodiments, the bacteria are Agathobaculum sp. (e.g., Agathobaculum sp. Strain A) bacteria.

In some embodiments, the bacteria are a strain of Agathobaculum sp. In some embodiments, the Agathobaculum sp. strain is a strain comprising at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the nucleotide sequence (e.g., genomic sequence, 16S sequence, CRISPR sequence) of the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892). In some embodiments, the Agathobaculum sp. strain is the Agathobaculum sp. Strain A (ATCC Deposit Number PTA-125892).

In some embodiments, the bacteria are of the class Bacteroidia [phylum Bacteroidota]. In some embodiments, the bacteria are of order Bacteroidales. In some embodiments, the bacteria are of the family Porphyromonoadaceae. In some embodiments, the bacteria are of the family Prevotellaceae. In some embodiments, the bacteria are of the class Bacteroidia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria are of the class Bacteroidia that stain Gram negative. In some embodiments, the bacteria are of the class Bacteroidia wherein the bacteria is diderm and the bacteria stain Gram negative.

In some embodiments, the bacteria are of the class Clostridia [phylum Firmicutes]. In some embodiments, the bacteria are of the order Eubacteriales. In some embodiments, the bacteria are of the family Oscillispiraceae. In some embodiments, the bacteria are of the family Lachnospiraceae. In some embodiments, the bacteria are of the family Peptostreptococcaceae. In some embodiments, the bacteria are of the family Clostridiales family XII/Incertae sedis 41. In some embodiments, the bacteria are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm. In some embodiments, the bacteria are of the class Clostridia that stain Gram negative. In some embodiments, the bacteria are of the class Clostridia that stain Gram positive. In some embodiments, the bacteria are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram negative. In some embodiments, the bacteria are of the class Clostridia wherein the cell envelope structure of the bacteria is monoderm and the bacteria stain Gram positive.

In some embodiments, the bacteria are of the class Negativicutes [phylum Firmicutes]. In some embodiments, the bacteria are of the order Veillonellales. In some embodiments, the bacteria are of the family Veillonelloceae. In some embodiments, the bacteria are of the order Selenomonadales. In some embodiments, the bacteria are of the family Selenomonadaceae. In some embodiments, the bacteria are of the family Sporomusaceae. In some embodiments, the bacteria are of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria are of the class Negativicutes that stain Gram negative. In some embodiments, the bacteria are of the class Negativicutes wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.

In some embodiments, the bacteria are of the class Synergistia [phylum Synergistota]. In some embodiments, the bacteria are of the order Synergistales. In some embodiments, the bacteria are of the family Synergistaceae. In some embodiments, the bacteria are of the class Synergistia wherein the cell envelope structure of the bacteria is diderm. In some embodiments, the bacteria are of the class Synergistia that stain Gram negative. In some embodiments, the bacteria are of the class Synergistia wherein the cell envelope structure of the bacteria is diderm and the bacteria stain Gram negative.

In some embodiments, the bacteria are bacteria that produce metabolites, e.g., the bacteria produce butyrate, iosine, proprionate, or tryptophan metabolites.

In some embodiments, the bacteria produce butyrate. In some embodiments, the bacteria are from the genus Blautia; Christensella; Copracoccus; Eubacterium; Lachnosperacea; Megasphaera; or Roseburia.

In some embodiments, the bacteria produce iosine. In some embodiments, the bacteria are from the genus Bfidobacterium; Lactobacillus; or Olsenella.

In some embodiments, the bacteria produce proprionate. In some embodiments, the bacteria are from the genus Akkermansia; Bacteroides; Dialister; Eubacterium; Megasphaera; Parabacteriodes; Prevotella; Ruminococcus; or Veillonella.

In some embodiments, the bacteria produce tryptophan metabolites. In some embodiments, the bacteria are from the genus Lactobacillus or Peptostreptococcus.

In some embodiments, the bacteria are bacteria that produce inhibitors of histone deacetylase 3 (HDAC3). In some embodiments, the bacteria are from the species Bariatricus massiliensis. Faecalibacterium prausnitzii. Megasphaera massiliensis or Roseburia intestinalis.

In some embodiments, the bacteria are of the genus Cutibacterium.

In some embodiments, the bacteria are Cutibacterium avidum.

In some embodiments, the bacteria are from the genus Lactobacillus.

In some embodiments, the bacteria are from the species Lactobacillus gasseri.

In some embodiments, the bacteria are from the genus Dysosmobacter.

In some embodiments, the bacteria are from the species Dysosmobacter welbionis.

In some embodiments, the bacteria of the genus Leuconostoc.

In some embodiments, the bacteria of the genus Lactobacillus.

In some embodiments, the bacteria are of the genus Akkermansia; Bacillus; Blautia; Cupriavidus; Enhydrobacter, Faecalibacterium; Lactobacillus; Lactococcus; Micrococcus; Morganella; Propionibacterium; Proteus; Rhizobium; or Streptococcus.

In some embodiments, the bacteria are Leuconostoc holzapfelii bacteria.

In some embodiments, the bacteria are Akkermansia muciniphila; Cupriavidus metallidurans; Faecalibacterium prausnitzii; Lactobacillus casei; Lactobacillus plantarum; Lactobacillus paracasei; Lactobacillus plantarum; Lactobacillus rhamnosus; Lactobacillus sakei; or Streptococcus pyogenes bacteria.

In some embodiments, the bacteria are Lactobacillus casei; Lactobacillus plantarum; Lactobacillus paracasei; Lactobacillus plantarum; Lactobacillus rhamnosus; or Lactobacillus sakei bacteria.

In some embodiments, the bacteria are Megasphaera sp. bacteria (e.g., from the strain with accession number NCIMB 43385, NCIMB 43386 or NCIMB 43387).

In some embodiments, the bacteria are Megasphaera massiliensis bacteria (e.g., from the strain with accession number NCIMB 42787, NCIMB 43388 or NCIMB 43389).

In some embodiments, the bacteria are Megasphaera massiliensis bacteria (e.g., from the strain with accession number DSM 26228).

In some embodiments, the bacteria are Bacillus amyloliquefaciens bacteria (e.g., from the strain with accession number NCIMB 43088, NCIMB 43087, or NCIMB 43086).

In some embodiments, the bacteria are Parabacteroides distasonis bacteria (e.g., from the strain with accession number NCIMB 42382).

In some embodiments, the bacteria are Megasphaera massiliensis bacteria (e.g., from the strain with accession number NCIMB 43388 or NCIMB 43389), or a derivative thereof. See, e.g., WO 2020/120714. In some embodiments, the Megasphaera massiliensis bacteria is a strain comprising at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the nucleotide sequence (e.g., genomic sequence, 16S sequence, and/or CRISPR sequence) of Megasphaera massiliensis bacteria from the strain with accession number NCIMB 43388 or NCIMB 43389. In some embodiments, the Megasphaera massiliensis bacteria is the strain with accession number NCIMB 43388 or NCIMB 43389.

In some embodiments, the bacteria are Megasphaera massiliensis bacteria strain deposited under accession number NCIMB 42787, or a derivative thereof. See, e.g., WO 2018/229216. In some embodiments, the Megasphaera massiliensis bacteria is a strain comprising at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the nucleotide sequence (e.g. genomic sequence, 16S sequence, and/or CRISPR sequence) of the Megasphaera massiliensis bacteria strain deposited under accession number NCIMB 42787. In some embodiments, the Megasphaera massiliensis bacteria is the strain deposited under accession number NCIMB 42787.

In some embodiments, the bacteria are Megasphaera spp. bacteria from the strain with accession number NCIMB 43385, NCIMB 43386 or NCIMB 43387, or a derivative thereof. See, e.g., WO 2020/120714. In some embodiments, the Megasphaera sp. bacteria is a strain comprising at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the nucleotide sequence (e.g. genomic sequence, 16S sequence, and/or CRISPR sequence) of the Megasphaera sp. from a strain with accession number NCIMB 43385, NCIMB 43386 or NCIMB 43387. In some embodiments, the Megasphaera sp. bacteria is the strain with accession number NCIMB 43385, NCIMB 43386 or NCIMB 43387.

In some embodiments, the bacteria are Parabacteroides distasonis bacteria deposited under accession number NCIMB 42382, or a derivative thereof. See, e.g., WO 2018/229216. In some embodiments, the Parabacteroides distasonis bacteria is a strain comprising at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the nucleotide sequence (e.g. genomic sequence, 16S sequence, and/or CRISPR sequence) of the Parabacteroides distasonis bacteria deposited under accession number NCIMB 42382. In some embodiments, the Parabacteroides distasonis bacteria is the strain deposited under accession number NCIMB 42382.

In some embodiments, the bacteria are Megasphaera massiliensis bacteria deposited under accession number DSM 26228, or a derivative thereof. See, e.g., WO 2018/229216. In some embodiments, the Megasphaera massiliensis bacteria is a strain comprising at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the nucleotide sequence (e.g., genomic sequence, 16S sequence, and/or CRISPR sequence) of Megasphaera massiliensis bacteria deposited under accession number DSM 26228. In some embodiments, the Megasphaera massiliensis bacteria is the strain deposited under accession number DSM 26228.

In some embodiments, the bacteria are Bacillus amyloliquefaciens bacteria (e.g., from the strain with accession number NCIMB 43088, NCIMB 43087, or NCIMB 43086, or a derivative thereof. See, e.g., WO 2019/236806. In some embodiments, the Bacillus amyloliquefaciens bacteria is a strain comprising at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the nucleotide sequence (e.g., genomic sequence, 16S sequence, and/or CRISPR sequence) of Bacillus amyloliquefaciens bacteria from the strain with accession number NCIMB 43088, NCIMB 43087, or NCIMB 43086. In some embodiments, the Bacillus amyloliquefaciens bacteria is the strain with accession number NCIMB 43088, NCIMB 43087, or NCIMB 43086. In some embodiments, the Bacillus amyloliquefaciens bacteria is the strain with accession number NCIMB 43088.

In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×10⁷to about 2×10¹²(e.g., about 3×10¹⁰or about 1.5×10¹¹or about 1.5×10¹²) cells (e.g., wherein cell number is determined by total cell count, which is determined by Coulter counter), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule. In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×10¹⁰to about 2×10¹²(e.g., about 1.6×10¹¹or about 8×10¹¹or about 9.6×10¹¹about 12.8×10¹¹or about 1.6×10¹²) cells (e.g., wherein cell number is determined by total cell count, which is determined by Coulter counter), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.

In some embodiments, the pharmaceutical agent comprises bacteria and the dose of bacteria is about 1×10⁹, about 3×10⁹, about 5×10⁹, about 1.5×10¹⁰, about 3×10¹⁰, about 5×10¹⁰, about 1.5×10¹¹, about 1.5×10¹², or about 2×10²cells, wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.

In some embodiments, the pharmaceutical agent comprises a powder comprising bacteria and the dose of the pharmaceutical agent (e.g., a powder comprising bacteria) is about 10 mg to about 3500 mg, wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.

In some embodiments, the pharmaceutical agent comprises a powder comprising bacteria and the dose of the pharmaceutical agent (e.g., a powder comprising bacteria) is about 30 mg to about 1300 mg (by weight of bacteria powder) (about 25, about 30, about 35, about 50, about 75, about 100, about 120, about 150, about 250, about 300, about 350, about 400, about 500, about 600, about 700, about 750, about 800, about 900, about 1000, about 1100, about 1200, about 1250, about 1300, about 2000, about 2500, about 3000, or about 3500 mg wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.

In some embodiments, the pharmaceutical agent comprises bacteria and the dose of pharmaceutical agent (e.g., bacteria) is about 2×10⁶to about 2×10¹⁶particles (e.g., wherein particle count is determined by NTA (nanoparticle tracking analysis)), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.

In some embodiments, the pharmaceutical agent comprises bacteria and the dose of pharmaceutical agent (e.g., bacteria) is about 5 mg to about 900 mg total protein (e.g., wherein total protein is determined by Bradford assay or BCA), wherein the dose is per capsule or tablet or per total number of minitablets in a capsule.

In some embodiments, the solid dosage form further comprises one or more additional therapeutic agents.

In some aspects, the disclosure provides a method of treating a subject (e.g., human) (e.g., a subject in need of treatment), the method comprising administering to the subject a pharmaceutical agent, a pharmaceutical composition or a solid dosage form provided herein. In some aspects, the disclosure provides use of a pharmaceutical agent, a pharmaceutical composition or a solid dosage form provided herein for the preparation of a medicament for treating a subject (e.g., human) (e.g., a subject in need of treatment).

In some embodiments, the pharmaceutical agent, pharmaceutical composition or solid dosage form is orally administered (e.g., is for oral administration).

In some embodiments, the pharmaceutical agent, pharmaceutical composition or solid dosage form is administered to a subject that is in a fed or fasting state. In some embodiments, the pharmaceutical agent, pharmaceutical composition or solid dosage form is administered to a subject on an empty stomach (e.g., one hour before eating or two hours after eating). In some embodiments, the pharmaceutical agent, pharmaceutical composition or solid dosage form is administered to a subject one hour before eating. In some embodiments, the pharmaceutical agent, pharmaceutical composition or solid dosage form is administered to a subject two hours after eating.

In some embodiments, the pharmaceutical agent, pharmaceutical composition or solid dosage form is administered (e.g., is for administration) 1, 2, 3, or 4 times a day.

In some embodiments, the pharmaceutical composition or solid dosage form provides release of the pharmaceutical agent in the small intestine, e.g., in the upper small intestine, of the pharmaceutical agent contained in the solid dosage form.

In some embodiments, the pharmaceutical composition or solid dosage form delivers the pharmaceutical agent to the small intestine, wherein the pharmaceutical agent can act on immune cells and/or epithelial cells in the small intestine, e.g., in the upper small intestine, e.g., to cause effects throughout the body (e.g., systemic effect).

In some embodiments, the pharmaceutical agent provides one or more beneficial immune effects outside the gastrointestinal tract, e.g., when orally administered.

In some embodiments, the pharmaceutical agent modulates immune effects outside the gastrointestinal tract in the subject, e.g., when orally administered.

In some embodiments, the pharmaceutical agent causes a systemic effect (e.g., an effect outside of the gastrointestinal tract), e.g., when orally administered.

In some embodiments, the pharmaceutical agent acts on immune cells and/or epithelial cells in the small intestine (e.g., upper small intestine) (e.g., causing a systemic effect (e.g., an effect outside of the gastrointestinal tract), e.g., when orally administered.

In some embodiments, the pharmaceutical agent, pharmaceutical composition or solid dosage form is administered orally and has one or more beneficial immune effects outside the gastrointestinal tract (e.g., interaction between the agent and cells in the small intestine modulates a systemic immune response).

In some embodiments, the pharmaceutical agent, pharmaceutical composition or solid dosage form is administered orally and modulates immune effects outside the gastrointestinal tract (e.g., interaction between agent and cells in the small intestine (e.g., upper small intestine) modulates a systemic immune response).

In some embodiments, the pharmaceutical agent, pharmaceutical composition or solid dosage form is administered orally and activates innate antigen presenting cells (e.g., in the small intestine, e.g., upper small intestine).

In some embodiments, the subject is in need of treatment (and/or prevention) of a cancer.

In some embodiments, the subject is in need of treatment (and/or prevention) of an autoimmune disease.

In some embodiments, the subject is in need of treatment (and/or prevention) of an inflammatory disease.

In some embodiments, the subject is in need of treatment (and/or prevention) of a metabolic disease.

In some embodiments, the subject is in need of treatment (and/or prevention) of a dysbiosis.

In some embodiments, the pharmaceutical agent, pharmaceutical composition or solid dosage form is administered in combination with a therapeutic agent (e.g., additional therapeutic agent).

In some aspects, the disclosure provides a cryoprotectant solution, e.g., for use in preparing a pharmaceutical agent, e.g, that comprises bacteria, as described herein.

In some embodiments, the cryoprotectant solution is mixed with the pellet in a ratio of about 0.2 to about 0.5 gram (g) cryoprotectant solution per gram of pellet; about 0.05 to about 0.25 gram (g) cryoprotectant solution per gram of pellet; about 0.06 to about 0.1 gram (g) cryoprotectant solution per gram of pellet; or about 0.15 to about 0.2 gram (g) cryoprotectant solution per gram of pellet. In some embodiments, the cryoprotectant solution is mixed with the pellet in a ratio of about 0.4 gram (g) cryoprotectant solution per gram of pellet. In some embodiments, the cryoprotectant solution is mixed with the pellet in a ratio of about 0.18 gram (g) cryoprotectant solution per gram of pellet. In some embodiments, the cryoprotectant solution is mixed with the pellet in a ratio of about 0.1 gram (g) cryoprotectant solution per gram of pellet. In some embodiments, the cryoprotectant solution is mixed with the pellet in a ratio of about 0.08 gram (g) cryoprotectant solution per gram of pellet.

In some embodiments, the cryoprotectant solution comprises sucrose. In some embodiments, the cryoprotectant solution comprises dextran. In some embodiments, the cryoprotectant solution comprises sucrose and dextran. In some embodiments, the cryoprotectant solution comprises sucrose and dextran in equivalent amounts (e.g., on a percent weight by weight basis). In some embodiments, the cryoprotectant solution comprises sucrose, dextran, and L-cysteine HCl. In some embodiments, the cryoprotectant solution does not comprise L-cysteine HCl.

In some embodiments, the cryoprotectant solution comprises about 0.05% to about 0.6% (weight/weight) L-cysteine HCl. In some embodiments, the cryoprotectant solution comprises about 0.1% to about 0.5% (weight/weight) L-cysteine HCl. In some embodiments, the cryoprotectant solution comprises about 0.15% to about 0.45% (weight/weight) L-cysteine HCl.

In some embodiments, the cryoprotectant solution comprises about 0.2% (weight/weight) L-cysteine HCl.

In some embodiments, the cryoprotectant solution comprises about 59.8% (weight/weight) water.

In some embodiments, the cryoprotectant solution comprises about 0.4% (weight/weight) L-cysteine HCl.

In some embodiments, the cryoprotectant solution comprises about 59.6% (weight/weight) water.

In certain embodiments, the cryoprotectant solution provided herein comprises: (i) about 20% (weight/weight) sucrose; (ii) about 20% (weight/weight) dextran; (iii) about 0.2% (weight/weight) L-cysteine HCl; and (iv) about 59.8% (weight/weight) water.

In certain embodiments, the cryoprotectant provided herein comprises: (i) about 50% (weight/weight) sucrose; (ii) about 50% (weight/weight) dextran; and (iii) about 1% (weight/weight) L-cysteine HCl.

In certain embodiments, the cryoprotectant provided herein comprises: (i) about 50% (weight/weight) sucrose; and (ii) about 50% (weight/weight) dextran.

In some embodiments, the freeze-dried powder comprises about 6% to about 12% (weight/weight) sucrose. In some embodiments, the freeze-dried powder comprises about 8% to about 12% (weight/weight) sucrose. In some embodiments, the freeze-dried powder comprises about 11% (weight/weight) sucrose. In some embodiments, the freeze-dried powder comprises about 6% to about 12% (weight/weight) dextran. In some embodiments, the freeze-dried powder comprises about 8% to about 12% (weight/weight) dextran. In some embodiments, the freeze-dried powder comprises about 11% (weight/weight) dextran. In some embodiments, the freeze-dried powder comprises about 6% to about 12% (weight/weight) sucrose and about 6% to about 12% (weight/weight) dextran. In some embodiments, the freeze-dried powder comprises about 8% to about 12% (weight/weight) sucrose and about 8% to about 12% (weight/weight) dextran. In some embodiments, the freeze-dried powder comprises about 11% (weight/weight) sucrose and about 11% (weight/weight) dextran. In some embodiments, the freeze-dried powder comprises about 0.01% (weight/weight) L-cysteine HCl. In some embodiments, the pharmaceutical agent comprises about 0.1% to about 0.3% (weight/weight) L-cysteine HCl. In some embodiments, the pharmaceutical agent comprises about 0.15% to about 0.25% (weight/weight) L-cysteine HCl.

In some embodiments, the freeze-dried powder comprises about 23% to about 30% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21). In some embodiments, the freeze-dried powder comprises about 24% to about 28% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21). In some embodiments, the freeze-dried powder comprises about 26% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21). In some embodiments, the freeze-dried powder comprises about 21% to about 29% (weight/weight) sucrose. In some embodiments, the freeze-dried powder comprises about 23% to about 27% (weight/weight) sucrose. In some embodiments, the freeze-dried powder comprises about 25% (weight/weight) sucrose. In some embodiments, the freeze-dried powder comprises about 6% to about 11% (weight/weight) dextrose. In some embodiments, the freeze-dried powder comprises about 7% to about 10% (weight/weight) dextrose. In some embodiments, the freeze-dried powder comprises about 9% (weight/weight) dextrose. In some embodiments, the freeze-dried powder comprises about 4% to about 10% (weight/weight) glutamate. In some embodiments, the freeze-dried powder comprises about 5% to about 9% (weight/weight) glutamate. In some embodiments, the freeze-dried powder comprises about 7% (weight/weight) glutamate.

In some embodiments, the freeze-dried powder comprises about 23% to about 30% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21) and about 21% to about 29% (weight/weight) sucrose. In some embodiments, the freeze-dried powder comprises about 24% to about 28% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21) and about 23% to about 27% (weight/weight) sucrose. In some embodiments, the freeze-dried powder comprises about 0.05% to about 0.6% (weight/weight) L-cysteine HCl. In some embodiments, the freeze-dried powder comprises about 0.1% to about 0.5% (weight/weight) L-cysteine HCl.

In some embodiments, the cryoprotectant comprises about 27% to about 47% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21); about 27% to about 47% (weight/weight) sucrose; and about 8% to about 18% (weight/weight) dextrose. In some embodiments, the cryoprotectant comprises about 27% to about 47% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21); about 27% to about 47% (weight/weight) sucrose; and about 8% to about 18% (weight/weight) monosodium glutamate. In some embodiments, the cryoprotectant comprises about 27% to about 47% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21); about 27% to about 47% (weight/weight) sucrose; about 8% to about 18% (weight/weight) dextrose; and about 8% to about 18% (weight/weight) monosodium glutamate.

In certain embodiments, the cryoprotectant provided herein comprises: (i) about 37% (weight/weight) dried (dehydrated) maize glucose syrup (such as Glucidex), such as a dried maize glucose syrup with a dextrose equivalent (DE) of 21 (such as Glucidex 21); (ii) about 37% (weight/weight) sucrose; (iii) about 13% (weight/weight) dextrose; and (iv) about 13% (weight/weight) monosodium glutamate.

In certain embodiments, the freeze-dried powder comprises about 40% to about 70% (weight/weight) dried bacteria. In certain embodiments, the pharmaceutical agent comprises about 35% to about 70% (weight/weight) bacteria (e.g., freeze dried bacteria).

In certain embodiments, the freeze-dried powder comprises about 64% (weight/weight) dried bacteria.

In certain embodiments, the freeze-dried powder comprises about 15% to about 35% (weight/weight) bacteria (e.g., freeze dried bacteria). In certain embodiments, the freeze-dried powder comprises about 18% to about 30% (weight/weight) bacteria (e.g., freeze dried bacteria). In certain embodiments, the freeze-dried powder comprises about 25% (weight/weight) bacteria (e.g., freeze dried bacteria).

In certain embodiments, the freeze-dried powder comprises Prevotella bacteria.

In certain embodiments, the freeze-dried powder comprises Veillonella bacteria.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a graph showing Total Cells/Gram Stability Profile over time long-term (2-8° C. (abbreviation: 5° C.)) and accelerated (25° C. (abbreviation: 25° C.)) storage conditions for Prevotella histicola Strain Batch 1. The lower trace in the graph provides values for accelerated (25° C.) storage conditions. The upper trace in the graph provides values for long-term (2-8° C. (abbreviation: 5° C.)) storage conditions. Total Cell Count (TCC) was determined by Coulter counter.

FIG. 2 is a graph showing Water Content Stability Profile overtime long-term (2-8° C.) and accelerated (25° C.) storage conditions for Prevotella histicola Strain B Batch 1. Water content was determined by the Karl Fisher method.

FIG. 3 is a graph showing Total Cells/Gram Stability Profile over time long-term (2-8° C. (abbreviation: 5° C.)) and accelerated (25° C. (abbreviation: 25° C.)) storage conditions for Prevotella histicola Strain B Batch 2. Total Cell Count (TCC) was determined by Coulter counter.

FIG. 4 is a graph showing Water Content Stability Profile over time long-term (2-8° C. (abbreviation: 5° C.)) and accelerated (25° C.) storage conditions for Prevotella histicola Strain B Batch 2. The upper trace in the graph provides values for accelerated (25° C.) storage conditions. The lower trace in the graph provides values for long-term (2-8° C. (abbreviation: 5° C.)) storage conditions. Water content was determined by the Karl Fisher method.

FIG. 5 is a graph showing Total Cells/Gram Stability Profile over time long-term (2-8° C. (abbreviation: 5° C.)) and accelerated (25° C./60% RH (abbreviation: 25° C.)) storage conditions for Veillonella parvula Strain A Batch A. The trace to 6 months in the graph provides values for accelerated (25° C.) storage conditions. The trace to 12 months in the graph provides values for long-term (2-8° C. (abbreviation: 5° C.)) storage conditions. Total Cell Count (TCC) was determined by Coulter counter.

FIG. 6 is a graph showing Water Content Stability Profile over time long-term (2-8° C.) and accelerated (25° C.) storage conditions for Veillonella parvula Strain A Batch A. The trace to 6 months in the graph provides values for accelerated (25° C.) storage conditions. The trace to 12 months in the graph provides values for long-term (2-8° C. (abbreviation: 5° C.)) storage conditions. Water content was determined by the Karl Fisher method.

FIG. 7 is a graph showing Total Cells/Gram Stability Profile over time long-term (2-8° C. (abbreviation: 5° C.)) and accelerated (25° C./60% RH (abbreviation: 25° C.)) storage conditions for Veillonella parvula Strain A Batch D. The lower trace in the graph provides values for accelerated (25° C.) storage conditions. The upper trace in the graph provides values for long-term (2-8° C. (abbreviation: 5° C.)) storage conditions. Total Cell Count (TCC) was determined by Coulter counter.

FIG. 8 is a graph showing Water Content Stability Profile over time long-term (2-8° C. (abbreviation: 5° C.)) and accelerated (25° C.) storage conditions for Veillonella parvula Strain A Batch D. Water content was determined by the Karl Fisher method.

FIG. 9 is a graph showing Total Cells/Gram Stability Profile over time long-term (2-8° C. (abbreviation: 5° C.)) and accelerated (25° C. (abbreviation: 25° C.)) storage conditions for Prevotella histicola Strain Batch 1. The trace to 6 months in the graph provides values for accelerated (25° C.) storage conditions. The trace to 18 months in the graph provides values for long-term (2-8° C. (abbreviation: 5° C.)) storage conditions. Total Cell Count (TCC) was determined by Coulter counter.

FIG. 10 is a graph showing Water Content Stability Profile overtime long-term (2-8° C.) and accelerated (25° C.) storage conditions for Prevotella histicola Strain B Batch 1. Water content was determined by the Karl Fisher method.

FIG. 11 is a graph showing Total Cells/Gram Stability Profile over time long-term (2-8° C. (abbreviation: 5° C.)) and accelerated (25° C. (abbreviation: 25° C.)) storage conditions for Prevotella histicola Strain Batch 2. The trace to 6 months in the graph provides values for accelerated (25° C.) storage conditions. The trace to 18 months in the graph provides values for long-term (2-8° C. (abbreviation: 5° C.)) storage conditions. Total Cell Count (TCC) was determined by Coulter counter.

FIG. 12 is a graph showing Water Content Stability Profile overtime long-term (2-8° C.) and accelerated (25° C.) storage conditions for Prevotella histicola Strain B Batch 2. Water content was determined by the Karl Fisher method.

FIG. 13 is a graph showing Total Cells/Gram Stability Profile over time long-term (2-8° C. (abbreviation: 5° C.)) and accelerated (25° C. (abbreviation: 25° C.)) storage conditions for Prevotella histicola Strain Batch 4. Total Cell Count (TCC) was determined by Coulter counter.

FIG. 14 is a graph showing Water Content Stability Profile over time long-term (2-8° C.) and accelerated (25° C.) storage conditions for Prevotella histicola Strain B Batch 4. Water content was determined by the Karl Fisher method.

FIG. 15 is a graph showing Total Cells/Gram Stability Profile over time long-term (2-8° C. (abbreviation: 5° C.)) and accelerated (25° C. (abbreviation: 25° C.)) storage conditions for Prevotella histicola Strain Batch 5. Total Cell Count (TCC) was determined by Coulter counter.

FIG. 16 is a graph showing Water Content Stability Profile over time long-term (2-8° C.) and accelerated (25° C.) storage conditions for Prevotella histicola Strain B Batch 5. Water content was determined by the Karl Fisher method.

FIG. 17 is a graph showing Total Cells/Gram Stability Profile over time long-term (−20° C.) and accelerated ((2-8° C. (abbreviation: 5° C.)) storage conditions for Prevotella histicola Strain Batch i. The trace to 6 months in the graph provides values for accelerated (2-8° C. (abbreviation: 5° C.)) storage conditions. The trace to 24 months in the graph provides values for long-term ((−20° C.) storage conditions. Total Cell Count (TCC) was determined by Coulter counter.

FIG. 18 is a graph showing Water Content Stability Profile over time long-term (−20° C.) and accelerated (2-8° C. (abbreviation: 5° C.)) storage conditions for Prevotella histicola Strain B Batch i. Water content was determined by the Karl Fisher method.

DETAILED DESCRIPTION

In certain aspects, provided herein are pharmaceutical agents (such as powders) comprising bacteria (e.g., freeze dried bacteria), wherein the bacteria in the pharmaceutical agent are present at a total cell count (TCC) of at least 1×10¹¹cells/gram of the pharmaceutical agent.

In certain aspects provided herein are pharmaceutical agents (such as powders) that comprise bacteria. In certain embodiments, the pharmaceutical agents maintain their stability, e.g., for three, six, twelve, eighteen and/or twenty-four months under long-term (2-8° C.) and/or accelerated (23-27° C. (optionally at 60% relative humidity (RH))) storage conditions, e.g., as determined by total cell count (TCC), e.g., as determined by Coulter counter and described herein. In certain embodiments, the pharmaceutical agents maintain their stability, e.g., for three, six, twelve, eighteen and/or twenty-four months under long-term (−20° C.) and/or accelerated (2-8° C.) storage conditions, e.g., as determined by total cell count (TCC), e.g., as determined by Coulter counter and described herein.

In certain aspects provided herein are pharmaceutical agents (such as powders) that comprise bacteria. In some embodiments, the water content of the pharmaceutical agents is between about 0.5% and about 9/6, between about 1% and about 8%, between about 1% and about 6%, (e.g., about 1.7%, e.g., 1.8%, e.g., about 2%, e.g., about 2.2%, e.g., about 2.3%, e.g., about 2.4%, e.g., about 2.8%, e.g., about 2.9%, e.g., about 3%, e.g., about 3.1%, e.g., about 3.2%, e.g., about 3.3%, e.g., about 3.5%, e.g., about 3.6%, e.g., about 4%, e.g., about 4.5%, e.g., about 5%, e.g., about 5.3%, e.g., about 5.4%, or e.g., about 7.8%), e.g., as determined by the Karl-Fischer method for water content analysis provided in Ph. Eur. method 2.5.12, and as described herein. In some embodiments, the pharmaceutical agents maintain their water content, e.g., for three, six, twelve, eighteen and/or twenty-four months under long-term (2-8° C.) and/or accelerated (25° C. (optionally at 60% RH)) storage conditions. In certain embodiments, the pharmaceutical agents maintain their water content, e.g., for three, six, twelve, eighteen and/or twenty-four months under long-term (−20) and/or accelerated (2-8° C.) storage conditions, e.g., as determined by total cell count (TCC), e.g., as determined by Coulter counter and described herein.

In certain aspects provided herein are pharmaceutical agents (such as powders) that comprise bacteria and a cryoprotectant.

Definitions

The term “about” when used before a numerical value indicates that the value may vary within a reasonable range, such as within ±10%, ±5% or ±1% of the stated value.

“Adjuvant” or “Adjuvant therapy” broadly refers to an agent that affects an immunological or physiological response in a subject (e.g., human). For example, an adjuvant might increase the presence of an antigen over time or to an area of interest like a tumor, help absorb an antigen presenting cell antigen, activate macrophages and lymphocytes and support the production of cytokines. By changing an immune response, an adjuvant might permit a smaller dose of an immune interacting agent to increase the effectiveness or safety of a particular dose of the immune interacting agent. For example, an adjuvant might prevent T cell exhaustion and thus increase the effectiveness or safety of a particular immune interacting agent.

“Administration” broadly refers to a route of administration of a composition (e.g., a pharmaceutical composition such as a solid dosage form of a pharmaceutical agent as described herein) to a subject. Examples of routes of administration include oral administration, rectal administration, topical administration, inhalation (nasal) or injection. Administration by injection includes intravenous (IV), intramuscular (IM), intratumoral (IT) and subcutaneous (SC) administration. A pharmaceutical composition described herein can be administered in any form by any effective route, including but not limited to intratumoral, oral, parenteral, enteral, intravenous, intraperitoneal, topical, transdermal (e.g., using any standard patch), intradermal, ophthalmic, (intra)nasally, local, non-oral, such as aerosol, inhalation, subcutaneous, intramuscular, buccal, sublingual, (trans)rectal, vaginal, intra-arterial, and intrathecal, transmucosal (e.g., sublingual, lingual, (trans)buccal, (trans)urethral, vaginal (e.g., trans- and perivaginally), implanted, intravesical, intrapulmonary, intraduodenal, intragastrical, and intrabronchial. In preferred embodiments, a pharmaceutical composition described herein is administered orally, rectally, intratumorally, topically, intravesically, by injection into or adjacent to a draining lymph node, intravenously, by inhalation or aerosol, or subcutaneously. In another preferred embodiment, a pharmaceutical composition described herein is administered orally, intratumorally, or intravenously. In another embodiment, a pharmaceutical composition described herein is administered orally.

As used herein, the term “antibody” may refer to both an intact antibody and an antigen binding fragment thereof. Intact antibodies are glycoproteins that include at least two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds. Each heavy chain includes a heavy chain variable region (abbreviated herein as V_H) and a heavy chain constant region. Each light chain includes a light chain variable region (abbreviated herein as V_L) and a light chain constant region. The V_Hand V_Lregions can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDR), interspersed with regions that are more conserved, termed framework regions (FR). Each V_Hand V_Lis composed of three CDRs and four FRs, arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4. The variable regions of the heavy and light chains contain a binding domain that interacts with an antigen. The term “antibody” includes, for example, monoclonal antibodies, polyclonal antibodies, chimeric antibodies, humanized antibodies, human antibodies, multispecific antibodies (e.g., bispecific antibodies), single-chain antibodies and antigen-binding antibody fragments.

The terms “antigen binding fragment” and “antigen-binding portion” of an antibody, as used herein, refer to one or more fragments of an antibody that retain the ability to bind to an antigen. Examples of binding fragments encompassed within the term “antigen-binding fragment” of an antibody include Fab, Fab′, F(ab′)₂, Fv, scFv, disulfide linked Fv, Fd, diabodies, single-chain antibodies, NANOBODIES®, isolated CDRH3, and other antibody fragments that retain at least a portion of the variable region of an intact antibody. These antibody fragments can be obtained using conventional recombinant and/or enzymatic techniques and can be screened for antigen binding in the same manner as intact antibodies.

“Cancer” broadly refers to an uncontrolled, abnormal growth of a host's own cells leading to invasion of surrounding tissue and potentially tissue distal to the initial site of abnormal cell growth in the host. Major classes include carcinomas which are cancers of the epithelial tissue (e.g., skin, squamous cells); sarcomas which are cancers of the connective tissue (e.g., bone, cartilage, fat, muscle, blood vessels, etc.); leukemias which are cancers of blood forming tissue (e.g., bone marrow tissue); lymphomas and myelomas which are cancers of immune cells; and central nervous system cancers which include cancers from brain and spinal tissue. “Cancer(s)” and “neoplasm(s)” are used herein interchangeably. As used herein, “cancer” refers to all types of cancer or neoplasm or malignant tumors including leukemias, carcinomas and sarcomas, whether new or recurring. Specific examples of cancers are: carcinomas, sarcomas, myelomas, leukemias, lymphomas and mixed type tumors. Non-limiting examples of cancers are new or recurring cancers of the brain, melanoma, bladder, breast, cervix, colon, head and neck, kidney, lung, non-small cell lung, mesothelioma, ovary, prostate, sarcoma, stomach, uterus and medulloblastoma. In some embodiments, the cancer comprises a solid tumor. In some embodiments, the cancer comprises a metastasis.

A “carbohydrate” refers to a sugar or polymer of sugars. The terms “saccharide,” “polysaccharide,” “carbohydrate,” and “oligosaccharide” may be used interchangeably. Most carbohydrates are aldehydes or ketones with many hydroxyl groups, usually one on each carbon atom of the molecule. Carbohydrates generally have the molecular formula C_nH_2nO_n. A carbohydrate may be a monosaccharide, a disaccharide, trisaccharide, oligosaccharide, or polysaccharide. The most basic carbohydrate is a monosaccharide, such as glucose, sucrose, galactose, mannose, ribose, arabinose, xylose, and fructose. Disaccharides are two joined monosaccharides. Exemplary disaccharides include sucrose, maltose, cellobiose, and lactose. Typically, an oligosaccharide includes between three and six monosaccharide units (e.g., raffinose, stachyose), and polysaccharides include six or more monosaccharide units. Exemplary polysaccharides include starch, glycogen, and cellulose. Carbohydrates may contain modified saccharide units such as 2′-deoxyribose wherein a hydroxyl group is removed, 2′-fluororibose wherein a hydroxyl group is replaced with a fluorine, or N-acetylglucosamine, a nitrogen-containing form of glucose (e.g., 2′-fluororibose, deoxyribose, and hexose). Carbohydrates may exist in many different forms, for example, conformers, cyclic forms, acyclic forms, stereoisomers, tautomers, anomers, and isomers.

“Cellular augmentation” broadly refers to the influx of cells or expansion of cells in an environment that are not substantially present in the environment prior to administration of a composition and not present in the composition itself. Cells that augment the environment include immune cells, stromal cells, bacterial and fungal cells. Environments of particular interest are the microenvironments where cancer cells reside or locate. In some instances, the microenvironment is a tumor microenvironment or a tumor draining lymph node. In other instances, the microenvironment is a pre-cancerous tissue site or the site of local administration of a composition or a site where the composition will accumulate after remote administration.

“Clade” refers to the OTUs or members of a phylogenetic tree that are downstream of a statistically valid node in a phylogenetic tree. The clade comprises a set of terminal leaves in the phylogenetic tree that is a distinct monophyletic evolutionary unit and that share some extent of sequence similarity.

A “combination” of bacteria from two or more strains includes the physical co-existence of the bacteria, either in the same material or product or in physically connected products, as well as the temporal co-administration or co-localization of the bacteria from the two or more strains.

The term “decrease” or “deplete” means a change, such that the difference is, depending on circumstances, at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 1/100, 1/1000, 1/10,000, 1/100,000, 1/1,000,000 or undetectable after treatment when compared to a pre-treatment state. Properties that may be decreased include the number of immune cells, bacterial cells, stromal cells, myeloid derived suppressor cells, fibroblasts, metabolites; the level of a cytokine; or another physical parameter (such as ear thickness (e.g., in a DTH animal model) or tumor size).

“Dysbiosis” refers to a state of the microbiota or microbiome of the gut or other body area, including, e.g., mucosal or skin surfaces (or any other microbiome niche) in which the normal diversity and/or function of the host gut microbiome ecological networks “microbiome”) are disrupted. A state of dysbiosis may result in a diseased state, or it may be unhealthy under only certain conditions or only if present for a prolonged period. Dysbiosis may be due to a variety of factors, including, environmental factors, infectious agents, host genotype, host diet and/or stress. A dysbiosis may result in: a change (e.g., increase or decrease) in the prevalence of one or more bacteria types (e.g., anaerobic), species and/or strains, change (e.g., increase or decrease) in diversity of the host microbiome population composition; a change (e.g., increase or reduction) of one or more populations of symbiont organisms resulting in a reduction or loss of one or more beneficial effects; overgrowth of one or more populations of pathogens (e.g., pathogenic bacteria); and/or the presence of, and/or overgrowth of, symbiotic organisms that cause disease only when certain conditions are present.

The term “ecological consortium” is a group of bacteria which trades metabolites and positively co-regulates one another, in contrast to two bacteria which induce host synergy through activating complementary host pathways for improved efficacy.

The term “effective dose” or “effective amount” is an amount of a pharmaceutical agent that is effective to achieve a desired therapeutic response in a subject for a particular agent, composition, and mode of administration.

As used herein, “engineered bacteria” are any bacteria that have been genetically altered from their natural state by human activities, and the progeny of any such bacteria. Engineered bacteria include, for example, the products of targeted genetic modification, the products of random mutagenesis screens and the products of directed evolution.

The term “epitope” means a protein determinant capable of specific binding to an antibody or T cell receptor. Epitopes usually consist of chemically active surface groupings of molecules such as amino acids or sugar side chains. Certain epitopes can be defined by a particular sequence of amino acids to which an antibody is capable of binding.

The term “gene” is used broadly to refer to any nucleic acid associated with a biological function. The term “gene” applies to a specific genomic sequence, as well as to a cDNA or an mRNA encoded by that genomic sequence.

“Identity” as between nucleic acid sequences of two nucleic acid molecules can be determined as a percentage of identity using known computer algorithms such as the “FASTA” program, using for example, the default parameters as in Pearson et al. (1988) Proc. Natl. Acad. Sci. USA 85:2444 (other programs include the GCG program package (Devereux, J., et al., Nucleic Acids Research 12(I):387 (1984)), BLASTP, BLASTN, FASTA Atschul, S. F., et al., J Molec Biol 215:403 (1990); Guide to Huge Computers, Mrtin J. Bishop, ed., Academic Press, San Diego, 1994, and Carillo et al. (1988) SIAM J Applied Math 48:1073). For example, the BLAST function of the National Center for Biotechnology Information database can be used to determine identity. Other commercially or publicly available programs include, DNAStar “MegAlign” program (Madison, Wis.) and the University of Wisconsin Genetics Computer Group (UWG) “Gap” program (Madison Wis.)).

As used herein, the term “immune disorder” refers to any disease, disorder or disease symptom caused by an activity of the immune system, including autoimmune diseases, inflammatory diseases and allergies. Immune disorders include, but are not limited to, autoimmune diseases (e.g., psoriasis, atopic dermatitis, lupus, scleroderma, hemolytic anemia, vasculitis, type one diabetes, Grave's disease, rheumatoid arthritis, multiple sclerosis, Goodpasture's syndrome, pernicious anemia and/or myopathy), inflammatory diseases (e.g., acne vulgaris, asthma, celiac disease, chronic prostatitis, glomerulonephritis, inflammatory bowel disease, pelvic inflammatory disease, reperfusion injury, rheumatoid arthritis, sarcoidosis, transplant rejection, vasculitis and/or interstitial cystitis), and/or an allergies (e.g., food allergies, drug allergies and/or environmental allergies).

“Immunotherapy” is treatment that uses a subject's immune system to treat disease (e.g., immune disease, inflammatory disease, metabolic disease, cancer) and includes, for example, checkpoint inhibitors, cancer vaccines, cytokines, cell therapy, CAR-T cells, and dendritic cell therapy.

The term “increase” means a change, such that the difference is, depending on circumstances, at least 10%, 200%, 30%, 400%, 50%, 60%, 70%, 80%, 90%, 2-fold, 4-fold, 10-fold, 100-fold, 10{circumflex over ( )}3 fold, 10{circumflex over ( )}4 fold, 10{circumflex over ( )}5 fold, 10{circumflex over ( )}6 fold, and/or 10{circumflex over ( )}7 fold greater after treatment when compared to a pre-treatment state. Properties that may be increased include the number of immune cells, bacterial cells, stromal cells, myeloid derived suppressor cells, fibroblasts, metabolites; the level of a cytokine; or another physical parameter (such as ear thickness (e.g., in a DTH animal model) or tumor size).

“Innate immune agonists” or “immuno-adjuvants” are small molecules, proteins, or other agents that specifically target innate immune receptors including Toll-Like Receptors (TLR), NOD receptors, RLRs, C-type lectin receptors, STING-cGAS Pathway components, inflammasome complexes. For example, LPS is a TLR-4 agonist that is bacterially derived or synthesized and aluminum can be used as an immune stimulating adjuvant. immuno-adjuvants are a specific class of broader adjuvant or adjuvant therapy. Examples of STING agonists include, but are not limited to, 2′3′-cGAMP, 3′3′-cGAMP, c-di-AMP, c-di-GMP, 2′2′-cGAMP, and 2′3′-cGAM(PS)2 (Rp/Sp) (Rp, Sp-isomers of the bis-phosphorothioate analog of 2′3′-cGAMP). Examples of TLR agonists include, but are not limited to, TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR1O and TLRI 1. Examples of NOD agonists include, but are not limited to, N-acetylmuramyl-L-alanyl-D-isoglutamine (muramyldipeptide (MDP)), gamma-D-glutamyl-meso-diaminopimelic acid (iE-DAP), and desmuramylpeptides (DMP).

The “internal transcribed spacer” or “ITS” is a piece of non-functional RNA located between structural ribosomal RNAs (rRNA) on a common precursor transcript often used for identification of eukaryotic species in particular fungi. The rRNA of fungi that forms the core of the ribosome is transcribed as a signal gene and consists of the 8S, 5.8S and 28S regions with ITS4 and 5 between the 8S and 5.8S and 5.8S and 28S regions, respectively. These two intercistronic segments between the 18S and 5.8S and 5.8S and 28S regions are removed by splicing and contain significant variation between species for barcoding purposes as previously described (Schoch et al Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. PNAS 109:6241-6246. 2012). 18S rDNA is traditionally used for phylogenetic reconstruction however the ITS can serve this function as it is generally highly conserved but contains hypervariable regions that harbor sufficient nucleotide diversity to differentiate genera and species of most fungus.

The term “isolated” or “enriched” encompasses a microbe (such as a bacterium) or other entity or substance that has been (1) separated from at least some of the components with which it was associated when initially produced (whether in nature or in an experimental setting), and/or (2) produced, prepared, purified, and/or manufactured by the hand of man. Isolated microbes may be separated from at least about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, or more of the other components with which they were initially associated. In some embodiments, isolated microbes are more than about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or more than about 99% pure. As used herein, a substance is “pure” if it is substantially free of other components. The terms “purify,” “purifying” and “purified” refer to a microbe or other material that has been separated from at least some of the components with which it was associated either when initially produced or generated (e.g., whether in nature or in an experimental setting), or during any time after its initial production. A microbe or a microbial population may be considered purified if it is isolated at or after production, such as from a material or environment containing the microbe or microbial population, and a purified microbe or microbial population may contain other materials up to about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, or above about 90% and still be considered “isolated.” In some embodiments, purified microbes or microbial population are more than about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or more than about 99% pure. In the instance of microbial compositions provided herein, the one or more microbial types present in the composition can be independently purified from one or more other microbes produced and/or present in the material or environment containing the microbial type. Microbial compositions and the microbial components thereof are generally purified from residual habitat products.

As used herein a “lipid” includes fats, oils, triglycerides, cholesterol, phospholipids, fatty acids in any form including free fatty acids. Fats, oils and fatty acids can be saturated, unsaturated (cis or trans) or partially unsaturated (cis or trans).

The term “LPS mutant or lipopolysaccharide mutant” broadly refers to selected bacteria that comprises loss of LPS. Loss of LPS might be due to mutations or disruption to genes involved in lipid A biosynthesis, such as lpxA, lpxC, and lpxD. Bacteria comprising LPS mutants can be resistant to aminoglycosides and polymyxins (polymyxin B and colistin).

“Metabolite” as used herein refers to any and all molecular compounds, compositions, molecules, ions, co-factors, catalysts or nutrients used as substrates in any cellular or microbial metabolic reaction or resulting as product compounds, compositions, molecules, ions, co-factors, catalysts or nutrients from any cellular or microbial metabolic reaction.

“Microbe” refers to any natural or engineered organism characterized as a archaeaon, parasite, bacterium, fungus, microscopic alga, protozoan, and the stages of development or life cycle stages (e.g., vegetative, spore (including sporulation, dormancy, and germination), latent, biofilm) associated with the organism. Examples of gut microbes include: Actinomyces graevenitzii, Actinomyces odontolyticus, Akkermansia muciniphila, Bacteroides caccae, Bacteroides fragilis, Bacteroides putredinis, Bacteroides thetaiotaomicron, Bacteroides vultagus, Bifidobacterium adolescentis, Bifidobacterium bifidum, Bilophila wadsworthia, Blautia, Butyrivibrio, Campylobacter gracilis, Clostridia cluster III, Clostridia cluster IV, Clostridia cluster IX (Acidaminococcaceae group), Clostridia cluster XI, Clostridia cluster XIII (Peptostreptococcus group), Clostridia cluster XIV, Clostridia cluster XV, Collinsella aerofaciens, Coprococcus, Corynebacterium sunsvallense, Desulfomonas pigra, Dorea formicigenerans, Dorea longicatena, Escherichia col, Eubacterium hadrum, Eubacterium rectale, Faecalibacteria prausnitzii, Gemella, Lactococcus, Lanchnospira, Mollicutes cluster XVI, Mollicutes cluster XVIII, Prevotella, Rothia mucilaginosa, Ruminococcus callidus, Ruminococcus gnavus, Ruminococcus torques, and Streptococcus.

“Microbiome” broadly refers to the microbes residing on or in body site of a subject or patient. Microbes in a microbiome may include bacteria, viruses, eukaryotic microorganisms, and/or viruses. Individual microbes in a microbiome may be metabolically active, dormant, latent, or exist as spores, may exist planktonically or in biofilms, or may be present in the microbiome in sustainable or transient manner. The microbiome may be a commensal or healthy-state microbiome or a disease-state microbiome. The microbiome may be native to the subject or patient, or components of the microbiome may be modulated, introduced, or depleted due to changes in health state (e.g., precancerous or cancerous state) or treatment conditions (e.g., antibiotic treatment, exposure to different microbes). In some aspects, the microbiome occurs at a mucosal surface. In some aspects, the microbiome is a gut microbiome. In some aspects, the microbiome is a tumor microbiome.

A “microbiome profile” or a “microbiome signature” of a tissue or sample refers to an at least partial characterization of the bacterial makeup of a microbiome. In some embodiments, a microbiome profile indicates whether at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or more bacterial strains are present or absent in a microbiome. In some embodiments, a microbiome profile indicates whether at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or more cancer-associated bacterial strains are present in a sample. In some embodiments, the microbiome profile indicates the relative or absolute amount of each bacterial strain detected in the sample. In some embodiments, the microbiome profile is a cancer-associated microbiome profile. A cancer-associated microbiome profile is a microbiome profile that occurs with greater frequency in a subject who has cancer than in the general population. In some embodiments, the cancer-associated microbiome profile comprises a greater number of or amount of cancer-associated bacteria than is normally present in a microbiome of an otherwise equivalent tissue or sample taken from an individual who does not have cancer.

“Modified” in reference to a bacteria broadly refers to a bacteria that has undergone a change from its wild-type form. Bacterial modification can result from engineering bacteria. Examples of bacterial modifications include genetic modification, gene expression modification, phenotype modification, formulation modification, chemical modification, and dose or concentration. Examples of improved properties are described throughout this specification and include, e.g., attenuation, auxotrophy, homing, or antigenicity. Phenotype modification might include, by way of example, bacteria growth in media that modify the phenotype of a bacterium such that it increases or decreases virulence.

An “oncobiome” as used herein comprises tumorigenic and/or cancer-associated microbiota, wherein the microbiota comprises one or more of a virus, a bacterium, a fungus, a protist, a parasite, or another microbe.

“Oncotrophic” or “oncophilic” microbes and bacteria are microbes that are highly associated or present in a cancer microenvironment. They may be preferentially selected for within the environment, preferentially grow in a cancer microenvironment or hone to a said environment.

“Operational taxonomic units” and “OTU(s)” refer to a terminal leaf in a phylogenetic tree and is defined by a nucleic acid sequence, e.g., the entire genome, or a specific genetic sequence, and all sequences that share sequence identity to this nucleic acid sequence at the level of species. In some embodiments the specific genetic sequence may be the 16S sequence or a portion of the 16S sequence. In other embodiments, the entire genomes of two entities are sequenced and compared. In another embodiment, select regions such as multilocus sequence tags (MLST), specific genes, or sets of genes may be genetically compared. For 16S, OTUs that share ≥97% average nucleotide identity across the entire 16S or some variable region of the 16S are considered the same OTU. See e.g., Claesson M J, Wang Q, O'Sullivan O, Greene-Diniz R, Cole J R, Ross R P, and O'Toole P W. 2010. Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res 38: e200. Konstantinidis K T, Ramette A, and Tiedje J M. 2006. The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci 361: 1929-1940. For complete genomes, MLSTs, specific genes, other than 16S, or sets of genes OTUs that share ≥95% average nucleotide identity are considered the same OTU. See e.g., Achtman M, and Wagner M. 2008. Microbial diversity and the genetic nature of microbial species. Nat. Rev. Microbiol. 6: 431-440. Konstantinidis K T, Ramette A, and Tiedje J M. 2006. The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci 361: 1929-1940. OTUs are frequently defined by comparing sequences between organisms. Generally, sequences with no more than 95% sequence identity are not considered to form part of the same OTU. OTUs may also be characterized by any combination of nucleotide markers or genes, in particular highly conserved genes (e.g., “house-keeping” genes), or a combination thereof. Operational Taxonomic Units (OTUs) with taxonomic assignments made to, e.g., genus, species, and phylogenetic clade are provided herein.

As used herein, a gene is “overexpressed” in a bacteria if it is expressed at a higher level in an engineered bacteria under at least some conditions than it is expressed by a wild-type bacteria of the same species under the same conditions. Similarly, a gene is “underexpressed” in a bacteria if it is expressed at a lower level in an engineered bacteria under at least some conditions than it is expressed by a wild-type bacteria of the same species under the same conditions.

As used herein, the term “pharmaceutical agent” refers to an agent for therapeutic use. In some embodiments, a pharmaceutical agent is a composition comprising bacteria that can be used to treat and/or prevent a disease and/or condition. In some embodiments, a medicinal product, medical food, a food product, or a dietary supplement comprises a pharmaceutical agent. In some embodiments, the pharmaceutical agent is a powder that contains the bacteria. The powder can include one or more additional components in addition to the bacteria, such as a cryoprotectant.

The terms “polynucleotide,” and “nucleic acid” are used interchangeably. They refer to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides, or analogs thereof. Polynucleotides may have any three-dimensional structure, and may perform any function. The following are non-limiting examples of polynucleotides: coding or non-coding regions of a gene or gene fragment, loci (locus) defined from linkage analysis, exons, introns, messenger RNA (mRNA), micro RNA (miRNA), silencing RNA (siRNA), transfer RNA, ribosomal RNA, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers. A polynucleotide may comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, modifications to the nucleotide structure may be imparted before or after assembly of the polymer. A polynucleotide may be further modified, such as by conjugation with a labeling component. In all nucleic acid sequences provided herein, U nucleotides are interchangeable with T nucleotides.

As used herein, the term “preventing” a disease or condition in a subject refers to administering to the subject to a pharmaceutical treatment, e.g., the administration of one or more agents (e.g., pharmaceutical agent), such that onset of at least one symptom of the disease or condition is delayed or prevented.

As used herein, a substance is “pure” if it is substantially free of other components. The terms “purify,” “purifying” and “purified” refer to a microbe preparation or other material that has been separated from at least some of the components with which it was associated either when initially produced or generated (e.g., whether in nature or in an experimental setting), or during any time after its initial production. A microbe preparation or compositions may be considered purified if it is isolated at or after production, such as from one or more other bacterial components, and a purified microbe or microbial population may contain other materials up to about 10%, about 20%, about 30%, about 40%, about 50% a, about 60%, about 70%, about 80%, about 90%, or above about 90% and still be considered “purified.” In some embodiments, purified microbes are more than about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or more than about 99% pure. Microbe compositions (or preparations) are, e.g., purified from residual habitat products.

“Residual habitat products” refers to material derived from the habitat for microbiota within or on a subject. For example, fermentation cultures of microbes can contain contaminants, e.g., other microbe strains or forms (e.g., bacteria, virus, mycoplasm, and/or fungus). For example, microbes live in feces in the gastrointestinal tract, on the skin itself, in saliva, mucus of the respiratory tract, or secretions of the genitourinary tract (i.e., biological matter associated with the microbial community). Substantially free of residual habitat products means that the microbial composition no longer contains the biological matter associated with the microbial environment on or in the culture or human or animal subject and is 100% free, 99% free, 98% free, 97% free, 96% free, or 95% free of any contaminating biological matter associated with the microbial community. Residual habitat products can include abiotic materials (including undigested food) or it can include unwanted microorganisms. Substantially free of residual habitat products may also mean that the microbial composition contains no detectable cells from a culture contaminant or a human or animal and that only microbial cells are detectable. In one embodiment, substantially free of residual habitat products may also mean that the microbial composition contains no detectable viral (including bacteria, viruses (e.g., phage)), fungal, mycoplasmal contaminants. In another embodiment, it means that fewer than 1×10⁻²%, 1×10⁻³%, 1×10⁻⁴%, 1×10⁻⁵%, 1×10⁻⁶%, 1×10⁻⁷%, 1×10⁻⁸% of the viable cells in the microbial composition are human or animal, as compared to microbial cells. There are multiple ways to accomplish this degree of purity, none of which are limiting. Thus, contamination may be reduced by isolating desired constituents through multiple steps of streaking to single colonies on solid media until replicate (such as, but not limited to, two) streaks from serial single colonies have shown only a single colony morphology. Alternatively, reduction of contamination can be accomplished by multiple rounds of serial dilutions to single desired cells (e.g., a dilution of 10⁻⁸or 10⁻⁹), such as through multiple 10-fold serial dilutions. This can further be confirmed by showing that multiple isolated colonies have similar cell shapes and Gram staining behavior. Other methods for confirming adequate purity include genetic analysis (e.g., PCR, DNA sequencing), serology and antigen analysis, enzymatic and metabolic analysis, and methods using instrumentation such as flow cytometry with reagents that distinguish desired constituents from contaminants.

As used herein, “specific binding” refers to the ability of an antibody to bind to a predetermined antigen or the ability of a polypeptide to bind to its predetermined binding partner. Typically, an antibody or polypeptide specifically binds to its predetermined antigen or binding partner with an affinity corresponding to a K_Dof about 10⁻⁷M or less, and binds to the predetermined antigen/binding partner with an affinity (as expressed by K_D) that is at least 10 fold less, at least 100 fold less or at least 1000 fold no more than its affinity for binding to a non-specific and unrelated antigen/binding partner (e.g., BSA, casein). Alternatively, specific binding applies more broadly to a two component system where one component is a protein, lipid, or carbohydrate or combination thereof and engages with the second component which is a protein, lipid, carbohydrate or combination thereof in a specific way.

“Strain” refers to a member of a bacterial species with a genetic signature such that it may be differentiated from closely-related members of the same bacterial species. The genetic signature may be the absence of all or part of at least one gene, the absence of all or part of at least on regulatory region (e.g., a promoter, a terminator, a riboswitch, a ribosome binding site), the absence (“curing”) of at least one native plasmid, the presence of at least one recombinant gene, the presence of at least one mutated gene, the presence of at least one foreign gene (a gene derived from another species), the presence at least one mutated regulatory region (e.g., a promoter, a terminator, a riboswitch, a ribosome binding site), the presence of at least one non-native plasmid, the presence of at least one antibiotic resistance cassette, or a combination thereof. Genetic signatures between different strains may be identified by PCR amplification optionally followed by DNA sequencing of the genomic region(s) of interest or of the whole genome. In the case in which one strain (compared with another of the same species) has gained or lost antibiotic resistance or gained or lost a biosynthetic capability (such as an auxotrophic strain), strains may be differentiated by selection or counter-selection using an antibiotic or nutrient/metabolite, respectively.

The terms “subject” or “patient” refers to any mammal. A subject or a patient described as “in need thereof” refers to one in need of a treatment (or prevention) for a disease. Mammals (i.e., mammalian animals) include humans, laboratory animals (e.g., primates, rats, mice), livestock (e.g., cows, sheep, goats, pigs), and household pets (e.g., dogs, cats, rodents). The subject may be a human. The subject may be a non-human mammal including but not limited to of a dog, a cat, a cow, a horse, a pig, a donkey, a goat, a camel, a mouse, a rat, a guinea pig, a sheep, a llama, a monkey, a gorilla or a chimpanzee. The subject may be healthy, or may be suffering from a cancer at any developmental stage, wherein any of the stages are either caused by or opportunistically supported of a cancer associated or causative pathogen, or may be at risk of developing a cancer, or transmitting to others a cancer associated or cancer causative pathogen. In some embodiments, a subject has lung cancer, bladder cancer, prostate cancer, plasmacytoma, colorectal cancer, rectal cancer, Merkel Cell carcinoma, salivary gland carcinoma, ovarian cancer, and/or melanoma. The subject may have a tumor. The subject may have a tumor that shows enhanced macropinocytosis with the underlying genomics of this process including Ras activation. In other embodiments, the subject has another cancer. In some embodiments, the subject has undergone a cancer therapy.

As used herein, a “systemic effect” in a subject treated with a pharmaceutical composition containing bacteria (e.g., a pharmaceutical agent comprising bacteria) of the instant invention means a physiological effect occurring at one or more sites outside the gastrointestinal tract. Systemic effect(s) can result from immune modulation (e.g., via an increase and/or a reduction of one or more immune cell types or subtypes (e.g., CD8+ T cells) and/or one or more cytokines). Such systemic effect(s) may be the result of the modulation by bacteria of the instant invention on immune or other cells (such as epithelial cells) in the gastrointestinal tract which then, directly or indirectly, result in the alteration of activity (activation and/or deactivation) of one or more biochemical pathways outside the gastrointestinal tract. The systemic effect may include treating or preventing a disease or condition in a subject.

As used herein, the term “treating” a disease in a subject or “treating” a subject having or suspected of having a disease refers to administering to the subject to a pharmaceutical treatment, e.g., the administration of one or more agents, such that at least one symptom of the disease is decreased or prevented from worsening. Thus, in one embodiment, “treating” refers inter alia to delaying progression, expediting remission, inducing remission, augmenting remission, speeding recovery, increasing efficacy of or decreasing resistance to alternative therapeutics, or a combination thereof.

As used herein, a value is “greater than” another value if it is higher by any amount (e.g., each of 100, 50, 20, 12, 11, 10.6, 10.1, 10.01, and 10.001 is at least 10). Similarly, as used herein, a value is “less than” another value if it is lower by any amount (e.g., each of 1, 2, 4, 6, 8, 9, 9.2, 9.4, 9.6, 9.8, 9.9, 9.99, 9.999 is no more than 10). In contrast, as used herein, a test value “is” an anchor value when the test value rounds to the anchor value (e.g., if “an ingredient mass is 10% of a total mass,” in which case 10% is the anchor value, the test values of 9.5, 9.6, 9.7, 9.8, 9.9, 10, 10.1, 10.2, 10.3, and 10.4 would also meet the “ingredient mass is 10% of the total mass” feature).

Bacteria

The pharmaceutical agent (e.g., and pharmaceutical compositions comprising the same) disclosed herein can comprise bacteria. For example, the pharmaceutical agent disclosed herein can comprise a powder comprising bacteria. Within a pharmaceutical agent that contains bacteria, the pharmaceutical agent can contain bacteria from one or more strains.

In some embodiments, the bacteria of the pharmaceutical agent are obtained are modified to reduce toxicity or other adverse effects, to enhance delivery) (e.g., oral delivery) (e.g., by improving acid resistance, muco-adherence and/or penetration and/or resistance to bile acids, digestive enzymes, resistance to anti-microbial peptides and/or antibody neutralization), to target desired cell types (e.g., M-cells, goblet cells, enterocytes, dendritic cells, macrophages), to enhance their immunomodulatory and/or therapeutic effect of the bacteria (e.g., either alone or in combination with another therapeutic agent), and/or to enhance immune activation or suppression by the bacteria (e.g., through modified production of polysaccharides, pili, fimbriae, adhesins). In some embodiments, the engineered bacteria described herein are modified to improve bacteria manufacturing (e.g., higher oxygen tolerance, stability, improved freeze-thaw tolerance, shorter generation times). For example, in some embodiments, the engineered bacteria described include bacteria harboring one or more genetic changes, such change being an insertion, deletion, translocation, or substitution, or any combination thereof, of one or more nucleotides contained on the bacterial chromosome or endogenous plasmid and/or one or more foreign plasmids, wherein the genetic change may result in the overexpression and/or underexpression of one or more genes. The engineered bacteria may be produced using any technique known in the art, including but not limited to site-directed mutagenesis, transposon mutagenesis, knock-outs, knock-ins, polymerase chain reaction mutagenesis, chemical mutagenesis, ultraviolet light mutagenesis, transformation (chemically or by electroporation), phage transduction, directed evolution, or any combination thereof.

Examples of taxonomic groups (e.g., class, order, family, genus, species or strain) of bacteria that can be used as a source of bacteria for a pharmaceutical agent described herein are provided herein (e.g., listed in Table 1, Table 2, Table 3, and/or Table 4 and/or elsewhere in the specification (e.g., Table J)). In some embodiments, the bacterial strain is a bacterial strain having a genome that has at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8% or 99.9% sequence identity to a strain listed herein. In some embodiments, the bacteria of the pharmaceutical agent are oncotrophic bacteria. In some embodiments, the bacteria of the pharmaceutical agent are immunomodulatory bacteria. In some embodiments, the bacteria of the pharmaceutical agent are immunostimulatory bacteria. In some embodiments, the bacteria of the pharmaceutical agent are immunosuppressive bacteria. In some embodiments, the bacteria of the pharmaceutical agent are immunomodulatory bacteria. In certain embodiments, the bacteria of the pharmaceutical agent are generated from a combination of bacterial strains provided herein. In some embodiments, the combination is a combination of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45 or 50 bacterial strains. In some embodiments, the combination includes the bacteria of the pharmaceutical agent are from bacterial strains listed herein and/or bacterial strains having a genome that has at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8% or 99.9% sequence identity to a strain listed herein (e.g., listed in Table 1, Table 2, Table 3, and/or Table 4 and/or elsewhere in the specification (e.g., Table J)). In certain embodiments, the bacteria of the pharmaceutical agent are generated from a bacterial strain provided herein. In some embodiments, the bacteria of the pharmaceutical agent are from a bacterial strain listed herein (e.g., listed in Table 1, Table 2, Table 3, and/or Table 4 and/or elsewhere in the specification (e.g., Table J)) and/or a bacterial strain having a genome that has at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8% or 99.9% sequence identity to a strain listed herein (e.g., listed in Table 1, Table 2, Table 3, and/or Table 4 and/or elsewhere in the specification (e.g., Table J)).

In some embodiments, the bacteria of the pharmaceutical agent are Gram negative bacteria.

In some embodiments, the Gram negative bacteria belong to the class Negativicutes. The Negativicutes represent a unique class of microorganisms as they are the only diderm members of the Firmicutes phylum. These anaerobic organisms can be found in the environment and are normal commensals of the oral cavity and GI tract of humans. The Negativicutes class includes the families Veillonellaceae, Selenomonadaceae, Acidaminococcaceae, and Sporomusaceae. The Negativicutes class includes the genera Megasphaera, Selenomonas, Propionospora, and Acidaminococcus. Exemplary Negativicutes species include, but are not limited to, Megasphaera sp., Selenomonas felix, Acidaminococcus intestine, and Propionospora sp.

In some embodiments, the bacteria of the pharmaceutical agent are Gram positive bacteria.

In some embodiments, the bacteria of the pharmaceutical agent are aerobic bacteria.

In some embodiments, the bacteria of the pharmaceutical agent are anaerobic bacteria. In some embodiments, the anaerobic bacteria comprise obligate anaerobes. In some embodiments, the anaerobic bacteria comprise facultative anaerobes.

In some embodiments, the bacteria of the pharmaceutical agent are acidophile bacteria.

In some embodiments, the bacteria of the pharmaceutical agent are alkaliphile bacteria.

In some embodiments, the bacteria of the pharmaceutical agent are neutralophile bacteria.

In some embodiments, the bacteria of the pharmaceutical agent are fastidious bacteria.

In some embodiments, the bacteria of the pharmaceutical agent are nonfastidious bacteria.

In some embodiments, the bacteria of the pharmaceutical agent are lyophilized.

In some embodiments, the bacteria of the pharmaceutical agent are gamma irradiated (e.g., at 17.5 or 25 kGy).

In some embodiments, the bacteria of the pharmaceutical agent are UV irradiated.

In some embodiments, the bacteria of the pharmaceutical agent are heat inactivated (e.g., at 50° C. for two hours or at 90° C. for two hours).

In some embodiments, the bacteria of the pharmaceutical agent are acid treated.

In some embodiments, the bacteria of the pharmaceutical agent are oxygen sparged (e.g., at 0.1 vvm for two hours).

The phase of growth can affect the amount or properties of bacteria. For example, bacteria can be isolated at the start of the log phase of growth, midway through the log phase, and/or once stationary phase growth has been reached for a bacterial culture.

In certain embodiments, the bacteria of the pharmaceutical agent are obligate anaerobic bacteria. Examples of obligate anaerobic bacteria include gram-negative rods (including the genera of Bacteroides, Prevotella, Porphyromonas, Fusobacterium, Bilophila and Sutterella spp.), gram-positive cocci (primarily Peptostreptococcus spp.), gram-positive spore-forming (Clostridium spp.), non-spore-forming bacilli (Actinomyces, Propionibacterium, Eubacterium, Lactobacillus and Bifidobacterium spp.), and gram-negative cocci (mainly Veillonella spp.). In some embodiments, the obligate anaerobic bacteria are of a genus selected from the group consisting of Agathobaculum, Atopobium, Blautia, Burkholderia, Dielma, Longicatena, Paraclostridium, Turicibacter, and Tyzzerella.

The Negativicutes class includes the families Veillonellaceae, Selenomonadaceae, Acidaminococcaceae, and Sporomusaceae. The Negativicutes class includes the genera Megasphaera, Selenomonas. Propionospora, and Acidaminococcus. Exemplary Negativicutes species include, but are not limited to, Megasphaera sp., Selenomonas felix, Acidaminococcus intestini, and Propionospora sp.

In some embodiments, the bacteria of the pharmaceutical agent are of the Negativicutes class.

In some embodiments, the bacteria of the pharmaceutical agent are of the Veillonellaceae family.

In some embodiments, the bacteria of the pharmaceutical agent are of the Selenomonadaceae family.

In some embodiments, the bacteria of the pharmaceutical agent are of the Acidaminococcaceae family.

In some embodiments, the bacteria of the pharmaceutical agent are of the Sporomusaceae family.

In some embodiments, the bacteria of the pharmaceutical agent are of the Megasphaera genus.

In some embodiments, the bacteria of the pharmaceutical agent are of the Selenomonas genus.

In some embodiments, the bacteria of the pharmaceutical agent are of the Propionospora genus.

In some embodiments, the bacteria of the pharmaceutical agent are of the Acidaminococcus genus.

In some embodiments, the bacteria of the pharmaceutical agent are Megasphaera sp. bacteria.

In some embodiments, the bacteria of the pharmaceutical agent are Selenomonas felix bacteria.

In some embodiments, the bacteria of the pharmaceutical agent are Acidaminococcus intestini bacteria.

In some embodiments, the bacteria of the pharmaceutical agent are Propionospora sp. bacteria.

The Oscillospriraceae family within the Clostridia class of microorganisms are common commensal organisms of vertebrates.

In some embodiments, the bacteria of the pharmaceutical agent are of the Clostridia class.

In some embodiments, the bacteria of the pharmaceutical agent are of the Oscillospriraceae family.

In some embodiments, the bacteria of the pharmaceutical agent are of the Faecalibacterium genus.

In some embodiments, the bacteria of the pharmaceutical agent are of the Fournierella genus.

In some embodiments, the bacteria of the pharmaceutical agent are of the Harryflintia genus.

In some embodiments, the bacteria of the pharmaceutical agent are of the Agathobaculum genus.

In some embodiments, the bacteria of the pharmaceutical agent are Faecalibacterium prausnitzii (e.g., Faecalibacterium prausnitzii Strain A) bacteria.

In some embodiments, the bacteria of the pharmaceutical agent are Fournierella massiliensis (e.g., Fournierella massiliensis Strain A) bacteria.

In some embodiments, the bacteria of the pharmaceutical agent are Harryflintia acetispora (e.g., Harryflintia acetispora Strain A) bacteria.

In some embodiments, the bacteria of the pharmaceutical agent are Agathobaculum sp. (e.g., Agathobaculum sp. Strain A) bacteria.

In some embodiments, the bacteria of the pharmaceutical agent are bacteria of a genus selected from the group consisting of Escherichia, Klebsiella, Lactobacillus, Shigella, and Staphylococcus.

In some embodiments, the bacteria of the pharmaceutical agent are a species selected from the group consisting of Blautia massiliensis, Paraclostridium benzoelyticum, Dielma fastidiosa, Longicatena caecimuris, Lactococcus lactis cremoris, Tyzzerella nexilis, Hungatella effluvia, Klebsiella quasipneumoniae subsp. Similipneumoniae, Klebsiella oxytoca, and Veillonella tobetsuensis.

In some embodiments, the bacteria of the pharmaceutical agent are a Prevotella bacteria selected from the group consisting of Prevotella albensis, Prevotella amnii, Prevotella bergensis, Prevotella bivia, Prevotella brevis, Prevotella bryantii, Prevotella buccae, Prevotella buccalis, Prevotella copri, Prevotella dentalis, Prevotella denticola, Prevotella disiens, Prevotella histicola, Prevotella intermedia, Prevotella maculosa, Prevotella marshii, Prevotella melaninogenica, Prevotella micans, Prevotella multiformis, Prevotella nigrescens, Prevotella oralis, Prevotella oris, Prevotella oulorum, Prevotella pallens, Prevotella salivae, Prevotella stercorea, Prevotella tannerae, Prevotella timonensis, Prevotella jejuni, Prevotella aurantiaca, Prevotella baroniae, Prevotella colorans, Prevotella corporis, Prevotella dentasini, Prevotella enoeca, Prevotella falsenii, Prevotellafusca, Prevotella heparinolytica, Prevotella loescheii, Prevotella multisaccharivorax, Prevotella nanceiensis, Prevotella oryzae, Prevotella paludivivens, Prevotella pleuritidis, Prevotella ruminicola, Prevotella saccharolytica Prevotella scopos, Prevotella shahii, Prevotella zoogleoformans, and Prevotella veroralis.

In some embodiments, the bacteria of the pharmaceutical agent are a strain of bacteria comprising a genomic sequence that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the genomic sequence of the strain of bacteria deposited with the ATCC Deposit number as provided in Table 3. In some embodiments, the bacteria of the pharmaceutical agent are a strain of bacteria comprising a 16S sequence that is at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity (e.g., at least 99.5% sequence identity, at least 99.6% sequence identity, at least 99.7% sequence identity, at least 99.8% sequence identity, at least 99.9% sequence identity) to the 16S sequence of the strain of bacteria deposited with the ATCC Deposit number as provided in Table 3.

The Negativicutes class includes the families Veillonellaceae, Selenomonadaceae, Acidaminococcaceae, and Sporomusaceae. The Negativicutes class includes the genera Megasphaera, Selenomonas, Propionospora, and Acidaminococcus. Exemplary Negativicutes species include, but are not limited to, Megasphaera sp., Selenomonas felix, Acidaminococcus intestini, and Propionospora sp.