Compositions and methods for treatment of allergy

Abstract

To provide compositions and methods for the treatment of allergy, such as food allergy.SOLUTION: A method for treating a food allergy, the method comprising administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains selected from the group consisting of Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Dorea longicatena, Erysipelotrichaceae bacterium, and Subdolinogranulum spp.SELECTED DRAWING: Figure 3-4

Description

[Technical Field]

[0001] Related Applications This application claims the benefit under 35 U.S.C. § 119(e) of U.S. Provisional Application No. 62 / 583,777, filed November 9, 2017; U.S. Provisional Application No. 62 / 637,355, filed March 1, 2018; and U.S. Provisional Application No. 62 / 721,786, filed August 23, 2018. The entire contents of each of these referenced applications are incorporated herein by reference.

[0002] FIELD OF THE INVENTION Provided herein are compositions and methods for treating allergies, such as food allergies. Also provided herein are compositions and methods for modulating immune responses associated with allergies and / or inducing immune tolerance or desensitization to allergies, such as food allergies. [Background technology]

[0003] Background of the Invention According to the World Health Organization's statistics on allergies, the incidence of allergies has been rising in developed countries over the past 50 years, and approximately 40-50% of school-age children worldwide are sensitive to at least one common allergen. See, for example, Pawankar R, et al. The WAO White Book on Allergy (Update 2013). Although allergies can develop during childhood, allergies can also develop or occur throughout life. The severity of allergic reactions upon exposure to allergens can range widely from mild to sometimes fatal reactions. Therefore, improved therapies for treating allergies and allergic reactions are desirable. Summary of the Invention

[0004] SUMMARY OF THE INVENTION Aspects of the present disclosure provide a method for treating allergy, comprising administering any of the compositions described herein. Also provided is a method for modulating an immune response associated with allergy, comprising administering any of the compositions described herein. Also provided is a method for inducing immune tolerance or hyposensitization to an, comprising administering any of the compositions described herein. Also provided is a method for modulating an immune response associated with allergy, comprising administering an antibiotic and administering any of the compositions described herein. Also provided is a method for inducing immune tolerance or hyposensitization to an, comprising administering an antibiotic and administering any of the compositions described herein.

[0005] Aspects of the present disclosure provide methods of treating food allergies, comprising administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains of a species selected from the group consisting of Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Dorea longicatena, Erysipelotrichaceae bacterium, and Subdolinogranulum spp. Aspects of the present disclosure provide methods of treating food allergies, comprising administering to a subject in need thereof an antibiotic and administering to the subject a therapeutically effective amount of a composition comprising two or more purified bacterial strains of a species selected from the group consisting of Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Dorea longicatena, Erysipelotrichaceae bacterium, and Subdolinogranulum spp. In some embodiments, the composition consists of purified bacterial strains Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Erysipelotrichaceae bacterium, and Subdolinogranulum spp. In some embodiments, the composition consists of purified bacterial strains Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Dorea longicatena, and Subdolinogranulum spp.

[0006] Aspects of the present disclosure provide methods for treating food allergies, comprising administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains of species selected from the group consisting of Clostridium indolis, Anaerostipes caccae, Lachnospiraceae bacterium, and Clostridium symbiosum. In some embodiments, the composition consists of the purified bacterial strains Clostridium indolis, Anaerostipes caccae, Lachnospiraceae bacterium, and Clostridium symbiosum. Aspects of the present disclosure provide methods for treating food allergies, comprising administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains of a species selected from the group consisting of Clostridium hathewayi, Clostridium bolteae, Sellimonas intestinalis, and Clostridium species. In some embodiments, the composition consists of the purified bacterial strains Clostridium hathewayi, Clostridium bolteae, Sellimonas intestinalis, and Clostridium species.

[0007] Aspects of the present disclosure provide methods for treating food allergies, comprising administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 1-8. Aspects of the present disclosure provide methods for treating food allergies, comprising administering to a subject in need thereof an antibiotic and administering to the subject a therapeutically effective amount of a composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 1-8. In some embodiments, the composition consists of purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence set forth as SEQ ID NOs: 1-5, 7, and 8. In some embodiments, the composition consists of purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence set forth as SEQ ID NOs: 1-6 and 8.

[0008] Aspects of the present disclosure provide methods of treating food allergies, comprising administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO: 10, SEQ ID NO: 11; SEQ ID NO: 13; and SEQ ID NO: 4. In some embodiments, the composition consists of purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleic acid sequence set forth as SEQ ID NO: 10, SEQ ID NO: 11; SEQ ID NO: 13; and SEQ ID NO: 4.

[0009] Aspects of the present disclosure provide methods of treating food allergies, comprising administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO:9, SEQ ID NO:1; SEQ ID NO:3; and SEQ ID NO:12. In some embodiments, the composition consists of purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence set forth as SEQ ID NO:9, SEQ ID NO:1; SEQ ID NO:3; and SEQ ID NO:12.

[0010] In some embodiments, the method results in suppression of IgE antibody production. In some embodiments, the method results in suppression of a Th2 immune response. In some embodiments, the method results in suppression of an immune response associated with food allergies. In some embodiments, the bacterial strains are lyophilized. In some embodiments, one or more of the bacterial strains are in spore form. In some embodiments, each of the bacterial strains is in spore form. In some embodiments, one or more of the strains are in vegetative form. In some embodiments, each of the bacterial strains is in vegetative form.

[0011] In some embodiments, the administration is oral administration. In some embodiments, the composition is formulated for oral delivery. In some embodiments, the composition is formulated for rectal delivery. In some embodiments, the composition is formulated for intestinal delivery. In some embodiments, the composition is formulated for colonic delivery. In some embodiments, the food allergy is selected from the group consisting of nut allergy, fish allergy, wheat allergy, milk allergy, peanut allergy, tree nut allergy, shellfish allergy, soy allergy, seed allergy, sesame seed allergy, and egg allergy. In some embodiments, the subject is a human.

[0012] In some embodiments, the composition further comprises one or more adjuvants. In some embodiments, the adjuvant is associated with allergy treatment or immune tolerance. Aspects of the present disclosure provide methods for modulating an immune response associated with food allergy, comprising administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains of a species selected from the group consisting of Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Dorea longicatena, Erysipelotrichaceae bacterium, and Subdolinogranulum spp. In some embodiments, the composition consists of purified bacterial strains Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Erysipelotrichaceae bacterium, and Subdolinogranulum spp. In some embodiments, the composition consists of purified bacterial strains Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Dorea longicatena, and Subdolinogranulum spp.

[0013] Aspects of the present disclosure provide methods for modulating an immune response associated with food allergy, comprising administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 1-8. In some embodiments, the composition consists of purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence set forth as SEQ ID NOs: 1-5, 7, and 8. In some embodiments, the composition consists of purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence set forth as SEQ ID NOs: 1-6 and 8.

[0014] Aspects of the present disclosure provide methods for modulating an immune response associated with food allergy, comprising administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO: 10, SEQ ID NO: 11; SEQ ID NO: 13; and SEQ ID NO: 4. In some embodiments, the composition consists of purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleic acid sequence set forth as SEQ ID NO: 10, SEQ ID NO: 11; SEQ ID NO: 13; and SEQ ID NO: 4.

[0015] Aspects of the present disclosure provide methods for modulating an immune response associated with food allergy, comprising administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO:9, SEQ ID NO:1; SEQ ID NO:3; and SEQ ID NO:12. In some embodiments, the composition consists of purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence set forth as SEQ ID NO:9, SEQ ID NO:1; SEQ ID NO:3; and SEQ ID NO:12.

[0016] In some embodiments, the method results in the induction of proliferation and / or accumulation of regulatory T cells. In some embodiments, the method results in the suppression of IgE antibody production. In some embodiments, the method results in the suppression of Th2 immune responses. In some embodiments, the bacterial strains are freeze-dried. In some embodiments, the bacterial strains are spray-dried. In some embodiments, one or more of the bacterial strains are in spore form. In some embodiments, each of the bacterial strains is in spore form. In some embodiments, one or more of the bacterial strains are in vegetative form. In some embodiments, each of the bacterial strains is in vegetative form.

[0017] In some embodiments, the administration is oral administration. In some embodiments, the composition is formulated for oral delivery. In some embodiments, the composition is formulated for rectal delivery. In some embodiments, the composition is formulated for intestinal delivery. In some embodiments, the composition is formulated for colonic delivery. In some embodiments, the food allergy is selected from the group consisting of nut allergy, fish allergy, wheat allergy, milk allergy, peanut allergy, tree nut allergy, shellfish allergy, soy allergy, seed allergy, sesame seed allergy, and egg allergy. In some embodiments, the subject is a human. In some embodiments, the composition further comprises one or more adjuvants. In some embodiments, the adjuvant is associated with allergy treatment or immune tolerance.

[0018] Aspects of the present disclosure provide methods for inducing immune tolerance or hyposensitization to food allergies, comprising administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains of a species selected from the group consisting of Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Dorea longicatena, Erysipelotrichaceae bacterium, and Subdolinogranulum spp. In some embodiments, the composition consists of purified bacterial strains Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Erysipelotrichaceae bacterium, and Subdolinogranulum spp. In some embodiments, the composition consists of purified bacterial strains Clostridium bolteae, Anaerotruncus colihominis, Ruminococcus torques, Clostridium symbiosum, Blautia producta, Dorea longicatena, and Subdolinogranulum spp.

[0019] Aspects of the present disclosure provide methods for inducing immune tolerance or hyposensitivity to food allergies, comprising administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains of species selected from the group consisting of Clostridium indolis, Anaerostipes caccae, Lachnospiraceae bacterium, and Clostridium symbiosum. In some embodiments, the composition consists of the purified bacterial strains Clostridium indolis, Anaerostipes caccae, Lachnospiraceae bacterium, and Clostridium symbiosum. Aspects of the present disclosure provide methods for inducing immune tolerance or hyposensitization to food allergies, comprising administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains of a species selected from the group consisting of Clostridium hathewayi, Clostridium bolteae, Sellimonas intestinalis, and Clostridium species. In some embodiments, the composition consists of the purified bacterial strains Clostridium hathewayi, Clostridium bolteae, Sellimonas intestinalis, and Clostridium species.

[0020] Aspects of the present disclosure provide methods for inducing immune tolerance or hyposensitization to food allergies, comprising administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 1-8. In some embodiments, the composition consists of purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence set forth as SEQ ID NOs: 1-5, 7, and 8. In some embodiments, the composition consists of purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence set forth as SEQ ID NOs: 1-6 and 8.

[0021] Aspects of the present disclosure provide methods of inducing immune tolerance or hyposensitization to food allergies, comprising administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO:10, SEQ ID NO:11; SEQ ID NO:13; and SEQ ID NO:4. In some embodiments, the composition consists of purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleic acid sequence set forth as SEQ ID NO:10, SEQ ID NO:11; SEQ ID NO:13; and SEQ ID NO:4.

[0022] Aspects of the present disclosure provide methods of inducing immune tolerance or hyposensitization to food allergies, comprising administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO:9, SEQ ID NO:1; SEQ ID NO:3; and SEQ ID NO:12. In some embodiments, the composition consists of purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence set forth as SEQ ID NO:9, SEQ ID NO:1; SEQ ID NO:3; and SEQ ID NO:12. In some embodiments, the method results in the induction of proliferation and / or accumulation of regulatory T cells. In some embodiments, the method results in the suppression of IgE antibody production. In some embodiments, the method results in the suppression of Th2 immune responses.

[0023] In some embodiments, the bacterial strains are freeze-dried. In some embodiments, the bacterial strains are spray-dried. In some embodiments, one or more of the bacterial strains are in spore form. In some embodiments, each of the bacterial strains is in spore form. In some embodiments, one or more of the bacterial strains are in vegetative form. In some embodiments, each of the bacterial strains is in vegetative form. In some embodiments, the administration is oral administration. In some embodiments, the composition is formulated for oral delivery. In some embodiments, the composition is formulated for rectal delivery. In some embodiments, the composition is formulated for intestinal delivery. In some embodiments, the composition is formulated for colonic delivery.

[0024] In some embodiments, the food allergy is selected from the group consisting of nut allergy, fish allergy, wheat allergy, milk allergy, peanut allergy, tree nut allergy, shellfish allergy, soy allergy, seed allergy, sesame seed allergy, and egg allergy. In some embodiments, the subject is a human. In some embodiments, the composition further comprises one or more adjuvants. In some embodiments, the adjuvant is associated with allergy treatment or immune tolerance.

[0025] Aspects of the present disclosure also provide a composition comprising three or more purified bacterial strains of a species selected from the group consisting of Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Erysipelotrichaceae bacterium, and Subdolinogranulum spp., and wherein the composition does not include Dorea longicatena. Aspects of the present disclosure also provide a composition comprising three or more purified bacterial strains selected from the group consisting of Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Dorea longicatena, and Subdolinogranulum spp., and wherein the composition does not include Erysipelotrichaceae bacterium.

[0026] Aspects of the present disclosure also provide a composition comprising three or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NOs:1-5, 7, and 8, wherein the composition does not include a bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence provided by SEQ ID NO:6. Aspects of the present disclosure also provide a composition comprising three or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NOs:1-6 and 8, wherein the composition does not include a bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence provided by SEQ ID NO:7.

[0027] In some embodiments, the composition induces the proliferation and / or accumulation of regulatory T cells. In some embodiments, the composition suppresses the production of IgE antibodies. In some embodiments, the composition suppresses one or more Th2 immune responses. In some embodiments, the composition further comprises one or more adjuvants. In some embodiments, the adjuvant is associated with allergy treatment or immune tolerance. Aspects of the present disclosure also provide pharmaceutical compositions comprising any of the compositions described herein and a pharmaceutically acceptable excipient. In some embodiments, the pharmaceutical composition is formulated for oral delivery. In some embodiments, the pharmaceutical composition is formulated for rectal delivery. In some embodiments, the pharmaceutical composition is formulated for intestinal delivery. In some embodiments, the pharmaceutical composition is formulated for colonic delivery. Aspects of the present disclosure also provide food products comprising any of the compositions described herein and nutrients.

[0028] Each of the limitations of the invention may cover various aspects of the invention. Thus, each of the limitations of the invention relating to any one element or combination of elements is expected to be encompassed in each aspect of the invention. The invention is not limited in its application to the details of construction and arrangement of components set forth in the following description or illustrated in the drawings. The invention is capable of other embodiments and of being practiced or carried out in various ways.

[0029] Brief description of the drawings The accompanying drawings are not intended to be drawn to scale. The figures are for illustrative purposes only and are not required for enablement of the present disclosure. For clarity, not every component may be labeled in every drawing. In the drawings: [Brief explanation of the drawings]

[0030] [Figure 1-2] Figure 1 shows the percentage of Foxp3+CD4+ regulatory T cells induced in the intestines of germ-free mice inoculated with Composition B compared to control mice ("GF"). The presented data are pooled from several independent experiments. To normalize between experiments, the average percentage of Foxp3-positive cells in the germ-free control mice was subtracted from each of the other mice in each experiment. Figure 2 shows the levels of IgE antibodies in serum samples obtained from germ-free mice inoculated with Composition B compared to control germ-free mice ("GF") and specific pathogen-free mice ("SPF").

[0031] [Figure 3-4]Figure 3 shows the percentage of Foxp3+ CD4+ regulatory T cells induced in the intestines of germ-free mice inoculated with Composition B, Composition C, or Composition D compared to control mice ("GF") and specific pathogen-free mice ("SPF"). The presented data are pooled from several independent experiments. To normalize between experiments, the average percentage of Foxp3-positive cells in the germ-free control mice was subtracted from each of the other mice in each experiment. Figure 4 shows the levels of IgE antibodies in serum samples obtained from germ-free mice inoculated with Composition B, Composition C, or Composition D compared to control germ-free ("GF") and specific pathogen-free ("SPF") mice.

[0032] [Figure 5] FIG. 5 shows the magnitude of regulatory T cell induction, measured as a percentage of Foxp3+CD4+ T cells, in germ-free mice inoculated with LBP1 or LBP2 compared to control mice (“GF”). [Figures 6A-6B] Figure 6A shows the amount of butyrate predicted to be produced in vitro by LBP2 or LBP1, and Figure 6B shows the amount of acetate predicted to be produced in vitro by LBP1 or LBP2. [Figure 6C-6D] Figure 6C shows the amount of butyrate produced in vivo as measured in ex vivo fecal samples from germ-free mice inoculated with LBP1 or LBP2, and Figure 6D shows the amount of acetate produced in vivo as measured in ex vivo fecal samples from germ-free mice inoculated with LBP1 or LBP2.

[0033] [Figure 7]Figure 7 is a schematic diagram showing the experimental food allergy model as described in Example 3. IL4raF709 mutant mice are pretreated with antibiotics for the times indicated by the boxes. OVA + Staphylococcal enterotoxin B (SEB) is administered to the mice at the time indicated by the arrow above the time axis. The bacterial mixture is administered to the mice at the time indicated by the hollow arrow below the time axis. Mice are challenged with OVA at the times indicated.

[0034] [Figures 8A-8C] Figure 8A shows the levels of IgE antibodies in serum samples obtained from mice inoculated with LBP1 or LBP2 compared to control mice (no bacteria, "NB"). Figure 8B shows the levels of OVA-specific IgE antibodies in serum samples obtained from mice inoculated with LBP1 or LBP2 compared to control mice (no bacteria, "NB"). Figure 8C shows the changes in body temperature of mice inoculated with LBP1 or LBP2 or control mice (no bacteria). [Figure 8D] FIG. 8D shows photomicrographs of tissue samples from mice inoculated with LBP1, LBP2, or no bacteria ("NB").

[0035] [Figure 9]Figure 9A shows the percentage of CD3+CD4+ cells in the spleen, mesenteric lymph node (MLN), and small intestine (SI) of mice inoculated with LBP1 or LBP2 compared to control mice (no bacteria). Figure 9B shows the percentage of CD4+IL4+ cells in the spleen, mesenteric lymph node (MLN), and small intestine (SI) of mice inoculated with LBP1 or LBP2 compared to control mice (no bacteria). Figure 9C shows the percentage of Foxp3+IL4+ cells in the spleen, mesenteric lymph node (MLN), and small intestine (SI) of mice inoculated with LBP1 or LBP2 compared to control mice (no bacteria). Figure 9D shows the percentage of GATA3-bright regulatory T cells in the spleen, mesenteric lymph node (MLN), and small intestine (SI) of mice inoculated with LBP1 or LBP2 compared to control mice (no bacteria). For each of Figures 9A-9D, white bars are control mice (no bacteria), black bars are mice inoculated with LBP1, and gray bars are mice inoculated with LBP2. **, ***, and **** represent statistical significance.

[0036] [Figure 10]Figure 10A shows the levels of mMCP-1 in serum samples from mice inoculated with LBP1 or LBP2 compared to control mice (no bacteria, "NB"). Figure 10B shows the levels of mast cells in the spleen, mesenteric lymph nodes (MLN), and small intestine (SI) of mice inoculated with LBP1 or LBP2 compared to control mice (no bacteria, "NB"). Figure 10C shows the levels of IgE+ mast cells in the spleen, mesenteric lymph nodes (MLN), and small intestine (SI) of mice inoculated with LBP1 or LBP2 compared to control mice (no bacteria, "NB"). Figure 10D shows the levels of IgE+ B cells in the spleen, mesenteric lymph nodes (MLN), and small intestine (SI) of mice inoculated with LBP1 or LBP2 compared to control mice (no bacteria, "NB"). For each of Figures 10B-10D, white bars are control mice (no bacteria), black bars are mice inoculated with LBP1, and gray bars are mice inoculated with LBP2. *, **, and *** indicate statistical significance.

[0037] [Figure 11] Figure 11A shows the amount of butyrate produced in vivo in germ-free mice inoculated with LBP1 or LBP2 at the indicated time points (days post-inoculation), as measured in ex vivo fecal samples. Figure 11B shows the amount of butyrate produced in vitro by LBP1, LBP2, Composition ("Comp") C, Composition D, or Composition B. Figure 11C shows the amount of butyrate produced in vivo in germ-free mice inoculated with Composition B at the indicated time points (D = days post-inoculation), as measured in ex vivo fecal samples. Figure 11D shows the amount of butyrate produced in vivo in germ-free mice inoculated with bacterial compositions at the indicated time points (D = days post-inoculation), as measured in ex vivo fecal samples. For each time point, the left column shows results from mice inoculated with Composition B, and the right column shows results from mice inoculated with Composition C.

[0038] [Figure 12]Figure 12A shows the amount of acetate produced in vivo in germ-free mice inoculated with LBP1 or LBP2 at the indicated time points (days post-inoculation), as measured in ex vivo fecal samples. Figure 12B shows the amount of acetate produced in vitro by LBP1, LBP2, Composition C, Composition D, or Composition B. Figure 12C shows the amount of acetate produced in vivo in germ-free mice inoculated with Composition B at the indicated time points (D = days post-inoculation), as measured in ex vivo fecal samples. Figure 12D shows the amount of acetate produced in vivo in germ-free mice inoculated with bacterial compositions at the indicated time points (D = days post-inoculation), as measured in ex vivo fecal samples. For each time point, the left column shows results from mice inoculated with Composition B, and the right column shows results from mice inoculated with Composition C.

[0039] [Figure 13] Figure 13 shows the percentage of Foxp3+ CD4+ regulatory T cells induced in the intestines of germ-free mice inoculated with LBP1, LBP2, Composition C, Composition D, or Composition B compared to control mice ("GF") and specific pathogen-free mice ("SPF"). The presented data are pooled from several independent experiments. To normalize between experiments, the average percentage of Foxp3-positive cells in the germ-free control mice was subtracted from each of the other mice in each experiment.

[0040] [Figure 14] Figure 14 shows the levels of IgE antibodies in serum samples obtained from germ-free mice inoculated with LBP1, LBP2, Composition C, Composition D, or Composition B compared to control germ-free ("GF") and specific pathogen-free ("SPF") mice. [Figures 15A-15B]Figure 15A shows the change in body temperature of mice inoculated with Composition C or control mice (no bacteria). Figure 15B shows the levels of mMCP-1 in serum samples from mice inoculated with Composition C compared to control mice (no bacteria, "NB"). The results shown in Figures 15A and 15B were obtained from the experimental food allergy model shown in Figure 7.

[0041] [Figures 16A-16D] Figure 16A shows the percentage of Foxp3+CD4+ regulatory T cells in the mesenteric lymph nodes (MLNs), spleens (SplNs), and gastrointestinal tract (small intestine) of mice inoculated with Composition C compared to control mice (no bacteria, "NB"). Figure 16B shows the percentage of Foxp3+IL4+ cells in the mesenteric lymph nodes (MLNs), spleens (SplNs), and gastrointestinal tract (small intestine) of mice inoculated with Composition C compared to control mice (no bacteria, "NB"). Figure 16C shows the percentage of Foxp3+GATA3+ cells in the mesenteric lymph nodes (MLNs), spleens (SplNs), and gastrointestinal tract (small intestine) of mice inoculated with Composition C compared to control mice (no bacteria, "NB"). Figure 16D shows the percentage of Foxp3-IL4+ cells in the mesenteric lymph nodes (MLNs), spleen (SplN) and gastrointestinal tract (small intestine) of mice inoculated with Composition C compared to control mice (no bacteria, "NB").

[0042] [Figure 16E] Figure 16E depicts a plot of microbial communities by principal component analysis (PCA) of species showing the fecal microbiome profile and changes to the microbiome due to inoculation with Composition C during allergic sensitization. Microbial species are shown for mice on day 0 (prior to antibiotic treatment), day 7 (after antibiotic treatment and prior to inoculation with Composition C), and days 14, 35, and 56 during the course of weekly allergen sensitization and inoculation with Composition C ("+Composition C"). The results shown in Figures 16A-16E are for the same experiment shown in Figures 15A and 15B.

[0043] [Figure 17] Figure 17A shows the mean change in body temperature (+ / - SEM) for mice inoculated with Composition C (+C) or control mice (no bacteria). Figure 17B shows the change in body temperature for individual mice inoculated with Composition C (+C) or control mice (no bacteria). Figure 17C shows the levels of mMCP-1 in serum samples from mice inoculated with Composition C (+C) compared to control mice (no bacteria, "NB"). SEM = standard error of the mean. The results in Figures 17A and 17B were obtained using the experimental food allergy model shown in Figure 7.

[0044] [Figures 18A-18D] Figure 18A shows the percentage of Foxp3+GATA3+ "Th2-type" regulatory T cells in the mesenteric lymph nodes (MLN), spleen (SPL), and small intestine (Sm Int) of mice inoculated with Composition C (+C) compared to control mice (no bacteria, "NB"). Figure 18B shows the percentage of Foxp3-GATA3- Th2 effector or T cells in the mesenteric lymph nodes (MLN), spleen (SPL), and small intestine (Sm Int) of mice inoculated with Composition C (+C) compared to control mice (no bacteria, "NB"). Figure 18C shows the percentage of Foxp3+ regulatory T cells in the mesenteric lymph nodes (MLN), spleen (SPL), and small intestine (Sm Int) of mice inoculated with Composition C (+C) compared to control mice (no bacteria, "NB"). Figure 18D shows the percentage of Foxp3- effector or T cells in the mesenteric lymph nodes (MLN), spleen (SPL) and small intestine (Sm Int) of mice inoculated with Composition C (+C) compared to control mice (no bacteria, "NB").

[0045] [Figure 18E]Figure 18E depicts a plot of microbial communities by principal component analysis (PCA) of species showing the fecal microbiome profile and changes to the microbiome due to inoculation with Composition C during allergic sensitization. Microbial species are shown for mice on day 0 (prior to antibiotic treatment and prior to inoculation with Composition C), and on days 28 and 63 during the course of weekly allergen sensitization and inoculation with Composition C ("+C"). The results shown in Figures 18A-18E are for the same experiment shown in Figures 17A-17C.

[0046] [Figure 19] Figure 19 is a schematic diagram showing the curative experimental food allergy model as described in Example 4. IL4raF709 mutant mice were sensitized with OVA plus Staphylococcal enterotoxin B (SEB) for 8 weeks, followed by 1 week of pretreatment with antibiotics ("Abx") as indicated. The bacterial mixture is administered to the mice at the time points indicated by the arrows below the time axis. [Figure 20] Figure 20A shows the mean change (+ / - SEM) in body temperature for mice inoculated with Composition C (+C) or control mice (no bacteria). Figure 20B shows the change in body temperature for individual mice inoculated with Composition C (+C) or control mice (no bacteria). Figure 20C shows the levels of mMCP-1 in serum samples from mice inoculated with Composition C (+C) compared to control mice (no bacteria, "NB"). SEM = standard error of the mean.

[0047] [Figure 21]Figure 21A shows the percentage of Foxp3+GATA3+ "Th2-type" regulatory T cells in the mesenteric lymph nodes (MLN), spleen (SPL), and small intestine (Sm Int) of mice inoculated with Composition C (+C) compared to control mice (no bacteria, "NB"). Figure 21B shows the percentage of Foxp3-GATA3- Th2 effector or T cells in the mesenteric lymph nodes (MLN), spleen (SPL), and small intestine (Sm Int) of mice inoculated with Composition C (+C) compared to control mice (no bacteria, "NB"). Figure 21C shows the percentage of total Foxp3+ regulatory T cells in the mesenteric lymph nodes (MLN), spleen (SPL), and small intestine (Sm Int) of mice inoculated with Composition C (+C) compared to control mice (no bacteria, "NB"). Figure 21D shows the percentage of total Foxp3- effector or T cells in the mesenteric lymph nodes (MLN), spleen (SPL), and small intestine (Sm Int) of mice inoculated with Composition C (+C) compared to control mice (no bacteria, "NB"). The results shown in Figures 21A-21D are for the same experiment shown in Figures 20A-20C.

[0048] [Figure 22] Figure 22A shows the levels of total IgE antibodies in serum samples obtained from mice inoculated with Composition C (+C) compared to control mice (no bacteria, "NB"). Figure 22B shows the levels of OVA-specific IgE antibodies in serum samples obtained from mice inoculated with Composition C (+C) compared to control mice (no bacteria, "NB"). The results shown in Figures 22A-22B are for the same experiment shown in Figures 20A-20C. [Figure 23]Figure 23A shows the mean change in body temperature (+ / - SEM) for mice inoculated with Composition C (+C), mice inoculated with Composition B (+B), or control mice ("NB," no bacteria). Figure 23B shows the change in body temperature for individual mice inoculated with Composition C (+C), individual mice inoculated with Composition B (+B), or control mice ("NB," no bacteria). SEM = standard error of the mean. The results shown in Figures 23A-23B were obtained from the experimental food allergy model shown in Figure 19.

[0049] [Figure 24] Figure 24A shows mMCP-1 levels in serum samples from curative food allergy model mice inoculated with Composition C (+C) or Composition B (+B) compared to control mice (no bacteria, "NB"). Figure 24B shows IgE antibody levels in serum samples obtained from curative food allergy model mice inoculated with Composition C (+C) or Composition B (+B) compared to control mice (no bacteria, "NB"). Figure 24C shows OVA-specific IgE antibody levels in serum samples obtained from model mice inoculated with Composition C (+C) or Composition B (+B) compared to control mice (no bacteria, "NB").

[0050] [Figure 25]Figure 25A shows the percentage of Foxp3+GATA3+ "Th2-type" regulatory T cells in the mesenteric lymph nodes (MLN), spleen (SPL), and small intestine (Sm Int) of mice inoculated with Composition C (+C) or Composition B (+B) compared to control mice (no bacteria, "NB"). Figure 25B shows the percentage of Foxp3-GATA3-Th2 effector or T cells in the mesenteric lymph nodes (MLN), spleen (SPL), and small intestine (Sm Int) of mice inoculated with Composition C (+C) or Composition B (+B) compared to control mice (no bacteria, "NB"). Figure 25C shows the percentage of Foxp3+ regulatory T cells in the mesenteric lymph nodes (MLN), spleen (SPL), and small intestine (Sm Int) of mice inoculated with Composition C (+C) or Composition B (+B) compared to control mice (no bacteria, "NB"). Figure 25D shows the percentage of Foxp3- effector or T cells in the mesenteric lymph nodes (MLN), spleen (SPL), and small intestine (Sm Int) of mice inoculated with Composition C (+C) or Composition B (+B) compared to control mice (no bacteria, "NB"). The results shown in Figures 25A-25D are for the same experiment as in Figures 23A-24C.

[0051] [Figure 26] Figure 26A shows the mean change in body temperature (+ / - SEM) for mice inoculated with Composition C (+C), Composition B (+B), or control mice ("no bacteria"). Figure 26B shows the change in body temperature for individual mice inoculated with Composition C (+C), Composition B (+B), or control mice ("no bacteria"). SEM = standard error of the mean. The results for Figures 26A and 26B are from the same experimental food allergy model shown in Figure 7.

[0052] [Figure 27]Figure 27A shows the level of mMCP-1 in serum samples from mice in the curative food allergy model inoculated with Composition C (+C), Composition B (+B), or control mice (no bacteria, "NB"). Figure 27B shows the level of total IgE antibodies in serum samples obtained from mice in the curative food allergy model inoculated with Composition C (+C), Composition B (+B), or control mice (no bacteria, "NB"). Figure 27C shows the level of OVA-specific IgE antibodies in serum samples obtained from mice in the curative food allergy model inoculated with Composition C (+C) or Composition B (+B) compared to control mice (no bacteria, "NB"). The results in Figures 27A-27C were obtained using the food allergy experimental model shown in Figure 19.

[0053] [Figure 28] Figure 28A shows the percentage of CD4+Foxp3+IL4+ "Th2-type" regulatory T cells in the small intestine (SI), spleen (SPL), and mesenteric lymph nodes (MLN) of mice inoculated with Composition C ("+C"), Composition B ("+B"), or control mice (no bacteria, "NB"). Figure 28B shows the percentage of CD4+Foxp3-IL4+ Th2 effector or T cells in the small intestine (SI), spleen (SPL), and mesenteric lymph nodes (MLN) of mice inoculated with Composition C ("+C"), Composition B ("+B"), or control mice (no bacteria, "NB"). The results for Figures 28A and 28B are from the same experiment as those for Figures 26A-27C.

[0054] [Figure 29]Figure 29 is a schematic diagram showing an experimental allergy model to assess the ability of bacterial compositions to affect the host microbiome and intestinal immune response. Specific pathogen-free ("SPF") mice were either treated or not with antibiotics for five consecutive days, as indicated by the horizontal bars. During the following 2-3 day "washout" period, mice were either inoculated with the bacterial composition (either raw or frozen preparations of the bacterial composition, as indicated by the arrows) or not (control mice). Dosing with the bacterial composition occurred twice in the first week and continued with intermittent weekly fecal pellet collection to monitor bacterial colonization and the fecal microbiome (as indicated by the vertical bars). Groups of mice were sacrificed at weeks 2 and 4 to monitor the intestinal immune response (indicated by the black "X").

[0055] [Figure 30] Figure 30A shows the percentage of total CD4+ T cells that were FoxP3+ and Helios- among live CD45+ lamina propria leukocytes isolated from the colons of mice that were treated with antibiotics ("+Abx") or not treated with antibiotics ("No Abx"), inoculated with Composition B ("+B"), or without bacteria ("NB"), and sacrificed either 2 or 4 weeks after the start of bacterial inoculation. Figure 30B shows the percentage of total CD4+ T cells that were FoxP3+ and Helios- among live CD45+ lamina propria leukocytes isolated from the colons of mice that were treated with antibiotics ("+Abx") and inoculated with Composition C ("+C"), or without bacteria ("NB"); or that did not receive antibiotics ("No Abx") and inoculated with Composition C ("+C"), Composition B ("+B"), or without bacteria ("NB"). Mice were either 2 or 4 weeks after the start of bacterial inoculation. The results in Figures 30A and 30B were obtained from the experimental model shown in Figure 29.

[0056] [Figure 31]Figure 31A shows plots of microbial communities by species principal component analysis (PCA) representing fecal microbiome profiles and changes to the microbiome of mice that received no antibiotics and were inoculated with Composition B (LBP) or no bacteria. Microbial communities are shown for mice on day 0 (prior to receiving a dose of Composition B) and days 13, 20, and 34 over the course of weekly inoculations with Composition B. Figure 31B shows plots of microbial communities by species principal component analysis (PCA) representing fecal microbiome profiles and changes to the microbiome of mice that received antibiotics and were inoculated with Composition B (antibiotics + LBP) or no bacteria ("antibiotics"). Microbial communities are shown for mice on day 0 (prior to inoculation with Composition B), day 6 (after antibiotic treatment and prior to inoculation with Composition B), and days 13, 20, and 34 over the course of weekly inoculations with Composition B. The results from Figures 31A and 31B show the fecal microbiome profiles of the mice from Figures 30A and 30B.

[0057] [Figure 32] Figure 32 shows a schematic diagram of a model for preventative food allergy experiments, similar to the experimental model shown in Figure 7, however, as indicated, the mice are not pre-treated with antibiotics prior to the start of inoculation with the bacterial composition. [Figure 33] Figure 33A shows an interim analysis of the levels of IgE antibodies in serum samples obtained 5 weeks after the start of inoculation with the bacterial composition. Mice were inoculated with LBP1, LBP2, or no bacteria (control mice, "NB"). Figure 33B shows an interim analysis of the levels of OVA-specific IgE antibodies in serum samples obtained 5 weeks after the start of inoculation with the bacterial composition, at which point the mice had not yet been sensitized and had not yet received an anaphylactic challenge for the full 8 weeks. The results shown in Figures 33A and 33B were obtained using the preventative food allergy model shown in Figure 32.

[0058] [Figure 34]Figure 34A shows the mean change in body temperature (+ / - SEM) for mice inoculated with LBP1, LBP2, or control mice ("NB," no bacteria). Figure 34B shows the change in body temperature for individual mice inoculated with LBP1, LBP2, or control mice ("NB," no bacteria). SEM = standard error of the mean. The results shown in Figures 34A and 34B were obtained using the experimental model shown in Figure 32. [Figure 35] Figure 35A shows the percentage of CD4+Foxp3+IL4+ "Th2-type" regulatory T cells in the spleen (SPL), mesenteric lymph nodes (MLN), and small intestine (SI) of mice inoculated with LBP1, LBP2, or control mice ("no bacteria"). Figure 35B shows the percentage of CD4+IL4+ (CD4+Foxp3-IL4+) Th2 effector or T cells in the spleen (SPL), mesenteric lymph nodes (MLN), and small intestine (SI) of mice inoculated with LBP1, LBP2, or control mice ("no bacteria"). The results shown in Figures 35A and 35B are from the same experiment as those in Figures 33A-34B.

[0059] Detailed Description of the Invention Current treatment regimens aimed at reducing allergies or allergic reactions focus on treating the symptoms of allergic immune responses, for example, with antihistamines, corticosteroids, or epinephrine.These methods fail to address the underlying undesired allergic immune responses stimulated upon contact or exposure to allergens.An additional approach is hyposensitization therapy, also known as allergen immunotherapy, which requires identifying the specific allergen that induces the allergic reaction, and then repeatedly administering the allergen to regulate the undesired immune response, effectively "desensitizing" the immune response to the allergen.However, identifying the specific allergen associated with allergy is not always feasible, and numerous, repeated administrations will result in low patient compliance.Allergen immunotherapy will also be impractical for individuals with allergies associated with severe allergic reactions.

[0060] In the context of food allergies, individuals are frequently advised to eliminate foods that contain or are likely to contain allergens that stimulate allergic reactions. Without control over food preparation or accurate food labeling, the risk of allergic reactions and exposure to allergens, even in very low amounts, remains high despite food avoidance. Furthermore, elimination of specific foods or food groups may lead to nutritional disorders and significantly impact a person's quality of life. Alternatively, methods are being explored to reduce the allergenicity of specific foods by reducing the amount of allergens in the food, for example, using processing methods. For example, see Verhoeckx et al. Food and Chem. Toxicology (2015) 80: 223-240; Bischoff et al. Gastroenterology (2005) 128(4): 1089-1113.

[0061] Provided herein are compositions and methods for treating allergies, such as food allergies, involving administering compositions of selected bacterial strains that modulate immune responses associated with allergies. Provided herein are compositions and methods for modulating immune responses associated with allergies, such as food allergies, for treating allergies in a subject. Also provided herein are compositions and methods for inducing immune tolerance or desensitization to allergies, such as food allergies.

[0062] The present invention is not limited in its application to the details of construction and the arrangement of components set forth in the following description or illustrated in the drawings. The invention is capable of other embodiments and of being practiced or carried out in various ways. Also, the phraseology and terminology used herein is for the purpose of description and should not be regarded as limiting. The use of "comprising," "including," "having," "containing," "relat- ing to," and variations thereof herein is meant to encompass the items listed thereafter and equivalents thereof as well as additional items.

[0063] Aspects of the present disclosure refer to compositions and methods for treating allergies, such as food allergies, in subjects. Also provided are compositions and methods for regulating allergy-related immune responses and / or inducing immune tolerance or hyposensitivity to allergies. Allergies are characterized by an unwanted immune response upon contact or exposure to a (non-self) substance that is typically considered harmless, called an allergen. In the general population, contact or exposure to an allergen does not induce a substantial immune response, and individuals are considered tolerant or insensitive to the allergen. Therefore, allergies may refer to a hypersensitivity reaction to an allergen.

[0064] Allergic reactions are driven by the Th2 immune response and involve the unwanted production and / or activation of allergen-specific antibodies, such as IgE antibodies, and allergen-specific lymphocytes, such as T cells and B cells. The progression of an allergic reaction can be divided into three phases: the sensitization phase, the effector phase, and the chronic phase. During the sensitization phase, allergens are internalized, processed, and presented by antigen-presenting cells, leading to the production of allergen-specific IgE antibodies. These antibodies can bind to high-affinity IgE receptors (e.g., FcεR1) present on mast cells and basal cells. During the effector phase, the interaction between the cell-bound allergen-specific IgE antibodies and the allergen leads to degranulation of mast cells and basophils, releasing histamine, leukotrienes, and other mediators, followed by the infiltration of other cells, such as basophils, eosinophils, and lymphocytes, into tissues. The chronic phase results from repeated allergic reactions and inflammation. Bischoff et al. Gastroenterology (2005) 128(4): 1089-1113.

[0065] The symptoms and severity of an allergy will depend on factors such as the type of immune response(s) involved, the duration and magnitude of the immune response(s), the amount of the allergen, and the site of contact / exposure to the allergen. Examples of allergic symptoms include, but are not limited to, skin rash, redness of the skin, hives, bumps / spots / weakness on the skin, itchy / watery eyes, headache, sneezing, wheezing, shortness of breath, chest tightness, cough, runny nose, sore throat, swelling, nausea, vomiting, diarrhea, and anaphylaxis. A subject may be contacted or exposed to an allergen that induces an allergic response through any route known in the art, such as ingestion, inhalation, injection, or direct contact. Symptoms associated with the allergic response may be localized to the site of contact or exposure to the allergen, such as an area of ​​the skin, respiratory tract, or gastrointestinal tract, a peripheral site, or may be systemic, such as in the case of anaphylaxis.

[0066] The immune response stimulated in response to contact or exposure to an allergen will be referred to as an allergic reaction. Generally, an allergic reaction will occur immediately, within about 30 minutes, or longer after contact or exposure to the allergen. Examples of allergies that can be treated in accordance with the compositions and methods provided herein include, but are not limited to, allergic asthma, allergic colitis, animal allergies, atopic allergies, hay fever, skin allergies, urticaria, atopic dermatitis, anaphylaxis, allergic rhinitis, drug or medicinal allergies, eczema (atopic dermatitis), food allergies, fungal allergies, insect allergies (including insect sting / insect venom allergies), mold allergies, plant allergies, and pollenosis. In some embodiments, the allergy is a food allergy.

[0067] Aspects of the present disclosure relate to treating food allergies and / or regulating immune responses associated with food allergies in subjects. Also provided herein is a method for inducing immune tolerance or hyposensitization to food allergies. As used herein, the term "food allergy" refers to an undesired allergic immune response to food, or specifically to the allergens present in food. In some embodiments, the allergic reaction associated with food allergies is induced following contact, for example, through the ingestion of food or food containing the same or similar allergens. As will be apparent to those skilled in the art, symptoms associated with food allergies will appear in the subject's gastrointestinal tract, for example, following the ingestion of food containing allergens; however, the allergic reaction may affect other areas, such as the respiratory tract or skin.

[0068] Food allergies are generally considered to be IgE-mediated immune responses; however, non-IgE-mediated food allergies and mixed IgE-mediated / non-IgE-mediated food allergies also exist. For example, see Fiocchi et al. "Food Allergy" World Allergy Organization: March 2017. IgE-mediated food allergies tend to occur immediately or within about two hours after contact with an allergen and include immediate gastrointestinal hypersensitivity, including urticaria (acute urticaria), angioedema, swelling, anaphylaxis, food-related exercise-induced anaphylaxis, oral allergy syndrome, and / or vomiting and pain. Non-IgE-mediated immune responses related to food allergies, also referred to as cell-mediated responses, are delayed hypersensitivity reactions and may include food protein-induced enterocolitis syndrome, food protein-induced allergic proctocolitis, allergic contact dermatitis, and Heiner's syndrome. A mixed or combined IgE-mediated / non-IgE-mediated immune response related to food allergy may involve both IgE- and T-cell-mediated effects and may include atopic dermatitis, eosinophilic esophagitis and / or eosinophilic gastroenteritis.

[0069] In contrast to food allergies, food intolerances are generally not thought to be mediated by the immune system, and onset occurs between about 30 minutes and up to 48 hours after exposure. In some embodiments, the compositions and methods described herein are used to treat IgE-mediated food allergies. In some embodiments, the compositions and methods described herein are used to regulate immune responses associated with IgE-mediated food allergies. In some embodiments, the compositions and methods described herein are used to induce immune tolerance or desensitization to IgE-mediated food allergies. The compositions and methods described herein may also be used in the context of non-IgE-mediated food allergies and / or mixed or combined IgE-mediated / non-IgE-mediated food allergies.

[0070] Examples of food allergies include, but are not limited to, peanut allergy, tree nut allergy, egg allergy, corn allergy, fruit allergy, milk allergy, garlic allergy, soy allergy, wheat allergy, seafood allergy, fish allergy (e.g., shellfish allergy), and seed allergy (e.g., sesame seed allergy). Non-limiting examples of foods containing allergens that may cause food allergies include abalone (abalone (perlemoen)), acerola, pollock, almonds, aniseed, apples, apricots, avocados, bananas, barley, bell peppers, Brazil nuts, buckwheat, cabbage, carp, carp, carrots, cashews, caster beans, celery, celery root, cherries, chestnuts, chickpeas (garbanzo beans, bengal gram), cocoa, coconut, cod, cottonseed, zucchini, crab, dates, eggs, figs, fish, linseed, frogs, cultivated plums, garlic, grapes, hazelnuts, kiwi fruit (Chinese kiwi fruit), and the like. gooseberry), lentils, lettuce, lobster, lupin (lupine), lychee, mackerel, maize (corn), mango, melon, milk, mustard, oat, oyster, peach, peanut (ground nuts), money Nuts), pears, pecans, persimmons, pine nuts, pineapple, pomegranate seeds, mustard seeds, potatoes, pumpkins, rice, rye, salmon, sesame seeds, shrimp (black tiger shrimp, brown shrimp, Yoshino shrimp, Indian shrimp, salmon shrimp, white shrimp), snails, soybeans (soybeans), squid, strawberries, sunflower seeds, tomatoes, tuna, turnips, walnuts, and wheat (bread wheat, pasta wheat, Kamut, spelt).

[0071] Also within the scope of this disclosure are compositions and methods that may be used to treat diseases or disorders associated with immune responses associated with a Th2 immune response(s). In some embodiments, the compositions and methods described herein are used to treat diseases or disorders associated with elevated levels of IgE antibodies. Examples of diseases or disorders that may be associated with elevated levels of IgE antibodies include, but are not limited to, hyper-IgE (Job's) syndrome, IgE myeloma, lymphoproliferative disorders, Sézary syndrome, Kimura's disease, parasitic diseases, HIV infection, vasculitis, systemic lupus erythematosus, and juvenile systemic lupus erythematosus.

[0072] In one aspect, the present disclosure provides compositions and methods of treatment for diseases or disorders, such as allergies (e.g., food allergies) in a subject. As used herein, "subject," "individual," and "patient" are used interchangeably and refer to a vertebrate, preferably a mammal, such as a human. Mammals include, but are not limited to, human primates, non-human primates, or murine, bovine, equine, canine, or feline species. In some embodiments, the subject is a human. In some embodiments, the human subject is a neonatal subject, a pediatric subject, an adolescent subject, an adult subject, or a geriatric subject.

[0073] In some embodiments, the subject has or is at risk of having an allergy, such as a food allergy. In some embodiments, the subject has had an allergic reaction or reaction after contact with or exposure to a specific food or food group containing an allergen. In some embodiments, the subject has a medical history related to allergies, such as food allergies. In some embodiments, the subject has a family history of allergies or allergies to specific allergens. For example, family history will affect the likelihood that a subject will have or develop an allergy, such as a food allergy. In addition, a subject who has a food allergy to a specific food (e.g., a specific allergen in a food) will also be more likely to have or develop a food allergy to a different food (e.g., a different specific allergen in a food).

[0074] In some embodiments, the subject has the risk factors associated with developing allergies.The examples of risk factors associated with developing food allergies include, but are not limited to, immature mucosal immune system, early introduction of solid food, genetically increased mucosal permeability, IgA deficiency or delayed IgA production, inappropriate challenge with commensal resident bacteria of the intestinal immune system, genetically determined bias toward Th2 immune response, polymorphisms of Th2 cytokine or IgE receptor genes, impaired enteric nervous system, immune system alterations (for example, low levels of TGF-β), and gastrointestinal infections (Bischoff et al. Gastroenterology (2005) 128 (4) 1089-1113).

[0075] Any of the compositions described herein may be administered to a subject in a therapeutically effective amount or a therapeutically effective dose for the treatment or prevention of a disease or disorder (e.g., food allergy). The term "treat" or "treatment" refers to reducing or alleviating one or more symptoms associated with a disease (e.g., an allergy, such as a food allergy). The term "prevent" or "prevention" encompasses prophylactic administration and will reduce the incidence or likelihood of a disease or disorder (e.g., a food allergy). In some embodiments, the composition reduces the incidence or likelihood of an allergic reaction, such as an allergic reaction associated with a food or food allergen.

[0076] Illustratively, in some embodiments, administration of a composition provided herein results in an altered microbiome in a subject, providing the effect of reducing the incidence or likelihood of an allergic reaction in the subject. Illustratively, in some embodiments, administration of a composition provided herein results in a healthy microbiome in a subject, providing the effect of reducing the incidence or likelihood of an allergic reaction in the subject. In some embodiments, administration of a composition provided herein results in a reduction or alleviation of one or more symptoms associated with allergies, such as symptoms associated with an allergic reaction.

[0077] In some embodiments, the compositions and methods described herein are used to induce immune tolerance to allergens associated with allergies (e.g., food allergies) or to desensitize the immune response to allergens associated with allergies (e.g., food allergies). As used herein, the terms "tolerance" and "immune tolerance" in the context of allergies refer to a reduced or non-responsive immune response to one or more stimuli, such as allergens associated with allergies. In particular, tolerance or immune tolerance refers to a sustained or prolonged reduced or non-responsive immune response to one or more stimuli. In contrast, the term "desensitize" in the context of allergies refers to a reversible state of reduced or non-responsive immune response to one or more stimuli, for example, during the course of a desensitization regimen.

[0078] In some embodiments, the compositions and methods described herein are used to regulate immune responses associated with allergies (e.g., food allergies). As will be apparent to one skilled in the art, the compositions and methods described herein will enhance one or more immune response(s) associated with allergies and reduce or suppress one or more other immune response(s) associated with allergies.

[0079] In some embodiments, the compositions and methods described herein induce the proliferation and / or accumulation of regulatory T cells, also referred to as "Tregs." Regulatory T cells may generally be characterized by the expression of FoxP3, CD25, and CD4. In some embodiments, administration of a composition described herein results in an increase in the proliferation and / or accumulation of regulatory T cells (e.g., total Tregs or allergen-specific Tregs) in a subject. In some embodiments, administration of a composition described herein results in an increase in the proliferation and / or accumulation of regulatory T cells (e.g., total Tregs or allergen-specific Tregs) at a specific site (e.g., the gastrointestinal tract) in a subject.

[0080] In some embodiments, administration of a composition described herein results in an increase in regulatory T cell counts of at least 1.1 fold, 1.2 fold, 1.3 fold, 1.4 fold, 1.5 fold, 2 fold, 3 fold, 4 fold, 5 fold, 6 fold, 7 fold, 8 fold, 9 fold, 10 fold, 20 fold, 30 fold, 40 fold, 50 fold, 10 ... 4 double, 10 5 In some embodiments, administration of a composition described herein results in an increase in the proliferation and / or accumulation of regulatory T cells (e.g., total Tregs or allergen-specific Tregs) of at least 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 10 ... 4 double, 10 5 This results in a 2-fold or greater increase in the proliferation and / or accumulation of regulatory T cells (e.g., total Tregs or allergen-specific Tregs).

[0081] In some embodiments, administration of a composition described herein results in at least a 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 125%, 150% or more increase in the expansion and / or accumulation of regulatory T cells (e.g., total Tregs or allergen-specific Tregs) compared to the quantity of regulatory T cells in the subject (or at a particular site in the subject) prior to administration of the composition. In some embodiments, administration of a composition described herein results in at least a 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 125%, 150% or more increase in the proliferation and / or accumulation of regulatory T cells (e.g., total Tregs or allergen-specific Tregs) compared to the quantity of regulatory T cells in another subject (e.g., a reference subject) that did not receive the composition.

[0082] The induction of Treg cells and the corresponding allergy treatment are intricately related. In some embodiments, in the treatment of one or more allergies, it is desirable to have Treg induction ranging in scope relative to the therapeutic efficacy for one or more allergies. In some embodiments, for a specific allergy treatment regimen, it is desirable to have a Treg response that is strong enough to induce the desired allergy treatment effect, but not so strong that it results in undesirable immunological events. In some embodiments, administration of the compositions described herein results in an increase in the proliferation and / or accumulation of regulatory T cells (e.g., total Tregs or allergen-specific Tregs) of between 1% and 20%, 2% and 19%, 3% and 17%, 4% and 16%, 4% and 15%, 5% and 15%, 6% and 14%, 7% and 13%, 8% and 12%, 5% and 10%, 5% and 15%, 10% and 15%, or 8% and 15% compared to the quantity of regulatory T cells in the subject (or at a specific site in the subject) prior to administration of the composition. In some embodiments, administration of a composition described herein results in an increase in the proliferation and / or accumulation of regulatory T cells (e.g., total Tregs or allergen-specific Tregs) of between 1% and 20%, 2% and 19%, 3% and 17%, 4% and 16%, 4% and 15%, 5% and 15%, 6% and 14%, 7% and 13%, 8% and 12%, 5% and 10%, 5% and 15%, 10% and 15%, or 8% and 15%, relative to the amount of regulatory T cells in another subject (e.g., a reference subject) that did not receive the composition.

[0083] In some embodiments, administration of a composition described herein results in an increase in regulatory T cell (e.g., total Tregs or allergen-specific Tregs) activity at a specific site (e.g., the gastrointestinal tract) in a subject. In some embodiments, administration of a composition described herein results in an increase in regulatory T cell activity of at least 1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 10 ... 4 double, 10 5In some embodiments, administration of a composition described herein results in an increase in the activity of regulatory T cells (e.g., total Tregs or allergen-specific Tregs) of at least 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 10 ... 4 double, 10 5 This results in a 2-fold or greater increase in the activity of regulatory T cells (e.g., total Tregs or allergen-specific Tregs).

[0084] In some embodiments, administration of a composition described herein results in an increase in the activity of regulatory T cells (e.g., total Tregs or allergen-specific Tregs) of at least 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 125%, 150% or more compared to the activity of regulatory T cells in the subject (or at a particular site in the subject) prior to administration of the composition. In some embodiments, administration of a composition described herein results in an increase in the activity of regulatory T cells (e.g., total Tregs or allergen-specific Tregs) of at least 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 125%, 150% or more compared to the activity of regulatory T cells in another subject (e.g., a reference subject) that did not receive the composition.

[0085] The abundance of regulatory T cells (e.g., total Tregs or allergen-specific Tregs) can be assessed by any method known in the art, such as by directly or indirectly assessing the activity of regulatory T cells, detecting a cell marker indicative of regulatory T cells (e.g., FoxP3), and / or measuring the production of one or more cytokines produced by regulatory T cells (e.g., IL-10).

[0086] In some embodiments, the compositions and methods described herein suppress the production of IgE antibodies. In some embodiments, the compositions and methods suppress the production of total IgE antibodies in a subject. In some embodiments, the compositions and methods suppress the production of IgE antibodies (e.g., allergen-specific IgE antibodies) that are specific to an allergen associated with allergy, e.g., a food allergen associated with food allergy. In some embodiments, administration of a composition described herein suppresses the production of IgE antibodies (e.g., total IgE antibodies or allergen-specific IgE antibodies) by at least 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 10 ... 4 double, 10 5 In some embodiments, administration of a composition described herein results in a level of IgE antibodies (e.g., total IgE antibodies or allergen-specific IgE antibodies) that is reduced by at least 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 10 ... 4 double, 10 5 The result is a 2-fold or more reduction in levels of IgE antibodies (e.g., total IgE antibodies or allergen-specific IgE antibodies).

[0087] In some embodiments, administration of a composition described herein results in a level of IgE antibodies (e.g., total IgE antibodies or allergen-specific IgE antibodies) that is reduced by at least 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% compared to the level of IgE antibodies (e.g., total IgE antibodies or allergen-specific IgE antibodies) in the subject (or a sample thereof) prior to administration of the composition. In some embodiments, administration of a composition described herein results in a level of IgE antibodies (e.g., total IgE antibodies or allergen-specific IgE antibodies) that is reduced by at least 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% compared to the level of IgE antibodies in another subject (e.g., a reference subject) that did not receive the composition.

[0088] In some embodiments, administration of a composition described herein results in a level of IgE antibodies (e.g., total IgE antibodies or allergen-specific IgE antibodies) that is reduced by between 0% and 50%, 30% and 45%, 35% and 45%, 30% and 40%, 35% and 40%, 40% and 50%, 40% and 45%, or 45% and 50% compared to the level of IgE antibodies (e.g., total IgE antibodies or allergen-specific IgE antibodies) in the subject (or a sample thereof) prior to administration of the composition. In some embodiments, administration of a composition described herein results in a level of IgE antibodies (e.g., total IgE antibodies or allergen-specific IgE antibodies) that is reduced by between 30% and 50%, 30% and 45%, 35% and 45%, 30% and 40%, 35% and 40%, 40% and 50%, 40% and 45%, or 45% and 50%, compared to the level of IgE antibodies in another subject (e.g., a reference subject) that did not receive the composition.

[0089] The presence and / or quantity of IgE antibodies in a subject, including the presence and / or quantity of allergen-specific IgE antibodies, can be assessed by methods known in the art. For example, a sample such as a blood or plasma sample can be obtained from a subject and subjected to analysis by, for example, immunoassays (e.g., radioallergosorbent test (RAST), fluorescent allergosorbent test (FAST), enzyme-linked immunosorbent assay (ELISA)) and protein arrays (e.g., see Fall et al. Methods Mol Biol (2009) 509: 107-122). The presence of allergen-specific IgE antibodies can also or alternatively be assessed using skin tests (e.g., skin prick tests).

[0090] In some embodiments, the compositions and methods described herein suppress one or more Th2 immune responses. In some embodiments, the compositions and methods described herein suppress the development or differentiation of Th2 cells (also known as type 2 helper T cells). In some embodiments, the compositions and methods described herein suppress the activity of Th2 cells. As will be apparent to those skilled in the art, Th2 cells are CD4+ cells that produce IL-4, IL-5, IL-6, IL-10, and / or IL-13 and promote IgE antibody responses and / or eosinophil activity. The differentiation of CD4+ cells into Th2 cells is promoted by the presence of IL-4 and / or IL-12 and the activation of the transcription factors STAT6 and GATA3 (see, e.g., Wan Trends Immunol. (2014) 35(6): 233-242; Zhu et al. J. Immunol. (2001) 166: 7276-7281). In some embodiments, the amount of IgE antibodies will be assessed as a marker of a Th2 immune response in a subject.

[0091] In some embodiments, administration of a composition described herein increases or decreases the Th2 immune response in a subject (or a sample thereof) by at least 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 10 ... 4 double, 10 5 In some embodiments, administration of a composition described herein results in a level of a Th2 immune response that is reduced by at least 1.5-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 10 ... 4 double, 10 5 This results in a 2-fold or more reduced Th2 immune response.

[0092] In some embodiments, administration of a composition described herein results in a level of a Th2 immune response that is reduced by at least 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% compared to the Th2 immune response in the subject (or a sample thereof) prior to administration of the composition. In some embodiments, administration of a composition described herein results in a Th2 immune response that is reduced by at least 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% compared to the Th2 immune response in another subject (e.g., a reference subject) that did not receive the composition.

[0093] The presence or level of Th2 immune response may be assessed using any method known in the art. The presence or level of Th2 immune response may be assessed by detecting and / or quantifying the number of Th2 cells in a sample obtained from a subject, for example, by detecting cell markers indicative of Th2 cells; assessing the transcriptional profile associated with Th2 cells; directly or indirectly assessing the activity of Th2 cells; and / or measuring the production of one or more cytokines (e.g., IL-4, IL-5, IL-6, IL-10, IL-13) produced by Th2 cells.

[0094] In some embodiments, administration of a composition provided herein results in a healthy microbiome that regulates immune responses associated with allergies (e.g., food allergies) in a subject. In some embodiments, administration of a composition provided herein results in a healthy microbiome that regulates immune responses associated with allergies (e.g., food allergies) in a subject. In some embodiments, administration of a composition provided herein results in a healthy microbiome that induces the accumulation and / or proliferation of regulatory T cells in a subject. In some embodiments, administration of a composition provided herein results in a healthy microbiome that suppresses the production of IgE antibodies in a subject. In some embodiments, administration of a composition provided herein results in a healthy microbiome that suppresses Th2 immune responses in a subject.

[0095] In some embodiments, a therapeutically effective amount of any of the compositions described herein is an amount sufficient to treat allergies. In some embodiments, a therapeutically effective amount of any of the compositions described herein is an amount sufficient to reduce one or more symptoms associated with allergies. In some embodiments, a therapeutically effective amount of any of the compositions described herein is an amount sufficient to regulate one or more immune responses associated with allergies, such as food allergies. For example, in some embodiments, a therapeutically effective amount of any of the compositions described herein is an amount sufficient to induce the proliferation and / or accumulation of regulatory T cells (Tregs) in a subject.

[0096] In some embodiments, a therapeutically effective amount of a composition induces proliferation and / or accumulation of Tregs in a specific site (e.g., the gastrointestinal tract) of a subject. In some embodiments, a therapeutically effective amount of any of the compositions described herein is an amount sufficient to suppress the production of IgE antibodies (e.g., total IgE antibodies or allergen-specific IgE antibodies). In some embodiments, a therapeutically effective amount of any of the compositions described herein is an amount sufficient to suppress one or more Th2 immune responses. In some embodiments, a therapeutically effective amount of any of the compositions described herein is an amount sufficient to allow a subject to survive allergen challenge (e.g., in the case of an anaphylactic allergic reaction upon unintentional exposure to peanut allergen).

[0097] As used herein, the term "therapeutically effective amount" may be used interchangeably with the term "effective amount." A therapeutically effective amount or effective amount of a composition, such as a pharmaceutical composition, as described herein is any amount that produces a desired response or outcome in a subject, such as those described herein, including, but not limited to, delaying the onset, halting the progression, alleviating or reducing the symptoms of a disease (e.g., allergy) treated using the methods described herein.

[0098] It should be understood that with respect to compositions containing bacterial strains, the term effective amount may be expressed as the number of bacteria or CFU administered. It should further be understood that multiple bacteria may be administered at once. Thus, even the administration of relatively small amounts of bacteria will have a therapeutic effect. Any of the methods described herein may be for treating allergies in a subject. As used herein, a method of treating allergies relates to alleviating or reducing at least one symptom associated with allergies, or delaying or preventing the onset of an allergic reaction upon contact or exposure to an allergen.

[0099] Methods relating to determining whether a subject has or is at risk of having an allergy, or whether a subject has or is at risk of having an allergic reaction in response to an allergen, are also within the scope of the present disclosure. In some embodiments, when it is determined that a subject has an allergy or is at risk of having an allergic reaction in response to an allergen, the subject is administered any of the compositions containing the bacterial strains described herein. Methods for determining whether a subject has or is at risk of having an allergy or whether a subject has an allergy in response to an allergen are known in the art, and include, for example, detecting the presence or level of IgE antibodies (e.g., total IgE antibodies, allergen-specific IgE antibodies), detecting the presence or level of one or more Th2 immune responses, or performing an allergy skin test. In some embodiments, the method relates to assessing whether a subject has or is at risk of having a food allergy. In some embodiments, when it is determined that a subject has a food allergy or is at risk of having an allergic reaction in response to a food allergen, the subject is administered any of the compositions containing the bacterial strains described herein.

[0100] Aspects of the present disclosure relate to the administration of compositions comprising bacterial strains. In some embodiments, the present disclosure provides bacterial strains comprising a 16S rDNA sequence that has sequence identity to the nucleic acid sequence of any one of the bacterial strain or species sequences described herein. In the context of two or more nucleic acid or amino acid sequences, the term "identical" or percent "identity" refers to two or more sequences or subsequences that are the same. Two sequences are "substantially identical" if they have a specified percentage of amino acid residues or nucleotides that are the same across a specific region or entire sequence of the nucleic acid or amino acid sequence when compared and aligned for maximum correspondence across a comparison window, or designated region, as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection (e.g., at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% sequence identity). Optionally, the identity exists over a region that is at least about 50 nucleotides in length, or more preferably over a region that is 100-500 or 1000 or more nucleotides in length. In some embodiments, the identity exists over the length of the 16S rRNA or 16S rDNA sequence.

[0101] In some embodiments, the bacterial strain has at least 60%, at least 70%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, 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%, at least 99%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8%, at least 99.9%, or up to 100% sequence identity across a specific region or across the entire sequence compared to any of the strains or bacterial species described herein. It will be apparent to those skilled in the art that the term "sequence identity" or "percent sequence identity" in the context of two or more nucleic acid or amino acid sequences refers to a degree of similarity between two or more sequences or portion(s) thereof.

[0102] In some embodiments, the composition comprises two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20) bacterial strains, wherein the two or more bacterial strains contain a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, and SEQ ID NO:13.

[0103] In some embodiments, the composition includes two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20) bacterial strains, wherein the two or more bacterial strains contain a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, and SEQ ID NO:8. In some embodiments, the composition comprises three or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20) bacterial strains, wherein two or more bacterial strains contain a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:7, and SEQ ID NO:8; and the composition does not contain a bacterial strain having a 16S rDNA sequence having at least 97% sequence identity to the nucleic acid sequence provided by SEQ ID NO:6. In some embodiments, the composition comprises two or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20) bacterial strains, wherein the two or more bacterial strains contain a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, and SEQ ID NO:8; and the composition does not contain a bacterial strain having a 16S rDNA sequence having at least 97% sequence identity to the nucleic acid sequence provided by SEQ ID NO:7.

[0104] In some embodiments, the composition includes seven bacterial strains, wherein the bacterial strains include a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:7, and SEQ ID NO:8. In some embodiments, the composition includes seven bacterial strains, wherein the bacterial strains include a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, or SEQ ID NO:8.

[0105] In some embodiments, the composition includes a bacterial strain having a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:7, and SEQ ID NO:8; and one or more additional bacterial strains. In some embodiments, the composition includes seven bacterial strains, wherein the bacterial strains include a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, or SEQ ID NO:8; and one or more additional bacterial strains.

[0106] In some embodiments, the composition consists of seven bacterial strains having 16S rDNA sequences with at least 97% sequence identity to the nucleic acid sequences of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:7, and SEQ ID NO:8. In some embodiments, the composition consists of seven bacterial strains having 16S rDNA sequences with at least 97% sequence identity to the nucleic acid sequences of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, or SEQ ID NO:8. In some embodiments, the composition includes two or more (e.g., three or four) bacterial strains, wherein the two or more bacterial strains contain a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO: 10, SEQ ID NO: 11; SEQ ID NO: 13; and SEQ ID NO: 4. In some embodiments, the composition consists of four bacterial strains, wherein the four bacterial strains contain a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence represented as SEQ ID NO: 10, SEQ ID NO: 11; SEQ ID NO: 13; and SEQ ID NO: 4.

[0107] In some embodiments, the composition includes two or more (e.g., three or four) bacterial strains, wherein the two or more bacterial strains contain a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO:9, SEQ ID NO:1; SEQ ID NO:3; and SEQ ID NO:12. In some embodiments, the composition consists of four bacterial strains, wherein the four bacterial strains contain a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence represented as SEQ ID NO:9, SEQ ID NO:1; SEQ ID NO:3; and SEQ ID NO:12.

[0108] Additionally or alternatively, two or more sequences may be assessed for alignment between the sequences. In the context of two or more nucleic acid or amino acid sequences, the term "alignment" or percent "alignment" refers to two or more sequences or subsequences that are the same. Two sequences are "substantially aligned" if they have a specified percentage of amino acid residues or nucleotides that are the same (e.g., at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.6%, 99.7%, 99.8%, or 99.9% identical) over a particular region or across the entire sequence when compared and aligned for maximum correspondence over a comparison window, or designated region, as measured using one of the sequence comparison algorithms below, or by manual alignment and visual inspection. Optionally, the alignment exists over a region that is at least about 50 nucleotides in length, or more preferably over a region that is 100-500 or 1000 or more nucleotides in length. In some embodiments, the identity exists over the length of the 16S rRNA or 16S rDNA sequence.

[0109] For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. Methods of alignment of sequences for comparison are well known in the art. See, for example, the local homology algorithm of Smith and Waterman (1970) Adv. Appl. Math. 2:482c, the homology alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443, 1970, the search for similarity method of Pearson and Lipman, Proc. Natl. Acad. Sci. USA 85:2444, 1988, by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, Madison, WI), or by manual alignment and visual inspection (see, for example, Brent et al., Current Protocols in Molecular Biology, John Wiley & Sons, Inc. (Ringbou ed., 2003)). Two examples of algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, described in Altschul et al., Nuc. Acids Res. 25:3389-3402, 1977; and Altschul et al., J. Mol. Biol. 215:403-410, 1990, respectively.

[0110] It should be understood that the terms "bacteria" and "bacterial strain" are interchangeable when used herein. A composition described herein containing multiple purified bacterial strains will also be referred to as a "live bacterial product."

[0111] In some embodiments, the compositions described herein contain bacteria belonging to the class Clostridia. In some embodiments, the compositions described herein contain bacteria belonging to the family Clostridia. In some embodiments, the compositions described herein contain bacteria belonging to the genus Clostridium. In some embodiments, the compositions described herein contain bacterial strains belonging to Clostridium clusters IV, XIVa, and / or XVII. In some embodiments, the compositions described herein contain bacterial strains belonging to Clostridium clusters IV, XIVa, and XVII. In some embodiments, the compositions described herein contain bacterial strains belonging to Clostridium clusters IV or XIVa. In some embodiments, the compositions described herein do not contain bacterial strains belonging to Clostridium cluster XVII. In some embodiments, the compositions described herein do not contain bacterial strains belonging to Clostridium cluster XVII. In some embodiments, the compositions described herein do not contain bacterial strains belonging to Clostridium cluster XVIII. In some embodiments, the compositions described herein do not contain bacterial strains belonging to Clostridium clusters XVI or XVIII.

[0112] In some embodiments, the compositions described herein contain two or more of the following bacterial strains: Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Dorea longicatena, Erysipelotrichaceae bacterium, Subdolinogranulum spp., Clostridium hathewayi, Clostridium indolis, Anaerostipes caccae, Lachnospiraceae bacterium, and Clostridium species.

[0113] In some embodiments, the compositions described herein contain two or more of the following bacterial strains: Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Dorea longicatena, Erysipelotrichaceae bacterium, and Subdolinogranulum spp. In some embodiments, the compositions include two or more (e.g., 3, 4, 5, 6, 7, or 8) of the following bacterial strains: Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Dorea longicatena, Erysipelotrichaceae bacterium, and Subdolinogranulum spp. In some embodiments, the composition includes two or more (e.g., 3, 4, 5, 6, 7, or 8) of the following bacterial strains and one or more additional bacterial strains: Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Dorea longicatena, Erysipelotrichaceae bacterium, and Subdolinogranulum spp.

[0114] In some embodiments, the compositions described herein contain two or more of the following bacterial strains: Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Erysipelotrichaceae bacterium, and Subdolinogranulum spp.; and the compositions do not contain Dorea longicatena. In some embodiments, the compositions described herein contain two or more of the following bacterial strains: Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Dorea longicatena, and Subdolinogranulum spp.; and the compositions do not contain Erysipelotrichaceae bacterium.

[0115] In some embodiments, the composition contains seven bacterial strains. In some embodiments, the composition consists of the following bacterial strains: Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Erysipelotrichaceae bacterium, and Subdolinogranulum spp. In some embodiments, the composition consists of the following bacterial strains: Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Dorea longicatena, and Subdolinogranulum spp. In some embodiments, the compositions described herein contain two or more (e.g., three or four) of the following bacterial strains: Clostridium indolis, Anaerostipes caccae, Lachnospiraceae bacterium, and Clostridium symbiosum. In some embodiments, the compositions described herein consist of the following bacterial strains: Clostridium indolis, Anaerostipes caccae, Lachnospiraceae bacterium, and Clostridium symbiosum.

[0116] In some embodiments, the compositions described herein contain two or more (e.g., three or four) of the following bacterial strains: Clostridium hathewayi, Clostridium bolteae, Sellimonas intestinalis, and Clostridium species. In some embodiments, the compositions described herein consist of the following bacterial strains: Clostridium hathewayi, Clostridium bolteae, Sellimonas intestinalis, and Clostridium species. In one aspect, the 16S rDNA sequence of the purified bacterial strain was compared to the 16S rDNA sequences of known bacterial species / strains in bacterial genome databases to identify the most closely related known bacterial species to the bacterial strains disclosed herein. It should be understood that multiple bacterial strains of the compositions disclosed herein will have the same most closely related bacterial species.

[0117] In one aspect, as demonstrated herein (e.g., in the Examples), the compositions and methods provided herein encompass the following bacteria: Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinalis, Clostridium symbiosum, Blautia producta, Dorea longicatena, Erysipelotrichaceae bacterium, and Subdolinogranulum spp. Exemplary bacterial strains of the compositions disclosed herein can also be identified by their 16S rRNA sequences (SEQ ID NOS: 1-8). Identifying bacteria by their sequences also allows for the identification of additional bacterial strains that are identical or highly similar to the exemplified bacteria. Illustratively, the 16S rRNA sequences of bacterial strains were used to identify their closest relatives (based on percent identity) through whole genome sequencing and by comparing these sequences to a 16S database (Table 1).

[0118] Additionally, based on whole-genome sequencing and comparison of the whole genome with whole-genome databases, the bacterial strains having the 16S rRNA sequences provided by SEQ ID NOS: 1-8 are most closely related to the following bacterial species: Clostridium bolteae 90A9, Anaerotruncus colihominis DSM 17241, Dracourtella massiliensis GD1, Clostridium symbiosum WAL-14163, Clostridium bacterium UC5.1-1D4, Dorea longicatena CAG:42, Erysipelotrichaceae bacterium 21_3, and Clostridium orbiscindens 1_3_50AFAA (see, for example, Table 1). Thus, in one aspect, each row in Table 1 should be understood to represent a highly similar and / or identical bacterial strain. In some embodiments, within the context of the present disclosure, the names of bacterial strains within a row in Table 1 may be used interchangeably.

[0119] Thus, for example, in some embodiments, the disclosure provides methods and compositions comprising the following bacteria: Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinalis, Clostridium symbiosum, Blautia producta, Dorea longicatena, Erysipelotrichaceae bacterium, and Subdolinogranulum spp. In some embodiments, the disclosure provides methods and compositions comprising the following bacteria: Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinalis, Clostridium symbiosum, Blautia producta, Erysipelotrichaceae bacterium, and Subdolinogranulum spp. In some embodiments, the present disclosure provides methods and compositions comprising the following bacteria: Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinalis, Clostridium symbiosum, Blautia producta, Dorea longicatena, and Subdolinogranulum spp.

[0120] Thus, for example, in some embodiments, the disclosure provides methods and compositions comprising the following bacteria: Clostridium bolteae, Anaerotruncus colihominis, Eubacterium fissicatena, Clostridium symbiosum, Blautia producta, Dorea longicatena, Erysipelotrichaceae bacterium, and Subdolinogranulum spp. In some embodiments, the disclosure provides methods and compositions comprising the following bacteria: Clostridium bolteae, Anaerotruncus colihominis, Eubacterium fissicatena, Clostridium symbiosum, Blautia producta, Erysipelotrichaceae bacterium, and Subdolinogranulum spp. In some embodiments, the present disclosure provides methods and compositions comprising the following bacteria: Clostridium bolteae, Anaerotruncus colihominis, Eubacterium fissicatena, Clostridium symbiosum, Blautia producta, Dorea longicatena, and Subdolinogranulum spp.

[0121] Thus, for example, in some embodiments, the disclosure provides methods and compositions comprising the following bacteria: Clostridium bolteae, Anaerotruncus colihominis, Drancourtella massiliensis, Clostridium symbiosum, Blautia producta, Dorea longicatena, Erysipelotrichaceae bacterium, and Subdolinogranulum spp. In some embodiments, the disclosure provides methods and compositions comprising the following bacteria: Clostridium bolteae, Anaerotruncus colihominis, Drancourtella massiliensis, Clostridium symbiosum, Blautia producta, Erysipelotrichaceae bacterium, and Subdolinogranulum spp. In some embodiments, the present disclosure provides methods and compositions comprising the following bacteria: Clostridium bolteae, Anaerotruncus colihominis, Drancourtella massiliensis, Clostridium symbiosum, Blautia producta, Dorea longicatena, and Subdolinogranulum spp.

[0122] Thus, for example, in some embodiments, the disclosure provides methods and compositions comprising the following bacteria: Clostridium bolteae, Anaerotruncus colihominis, Ruminococcus torques, Clostridium symbiosum, Blautia producta, Dorea longicatena, Erysipelotrichaceae bacterium, and Subdolinogranulum spp. In some embodiments, the disclosure provides methods and compositions comprising the following bacteria: Clostridium bolteae, Anaerotruncus colihominis, Ruminococcus torques, Clostridium symbiosum, Blautia producta, Erysipelotrichaceae bacterium, and Subdolinogranulum spp. In some embodiments, the present disclosure provides methods and compositions comprising the following bacteria: Clostridium bolteae, Anaerotruncus colihominis, Ruminococcus torques, Clostridium symbiosum, Blautia producta, Dorea longicatena, and Subdolinogranulum spp.

[0123] Thus, for example, in some embodiments, the disclosure provides methods and compositions comprising the following bacteria: Clostridium bolteae, Anaerotruncus colihominis, Ruminococcus torques, Clostridium symbiosum, Blautia producta, Dorea longicatena, Clostridium innocuum, and Subdolinogranulum spp. In some embodiments, the disclosure provides methods and compositions comprising the following bacteria: Clostridium bolteae, Anaerotruncus colihominis, Ruminococcus torques, Clostridium symbiosum, Blautia producta, Clostridium innocuum, and Subdolinogranulum spp.

[0124] Thus, for example, in some embodiments, the disclosure provides methods and compositions comprising the following bacteria: Clostridium bolteae, Anaerotruncus colihominis, Ruminococcus torques, Clostridium symbiosum, Blautia producta, Dorea longicatena, Erysipelotrichaceae bacterium, and Flavinofractor plautii. In some embodiments, the disclosure provides methods and compositions comprising the following bacteria: Clostridium bolteae, Anaerotruncus colihominis, Ruminococcus torques, Clostridium symbiosum, Blautia producta, Erysipelotrichaceae bacterium, and Flavinofractor plautii. In some embodiments, the present disclosure provides methods and compositions comprising the following bacteria: Clostridium bolteae, Anaerotruncus colihominis, Ruminococcus torques, Clostridium symbiosum, Blautia producta, Dorea longicatena, and Flavinofractor plautii.

[0125] Thus, for example, in some embodiments, the disclosure provides methods and compositions comprising the following bacteria: Clostridium bolteae, Anaerotruncus colihominis, Ruminococcus torques, Clostridium symbiosum, Blautia producta, Dorea longicatena, Erysipelotrichaceae bacterium, and Clostridium orbiscindens. In some embodiments, the disclosure provides methods and compositions comprising the following bacteria: Clostridium bolteae, Anaerotruncus colihominis, Ruminococcus torques, Clostridium symbiosum, Blautia producta, Erysipelotrichaceae bacterium, and Clostridium orbiscindens. In some embodiments, the present disclosure provides methods and compositions comprising the following bacteria: Clostridium bolteae, Anaerotruncus colihominis, Ruminococcus torques, Clostridium symbiosum, Blautia producta, Dorea longicatena, and Clostridium orbiscindens.

[0126] The homologies based on whole genome analysis are presented in Table 1. [Table 1]

[0127] In some embodiments, one or more of the bacterial strains are human-derived bacteria, meaning that one or more bacterial strains were obtained or identified from a human or a sample therefrom (e.g., a human donor). In some embodiments, one or more bacterial strains are human commensal bacteria, i.e., bacterial strains commonly found in a healthy human microbiome. In some embodiments of the compositions provided herein, all of the bacterial strains are human-derived bacteria. In some embodiments of the compositions provided herein, all of the bacterial strains are human commensal bacteria. In some embodiments of the compositions provided herein, the bacterial strains are derived from two or more human donors.

[0128] The bacterial strains used in the compositions provided herein are generally isolated from the microbiome of a healthy individual. In some embodiments, the compositions include strains originating from a single individual. In some embodiments, the compositions include strains originating from multiple individuals. In some embodiments, the compositions are obtained, isolated, and grown individually from multiple individuals. The individually grown bacterial compositions may then be combined to provide the compositions of the present disclosure. It should be understood that the origin of the bacterial strains in the compositions provided herein is not limited to human microbiomes from healthy individuals. In some embodiments, the bacterial strains originate from a human with a microbiome in a dysbiotic gut. In some embodiments, the bacterial strains originate from a non-human animal or the environment (e.g., soil or surface water). In some embodiments, the combinations of bacterial strains provided herein originate from multiple sources (e.g., a human and a non-human animal).

[0129] In some embodiments, the composition includes one or more anaerobes. In some embodiments, the composition includes only anaerobes. In some embodiments, the composition includes one or more facultative anaerobes. In some embodiments, the composition includes only facultative anaerobes. In some embodiments, the composition includes one or more obligate anaerobes. In some embodiments, the composition includes only obligate anaerobes.

[0130] In some embodiments, at least one (e.g., 1, 2, 3, 4, 5, or more) of the bacterial strains in the composition is a spore-forming bacteria. In some embodiments, at least one (e.g., 1, 2, 3, 4, 5, or more) of the bacterial strains in the composition is in a spore-forming form. In some embodiments, at least one (e.g., 1, 2, 3, 4, 5, or more) of the bacterial strains in the composition is a non-spore-forming bacteria. In some embodiments, at least one (e.g., 1, 2, 3, 4, 5, or more) of the bacterial strains in the composition is in a vegetative form. As described above, spore-forming bacteria can also be in a vegetative form. In some embodiments, at least one (e.g., 1, 2, 3, 4, 5, or more) of the bacterial strains in the composition is in a spore-forming form, and at least one (e.g., 1, 2, 3, 4, 5, or more) of the bacterial strains in the composition is in a vegetative form. In some embodiments, at least one bacterial strain that is thought to be capable of forming spores (i.e., a spore-forming bacteria) is present in the composition in a vegetative form. In some embodiments, at least one bacterial strain believed to be capable of forming spores is present in the composition in both spore and vegetative form.

[0131] It is assumed that the bacterial strains of the live bacterial products provided herein are alive and will be alive when they reach the target area (e.g., the intestine). Bacterial spores are considered alive in this regard. In some embodiments, bacteria administered as spores will germinate in the target area (e.g., the intestine). It should be further understood that not all of the bacteria are alive, and the composition may include a percentage (e.g., by weight) that is not alive. Additionally, in some embodiments, the composition includes bacterial strains that are not alive when administered or when the composition reaches the target area (e.g., the intestine). It should be understood that non-viable bacteria will still be useful by providing some nutrients and metabolites for other bacterial strains in the composition.

[0132] In some embodiments of any of the live bacterial products provided herein, the bacterial strain is purified. In some embodiments of any of the live bacterial products provided herein, the bacterial strain is isolated. Any of the bacterial strains described herein may be isolated and / or purified from a source, such as culture medium or a microbiome sample (e.g., feces). The bacterial strains used in the compositions provided herein are generally isolated from the microbiome of a healthy individual. However, bacterial strains may also be isolated from individuals considered unhealthy. In some embodiments, the compositions include strains originating from multiple individuals.

[0133] As used herein, the term "isolated" in reference to bacteria refers to bacteria that have been separated from one or more undesirable components, such as another bacterium or bacterial strain, one or more components of a growth medium, and / or one or more components of a sample, such as a fecal sample. In some embodiments, bacteria are substantially isolated from a source such that other components of the source are not detectable (e.g., below the level of detection). As also used herein, the term "purified" refers to a bacterial strain or composition, including one that has been separated from one or more components, such as contaminants. In some embodiments, the bacterial strain is substantially free of contaminants. In some embodiments, one or more bacterial strains of a composition may be purified independently from one or more other bacteria produced or present in the medium or sample containing the bacterial strain. In some embodiments, the bacterial strain is isolated or purified from a sample and then cultured under appropriate conditions for bacterial replication, e.g., anaerobic culture conditions. Bacteria grown under appropriate conditions for bacterial replication may subsequently be isolated / purified from the growth medium.

[0134] Compositions, including compositions for administration to a subject, such as pharmaceutical compositions, are also within the scope of this disclosure. In some embodiments, the composition comprises any of the bacterial strains described herein. In one aspect, the present disclosure provides a pharmaceutical composition comprising any of the bacterial strains described herein. In some embodiments, the pharmaceutical composition comprises a pharmaceutically acceptable excipient. In some embodiments, the pharmaceutical composition is formulated for oral administration. In some embodiments, the pharmaceutical composition is formulated for rectal administration. In some embodiments, the pharmaceutical composition is formulated for intestinal delivery. In some embodiments, the pharmaceutical composition is formulated for colonic delivery.

[0135] In some embodiments, the composition or pharmaceutical composition contains a bacterial strain. In some embodiments, the pharmaceutical composition contains a bacterial strain in powder form. In some embodiments, the pharmaceutical composition contains a lyophilized bacterial strain. In some embodiments, the pharmaceutical composition contains a spray-dried bacterial strain. In some embodiments, the pharmaceutical composition contains a lyophilized and a spray-dried bacterial strain. In some embodiments, the pharmaceutical composition is in the form of a capsule. In some embodiments, the pharmaceutical composition further comprises a pH-sensitive composition comprising one or more enteric polymers.

[0136] In some embodiments, one or more of the bacterial strains of the compositions, including pharmaceutical compositions and food products, are spray-dried. In some embodiments, a subset of the bacterial strains are spray-dried. The process of spray-drying refers to the production of a dry powder from a liquid containing the bacterial composition (see, for example, Ledet et al., Spray-Drying of Pharmaceuticals in "Lyophilized Biologics and Vaccines" pages 273-294, Springer). Generally, the process involves rapidly drying the bacterial composition with hot gas. The bacterial strains may be combined with pharmaceutical excipients before being combined with other bacterial strains, or multiple spray-dried bacterial strains may be combined while in spray-dried form, and a mixture of bacterial strains may be combined once and subsequently combined with pharmaceutical excipients.

[0137] In any of the compositions described herein, including pharmaceutical compositions and food products comprising bacterial strains, the bacterial strains are in any form, for example, an aqueous form such as a solution or suspension, embedded in a semi-solid form, in a powdered form, or in a freeze-dried form. In some embodiments, the composition or bacterial strain is lyophilized. In some embodiments, a subset of bacterial strains is lyophilized. Methods for lyophilizing compositions, particularly compositions comprising bacteria, are well known in the art. For example, see US 3,261,761; US ​​4,205,132; PCT Publications WO 2014 / 029578 and WO 2012 / 098358, which are incorporated herein by reference in their entirety. The bacteria may be lyophilized as a combination, and / or the bacteria may be lyophilized individually and combined prior to administration. The bacterial strains may be combined with the pharmaceutical excipients prior to being combined with other bacterial strains, or multiple lyophilized bacteria may be combined while in lyophilized form, and the mixture of bacteria may be combined once and subsequently combined with the pharmaceutical excipients. In some embodiments, the bacterial strains are lyophilized cakes. In some embodiments, the composition comprising one or more bacterial strains is a lyophilized cake.

[0138] Bacterial strains can be produced using fermentation techniques well known in the art. In some embodiments, bacteria are grown or produced using anaerobic fermenters, which can support the rapid growth of anaerobic species. The anaerobic fermenter can be, for example, a stirred tank reactor or a disposable WAVE Bioreactor. Culture media such as BL medium and EG medium, or similar animal-component-free versions of these media, can be used to support the growth of bacterial species. Bacterial products can be purified and concentrated from the fermentation broth by existing techniques such as centrifugation and filtration, and optionally dried and lyophilized by techniques well known in the art.

[0139] In some embodiments, the live bacterial product may be formulated for administration as a pharmaceutical composition. The term "pharmaceutical composition," as used herein, refers to a product that combines or results in a combination of at least one active ingredient, such as any of the bacterial strains described herein, with one or more inactive ingredients, and may include one or more pharmaceutically acceptable excipients.

[0140] An "acceptable" excipient refers to an excipient that must be compatible with the active ingredient and not harmful to the subject to which it is administered. In some embodiments, pharmaceutically acceptable excipients are selected based on the intended route of administration of the composition; for example, a composition for oral or nasal administration will contain different pharmaceutically acceptable excipients than a composition for rectal administration. Examples of excipients include sterile water, saline, solvents, bases, emulsifiers, suspending agents, surfactants, stabilizers, flavoring agents, fragrances, excipients, vehicles, preservatives, binders, diluents, isotonicity agents, soothing agents, fillers, disintegrants, buffers, coating agents, lubricants, coloring agents, sweeteners, thickeners, and solubilizers.

[0141] The pharmaceutical compositions of the present invention can be prepared according to methods well known and routinely practiced in the art (see, for example, Remington: The Science and Practice of Pharmacy, Mack Publishing Co. 20th ed. 2000). The pharmaceutical compositions described herein may further comprise any carrier or stabilizer in the form of a lyophilized formulation or aqueous solution. Acceptable excipients, carriers, or stabilizers may include, for example, buffers, antioxidants, preservatives, polymers, chelating agents, and / or surfactants. The pharmaceutical compositions are preferably manufactured under GMP conditions. The pharmaceutical compositions may be used orally, nasally, or parenterally in the form of, for example, capsules, tablets, pills, sachets, liquids, powders, granules, fine granules, film-coated formulations, pellets, troches, sublingual formulations, chewable tablets, buccal tablets, pastes, syrups, suspensions, elixirs, emulsions, liniments, ointments, salves, poultices, transdermal systems, lotions, inhalants, aerosols, injections, suppositories, etc. In some embodiments, the pharmaceutical compositions may be administered by injection, such as intravenous, intramuscular, subcutaneous, or intradermal administration.

[0142] In some embodiments, the composition comprising the bacterial strain is formulated for delivery to the intestine (e.g., the small intestine and / or colon). In some embodiments, the composition comprising the bacterial strain may be formulated with an enteric coating that increases the survival of the bacteria through the harsh environment of the stomach. The enteric coating resists the action of gastric juice in the stomach, allowing the bacteria of the composition therein to pass through the stomach and enter the intestine. The enteric coating may readily dissolve upon contact with intestinal fluid, allowing the bacteria encapsulated within the coating to be released into the intestinal tract. The enteric coating may be composed of polymers and copolymers well known in the art, such as the commercially available EUDRAGIT (Evonik Industries) (see, e.g., Zhang, AAPS PharmSciTech, 2016, 17 (1), 56-67).

[0143] Compositions containing bacterial strains may also be formulated for rectal delivery to the intestine (e.g., the colon). Thus, in some embodiments, compositions containing bacterial strains may be formulated for delivery by colonoscopy, endoscopy, sigmoidoscopy, or enema. Pharmaceutical preparations or formulations, and particularly pharmaceutical preparations for oral administration, may include additional components that enable efficient delivery of the compositions of the present disclosure to the intestine (e.g., the colon). Various pharmaceutical preparations that enable delivery of the composition to the intestine (e.g., the colon) can be used. Examples include pH-sensitive compositions, more specifically, buffered sachets or enteric polymers that release their contents when the pH becomes alkaline after the enteric polymer has passed through the stomach. When a pH-sensitive composition is used to formulate a pharmaceutical preparation, the pH-sensitive composition is preferably a polymer whose pH threshold for degradation of the composition is between about 6.8 and about 7.5.

[0144] This range of values ​​is the range that shifts to alkaline at the distal part of the stomach, and therefore is the preferred range for use in delivery to the colon.It should be further understood that each part of the intestine (for example, the duodenum, jejunum, ileum, cecum, colon and rectum) has different biochemical and chemical environments.For example, each part of the intestine has different pH, allowing targeted delivery by compositions with specific pH sensitivity.Therefore, the compositions provided herein can be formulated for delivery to the intestine or specific intestinal parts (for example, the duodenum, jejunum, ileum, cecum, colon and rectum) by providing a formulation with appropriate pH sensitivity (see, for example, Villena et al., Int J Pharm 2015, 487 (1-2): 314-9).

[0145] Pharmaceutical compositions for administration by additional or alternative routes are also within the scope of this disclosure. In some embodiments, the pharmaceutical composition is formulated for sublingual administration. In some embodiments, the pharmaceutical composition is formulated for administration by injection. In some embodiments, the pharmaceutical composition may include additional components that allow for efficient delivery of the composition of the present disclosure to a desired site, such as the gastrointestinal tract (e.g., the colon). In some embodiments, the pharmaceutical composition includes an adjuvant associated with providing a benefit in the treatment of allergies, hi some embodiments, the pharmaceutical composition includes one or more components of oral immunotherapy, epicutaneous immunotherapy, or sublingual immunotherapy.

[0146] Another embodiment of a pharmaceutical preparation useful for delivering a composition to the intestine (e.g., the colon) ensures delivery to the colon by delaying the release of the contents (e.g., a bacterial strain) for approximately 3 to 5 hours, corresponding to the transit time through the small intestine. In one embodiment of a pharmaceutical preparation for delayed release, a hydrogel is used as the shell. The hydrogel hydrates and swells upon contact with gastrointestinal fluid, resulting in effective release of the contents (primarily in the colon). Delayed-release dosage units include drug-containing compositions with materials that coat or selectively coat the administered drug or active ingredient. Examples of such selective coating materials include in vivo degradable polymers, gradually hydrolyzable polymers, gradually water-soluble polymers, and / or enzymatically degradable polymers. A wide variety of coating materials for efficiently delaying release are available, including, for example, cellulose-based polymers and copolymers, such as hydroxypropyl cellulose, acrylic acid polymers, and methacrylic acid polymers and copolymers, and copolymers, such as vinyl polymers and polyvinylpyrrolidone.

[0147] Additional examples of pharmaceutical compositions that allow for delivery to the intestine (e.g., colon) include bioadhesive compositions that specifically adhere to the colonic mucosa (e.g., polymers described in U.S. Pat. No. 6,368,586), and compositions that incorporate protease inhibitors to protect biologic preparations specifically within the gastrointestinal tract from deterioration due to protease activity. Another example of a system that allows delivery to the intestine (e.g., the colon) is a system that delivers a composition to the colon by pressure changes, such that the contents are released by utilizing the pressure changes caused by gas production during bacterial fermentation in the distal part of the stomach. A more specific example of such a system, but not limited to, is a capsule in which the contents are dispersed in a suppository base and coated with a hydrophobic polymer (e.g., ethylcellulose).

[0148] Further examples of systems that allow delivery of compositions to the intestine (e.g., the colon) include compositions that include a coating that can be removed by enzymes present in the digestive tract (e.g., the colon), such as carbohydrate hydrolases or carbohydrate reductases. More specific examples of such systems include, but are not limited to, systems that use food components such as non-starch polysaccharides, amylose, xanthan gum, and azopolymers. The compositions provided herein can also be delivered to a specific target area, such as the intestine, by delivery through a hole (e.g., a nasal tube) or through surgery. In addition, compositions provided herein formulated for delivery to a specific area (e.g., the cecum or colon) can be administered by a tube (e.g., directly into the small intestine). Combining a mechanical delivery method, such as a tube, with a chemical delivery method, such as a pH-specific coating, allows the compositions provided herein to be delivered to the desired target area (e.g., the cecum or colon).

[0149] The composition comprising the bacteria is formulated into a pharmaceutically acceptable dosage form by conventional methods known to those skilled in the art. The dosage regimen is adjusted to provide the optimal desired response (e.g., prophylactic or therapeutic effect). In some embodiments, the composition is in the form of a tablet, pill, capsule, powder, granules, solution, or suppository. In some embodiments, the pharmaceutical composition is formulated for oral administration. In some embodiments, the pharmaceutical composition comprises a bacterial strain and is formulated so that the bacteria, or a portion thereof, remain viable after passing through the subject's stomach. In some embodiments, the pharmaceutical composition is formulated for rectal administration, e.g., as a suppository. In some embodiments, the pharmaceutical composition is formulated for delivery to the intestine or a specific area of ​​the intestine (e.g., the colon) by providing an appropriate coating (e.g., a pH-specific coating, a coating that can be degraded by a target area-specific enzyme, or a coating that can bind to a receptor present in the target area).

[0150] The dosage of the active ingredient in the pharmaceutical compositions of the present invention can be varied to obtain an amount of the active ingredient that is effective to achieve the desired pharmaceutical response for a particular subject, composition, and mode of administration, without being toxic or deleterious in the subject. The selected dosage level will depend on a variety of factors, including the activity of the particular composition used in the present invention, the route of administration, the time of administration, the duration of treatment, other drugs, compounds, and / or materials used in combination with the particular composition used, the age, sex, weight, condition, overall health, and previous medical history of the subject being treated, and such factors.

[0151] A physician, veterinarian, or other trained practitioner can start a dose of the pharmaceutical composition at a level lower than that required to achieve the desired therapeutic effect and gradually increase the dosage until the desired effect (e.g., treatment of allergies, modulation of one or more immune responses associated with allergies) is achieved. Generally, the effective dose of the compositions of the invention for prophylactic treatment of a group of people as described herein will vary depending on many different factors, including the route of administration, the physiological condition of the subject, whether the subject is human or animal, other administered drugs, and the desired therapeutic effect. Dosage should be determined to optimize safety and effectiveness.

[0152] In some embodiments, the dosing regimen involves oral administration of a dose of any of the compositions described herein. In some embodiments, the dosing regimen involves oral administration of multiple doses of any of the compositions described herein. In some embodiments, any of the compositions described herein is administered to a subject 1, 2, 3, 4, 5, 6, 7, 8, 9, or at least 10 times or more. In some embodiments, any of the compositions described herein is administered to a subject in multiple doses at regular intervals, such as every two weeks, every month, every two months, every three months, every four months, every five months, every six months, or more. In some embodiments, one dose of any of the compositions described herein is administered, and a second dose of the composition is administered the next day (e.g., on consecutive days). In some embodiments, one dose of any of the compositions described herein is administered, and each additional dose of the composition is administered on consecutive days (e.g., the first dose on day 1, the second dose on day 2, the third dose on day 3, etc.).

[0153] In one aspect, the present disclosure provides a method comprising administering pharmaceutical compositions in multiple doses every day.In some embodiments, pharmaceutical compositions is administered every day for 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, 14 days, 15 days, 16 days, 17 days, 18 days, 19 days, 20 days, 21 days, 22 days, 23 days, 24 days, 25 days, 26 days, 27 days, 28 days, 29 days, 30 days, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, 12 months or more.

[0154] In some embodiments, the present disclosure provides methods that include administering one or more doses of the pharmaceutical composition and determining whether the subject is responding to the administration of the one or more doses of the pharmaceutical composition, e.g., by measuring levels of Treg cells, IgE cells, or performing a skin test, wherein if the response is not associated with the desired effect (e.g., insufficient levels of Treg cells, or a strong response to the skin test), additional doses of the pharmaceutical composition are administered.

[0155] In any of the methods described herein, one or more antibiotics may be administered to the subject prior to administration of any of the bacterial compositions described herein. In some embodiments, the one or more antibiotics are administered to rid the subject's gastrointestinal tract of bacterial strains associated with food allergies (see, e.g., Ho et al., Role of the Microbiome in Food Allergy. Curr Allergy Asthema Rep. 2018 Apr 5;18(4):27.). In some embodiments, the one or more antibiotics are administered to rid the subject's gastrointestinal tract of bacterial strains associated with undesirable immune responses that enhance allergic reactions.

[0156] In such embodiments, the antibiotic would be administered according to a regimen that does not diminish the effectiveness of the beneficial bacterial compositions provided herein (e.g., by removing the antibiotic from the body prior to administration of one or more beneficial bacterial compositions provided herein). In some embodiments, one or more antibiotics may be administered to a subject prior to any of the bacterial compositions provided herein. In some embodiments, the present disclosure provides methods comprising administering an antibiotic (e.g., vancomycin) followed by a single dose of a pharmaceutical composition. In some embodiments, the present disclosure provides methods comprising administering an antibiotic (e.g., vancomycin) followed by multiple doses of a pharmaceutical composition.

[0157] In some embodiments, administration of an antibiotic (e.g., vancomycin) followed by administration of a single or multiple doses of the pharmaceutical composition results in an increased abundance of the bacterial strain in the pharmaceutical composition compared to a method of administration that does not include an antibiotic. In some embodiments, administration of an antibiotic (e.g., vancomycin) followed by administration of a single or multiple doses of the pharmaceutical composition results in an increased duration of colonization of the bacterial strain in the pharmaceutical composition compared to a method that does not include an antibiotic. In some embodiments, the methods described herein do not include administering an antibiotic prior to the administration of the pharmaceutical composition described herein.

[0158] In some embodiments, the antibiotic is vancomycin, fidaxomycin, or ridinilazole. In some embodiments, the antibiotic is not vancomycin. Non-limiting examples of antibiotics that may be used in any of the methods provided herein include the cephalosporin antibiotics cephalexin, cefuroxime, cefadroxil, cefazolin, cephalothin, cefaclor, cefamandole, cefoxitin, cefprozil, ceftobiprole, clindamycin, ceftriaxone, cefotaxime, cefazolin, cefoperazone, cefuroxime, cefmetazole, fluoroquinolones, ciprofloxacin, revaquin, floxin, tequin, avelox, and norfloxacin. (norflox), tetracycline, minocycline, oxytetracycline, doxycycline, amoxicillin, ampicillin, penicillin V, dicloxacillin, benzylpenicillin, carbenicillin, vancomycin, and methicillin, ertapenem, doripenem, imipenem / cilastatin, meropenem, clavulanic acid, tazobactam, piperacillin, ceftriaxone, cefotaxime, cefazolin, fluoroquinolones, imipenem, meropenem, metronidazole, fidaximicin, or ridinilazole.

[0159] In some embodiments, any of the methods described herein may further include administering vancomycin to the subject prior to administering the pharmaceutical composition described herein. In some embodiments, the method does not include administering vancomycin to the subject prior to administering the pharmaceutical composition described herein. Administration of vancomycin has been found to alter the composition of the human gastrointestinal microbiota. See, e.g., Reijnders et al. Cell Metabolism (2016) 24(1): 63-72. While not wishing to be bound by any particular theory, it is believed that administration of vancomycin may aid in the engraftment of the bacterial strain(s) of the pharmaceutical composition described herein, for example, by clearing out other microorganisms present in the gastrointestinal tract.

[0160] In some embodiments, the antibiotic (e.g., vancomycin) is administered to the subject once as a single dose. In some embodiments, the antibiotic (e.g., vancomycin) is administered to the subject in multiple doses. In some embodiments, the antibiotic (e.g., vancomycin) is administered to the subject in at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more doses. The multiple doses of the antibiotic (e.g., vancomycin) may be administered to the subject at regular intervals prior to administering any of the pharmaceutical compositions described herein. In some embodiments, each of the multiple doses of the antibiotic (e.g., vancomycin) is administered on consecutive days (e.g., a first dose on day 1, a second dose on day 2, a third dose on day 3, etc.).

[0161] In some embodiments, an antibiotic (e.g., vancomycin) is administered to a subject for 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or more consecutive days. In some embodiments, an antibiotic (e.g., vancomycin) is administered each day for three consecutive days. In some embodiments, an antibiotic (e.g., vancomycin) is administered each day for five consecutive days. In some embodiments, an antibiotic (e.g., vancomycin) is administered to a subject for one day. In any of the embodiments described herein, a subject may receive one or more doses of a first antibiotic followed by one or more doses of a second antibiotic.

[0162] In some embodiments, the first dose in a single-dose or multiple-dose treatment regimen is administered on the same day as the administration of the final dose of antibiotic (e.g., vancomycin). In some embodiments, the first dose in a single-dose or multiple-dose treatment regimen is administered the day after the administration of the final dose of antibiotic (e.g., vancomycin). In some embodiments, the first dose in a single-dose or multiple-dose treatment regimen is administered two days after the administration of the final dose of antibiotic (e.g., vancomycin). In some embodiments, the methods provided herein allow for a washout day between the final dose of antibiotic (e.g., vancomycin) and the first dose of the pharmaceutical composition. In some embodiments, the first dose in a single-dose or multiple-dose treatment regimen is administered 3, 4, 5, 6, 10, or more days after the administration of the final dose of antibiotic (e.g., vancomycin). In some embodiments, the methods provided herein allow for multiple washout days between the final dose of antibiotic (e.g., vancomycin) and the first dose of the pharmaceutical composition.

[0163] Each dose of antibiotic (e.g., vancomycin) may be the same amount of antibiotic or a different amount of antibiotic. In some embodiments, the antibiotic (e.g., vancomycin) is administered in an amount sufficient to allow colonization of one or more bacterial strains of the pharmaceutical compositions described herein. In some embodiments, a subject receives between about 50 mg and 1 g, 100 mg and 750 mg, 100 mg and 500 mg, 200 mg and 750 mg, 200 mg and 500 mg, 300 mg and 750 mg, 300 mg and 500 mg, 100 mg and 400 mg, 100 mg and 300 mg, 100 mg and 200 mg, 200 mg and 400 mg, 200 mg and 300 mg, or 450 mg and 550 mg of antibiotic per day. Those skilled in the art will appreciate that the total amount of vancomycin administered to a subject per day may be administered in a single dose or over multiple doses, which add up to provide the total daily dose of antibiotic.

[0164] In some examples, the subject is administered about 500 mg of vancomycin per day prior to administration of any of the pharmaceutical compositions described herein. In some embodiments, the 500 mg of vancomycin per day is administered in a single dose (e.g., 500 mg). In some embodiments, the 500 mg of vancomycin per day is administered in multiple doses (e.g., 2, 3, 4, 5, or more) totaling 500 mg of vancomycin per day. In some embodiments, the 500 mg of vancomycin is administered in four doses of 125 mg of vancomycin per day. In some embodiments, the 500 mg of vancomycin is administered to the subject for one day. In some embodiments, the 500 mg of vancomycin is administered to the subject per day for two days. In some embodiments, the 500 mg of vancomycin is administered to the subject per day for three days. In some embodiments, the 500 mg of vancomycin is administered to the subject per day for four days. In some embodiments, 500 mg of vancomycin is administered per day to a subject for five days.

[0165] In some embodiments, the subject is administered about 250 mg of vancomycin per day prior to administration of any of the pharmaceutical compositions described herein. In some embodiments, the 250 mg of vancomycin per day is administered in a single dose (e.g., 250 mg). In some embodiments, the 250 mg of vancomycin per day is administered in multiple doses (e.g., 2, 3, 4, 5, or more) totaling 250 mg of vancomycin per day. In some embodiments, the 250 mg of vancomycin is administered in two doses of 125 mg of vancomycin per day. In some embodiments, the 250 mg of vancomycin is administered to the subject for one day. In some embodiments, the 250 mg of vancomycin is administered to the subject per day for two days. In some embodiments, the 250 mg of vancomycin is administered to the subject per day for three days. In some embodiments, the 250 mg of vancomycin is administered to the subject per day for four days. In some embodiments, 250 mg of vancomycin is administered per day to a subject for five days.

[0166] In some embodiments, the subject is administered about 125 mg of vancomycin per day prior to administration of any of the pharmaceutical compositions described herein. In some embodiments, the 125 mg of vancomycin per day is administered in a single dose (e.g., 125 mg). In some embodiments, the 125 mg of vancomycin per day is administered in multiple doses (e.g., 2, 3, 4, 5, or more), totaling 125 mg of vancomycin per day. In some embodiments, 125 mg of vancomycin is administered to the subject for one day. In some embodiments, 125 mg of vancomycin is administered to the subject per day for two days. In some embodiments, 125 mg of vancomycin is administered to the subject per day for three days. In some embodiments, 125 mg of vancomycin is administered to the subject per day for four days. In some embodiments, 125 mg of vancomycin is administered to the subject per day for five days.

[0167] In some embodiments, the present disclosure provides methods comprising administering one or more antibiotics to a subject, followed by administering any of the bacterial compositions to the subject one, two, three, four, five, six, seven, eight, nine, or at least ten or more times. In some embodiments, the present disclosure provides methods comprising administering one or more antibiotics to a subject, followed by administering any of the bacterial compositions described herein in multiple doses to the subject at regular intervals, such as every two weeks, every month, every two months, every three months, every four months, every five months, every six months, or more. In some embodiments, one dose of any of the compositions described herein is administered, and a second dose of the composition is administered the following day (e.g., on consecutive days). In some embodiments, one dose of any of the compositions described herein is administered, and each additional dose of the composition is administered on consecutive days (e.g., the first dose on day one, the second dose on day two, the third dose on day three, etc.).

[0168] In one aspect, the present disclosure provides methods comprising administering one or more antibiotics to a subject, followed by administering any of the bacterial compositions as multiple daily doses of the pharmaceutical composition. In some embodiments, the pharmaceutical composition is administered daily for 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, 14 days, 15 days, 16 days, 17 days, 18 days, 19 days, 20 days, 21 days, 22 days, 23 days, 24 days, 25 days, 26 days, 27 days, 28 days, 29 days, 30 days, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, 12 months or more.

[0169] While not wishing to be bound by any particular mechanism, in some embodiments, administration of the pharmaceutical compositions described herein may treat or reduce the incidence or severity of allergies by inducing an immune response (e.g., suppression of regulatory T cells, IgE antibodies) in a subject. In some embodiments, administration of the pharmaceutical compositions described herein may treat or reduce the incidence or severity of allergies by modulating the subject's microbiome. In some embodiments, administration of the pharmaceutical compositions described herein may treat or reduce the incidence or severity of allergies by increasing the presence or abundance of the bacterial strain of the pharmaceutical composition in the subject's microbiome.

[0170] In some embodiments, administration of the pharmaceutical compositions described herein may treat or reduce the incidence or severity of allergies by increasing the presence or abundance of bacterial strains not present in the pharmaceutical composition in the subject's microbiome. As shown herein, administration of the bacterial compositions of the present disclosure is associated with an overall shift in the subject's microbiome. It should further be understood that administration of the pharmaceutical compositions described herein may result in any combination of the described results. Thus, by way of illustration, food allergies in a subject are treated so that the subject's microbiome during treatment includes strains of the administered bacterial composition and bacterial strains associated with a healthy microbiome or a microbiome found in subjects without food allergies.

[0171] Generally, administration of multiple doses of a pharmaceutical composition described herein will provide enhanced colonization (engraftment) of one or more bacterial strains of the pharmaceutical composition compared to administration of a single dose of the pharmaceutical composition. In some embodiments, administration of multiple doses of a pharmaceutical composition described herein induces or enhances one or more beneficial immune responses in the treatment of allergies compared to administration of a single dose of the pharmaceutical composition. In some embodiments, administration of multiple doses of a pharmaceutical composition described herein provides increased abundance of one or more bacterial strains of the pharmaceutical composition compared to administration of a single dose of the pharmaceutical composition. In some embodiments, administration of multiple doses of a pharmaceutical composition described herein modulates (e.g., increases or decreases) the abundance of one or more bacterial strains not present in the pharmaceutical composition compared to administration of a single dose of the pharmaceutical composition.

[0172] In any of the aspects described herein, the pharmaceutical composition may be administered to a subject prior to, subsequent to, or simultaneously with an allergen immunotherapy regimen. Examples of allergen immunotherapy regimens include oral immunotherapy ("OIT"), sublingual immunotherapy ("SLIT", e.g., "allergy drops / tablets"), subcutaneous allergen administration (e.g., allergy injections), and epicutaneous immunotherapy (e.g., allergen patches). Generally, allergen immunotherapy regimens involve administering an allergen (e.g., a food allergen) to a subject in gradually increasing dosages to desensitize the subject to the allergen. Such immunotherapy may also be referred to as "tolerogenic" or "tolerogenic" vaccines.

[0173] In some embodiments, the pharmaceutical compositions described herein are used in combination with oral immunotherapy, which involves administering a tolerogenic antigen to induce a tolerogenic immune response. Any of the allergens described herein, such as food allergens, may be administered to a subject in an allergen immunotherapy regimen. In some embodiments, the allergen immunotherapy includes an allergen specific to a food allergy. In some embodiments, the food allergen is a peanut allergen, other nut allergen, milk allergen, or egg allergen. Examples of oral or sublingual immunotherapy include, but are not limited to, Hello, Peanut!® (Assured Bites, Inc.); AR101 (peanut allergen, Aimmune Therapeutics); AR201 (egg allergen, Aimmune Therapeutics); AR301 (walnut allergen, Aimmune Therapeutics); and SAR439794 (Sanofi). In some embodiments, the pharmaceutical composition is not administered to the subject prior to, subsequent to, or concurrently with an allergen immunotherapy regimen.

[0174] In some embodiments, in the methods provided herein, the subject is challenged with an allergen immunotherapy regimen to assess the subject's susceptibility to food allergy during or after administration of any one of the compositions provided herein according to any one of the methods provided herein. In some embodiments, any of the pharmaceutical compositions described herein can be administered to subjects simultaneously with oral immunotherapy or sublingual immunotherapy.Simultaneous administration can include the administration of pharmaceutical compositions and oral immunotherapy or sublingual immunotherapy within a specified period, preferably within 1 month, more preferably within 1 week, even more preferably within 1 day, and even more preferably within 1 hour.In some embodiments, material / agent can be administered repeatedly at the same time; it is simultaneous administration in two or more cases.

[0175] In embodiments, any of the pharmaceutical compositions described herein may be administered to a subject sequentially (e.g., before or after) or simultaneously with oral or sublingual immunotherapy. In some embodiments, bowel preparation is performed prior to administration of any of the compositions described herein. In some embodiments, a fecal sample is collected after administration of any of the compositions described herein to assess whether the bacterial strain of the composition has colonized in the subject's microbiome. In some embodiments, a fecal sample is collected after administration of any of the compositions described herein to analyze the composition of the subject's microbiome. In some embodiments, a fecal sample is collected after administration of any of the compositions described herein to analyze the composition of the subject's microbiome and to assess whether the bacterial strain of the composition has colonized in the subject's microbiome.

[0176] The compositions, including pharmaceutical compositions, disclosed herein include compositions containing selected bacterial strains. The amount of bacteria, including the amount of each bacterial strain in the compositions, including pharmaceutical compositions, may be expressed in terms of weight or number of bacteria and / or CFU (colony forming units). In some embodiments, the compositions, including pharmaceutical compositions, contain about 10, about 10 per dosage. 2 , about 10 3 , about 10 4 , about 10 5 , about 10 6 , about 10 7 , about 10 8 , about 10 9 , about 10 10 , about 10 11 , about 10 12 , about 10 13 In some embodiments, the compositions, including pharmaceutical compositions, contain about 10, about 10, or more of each of the bacterial strains. 2 , about 10 3 , about 10 4 , about 10 5 , about 10 6 , about 10 7 , about 10 8 , about 109 , about 10 10 , about 10 11 , about 10 12 , about 10 13 It should be further understood that each of the bacteria of a bacterial strain may be present in different amounts. Thus, by way of illustrative and non-limiting example, the composition may comprise 10 or more whole bacteria. 3 Bacteria A, 10 4 Bacteria B and 10 6 In some embodiments, the compositions, including pharmaceutical compositions, may contain about 10, about 10, or about 10 Bacterium C per dosage. 2 , about 10 3 , about 10 4 , about 10 5 , about 10 6 , about 10 7 , about 10 8 , about 10 9 , about 10 10 , about 10 11 , about 10 12 , about 10 13 In some embodiments, the compositions, including pharmaceutical compositions, contain about 10 CFU of each of the combined bacterial strains total per dosage. 1 , about 10 2 , about 10 3 , about 10 4 , about 10 5 , about 10 6 , about 10 7 , about 10 8 , about 10 9 , about 10 10 , about 10 11 , about 10 12 , about 10 13 or more CFU. As described above, each of the bacteria of the bacterial strain may be present in different amounts. In some embodiments, the compositions, including pharmaceutical compositions, contain about 10 CFU per dosage. -7 , about 10 -6 , about 10 -5 , about 10 -4 , about 10 -3 , about 10 -2 , about 10 -1In some embodiments, the compositions, including pharmaceutical compositions, contain more than about 10 grams of bacteria from each of the combined bacterial strains per dosage. -7 , about 10 -6 , about 10 -5 , about 10 -4 , about 10 -3 , about 10 -2 , about 10 -1 In some embodiments, the dosage is one administration device (e.g., one tablet, pill, or capsule). In some embodiments, the dosage is the amount administered in a specific period (e.g., one day or one week).

[0177] In some embodiments, compositions, including pharmaceutical compositions, contain 10 to 10 13 Between 10 2 ~10 13 Between 10 3 ~10 13 Between 10 4 ~10 13 Between 10 5 ~10 13 Between 10 6 ~10 13 Between 10 7 ~10 13 Between 10 8 ~10 13 Between 10 9 ~10 13 Between 10 10 ~10 13 Between 10 11 ~10 13 Between 10 12 ~10 13 Between 10 and 10 12 Between 10 2 ~10 12 Between 10 3 ~10 12 Between 10 4 ~10 12 Between 10 5 ~10 12 Between 10 6 ~10 12 Between 10 7 ~1012 Between 10 8 ~10 12 Between 10 9 ~10 12 Between 10 10 ~10 12 Between 10 11 ~10 12 Between 10 and 10 11 Between 10 2 ~10 11 Between 10 3 ~10 13 Between 10 4 ~10 13 Between 10 5 ~10 13 Between 10 6 ~10 13 Between 10 7 ~10 11 Between 10 8 ~10 11 Between 10 9 ~10 11 Between 10 10 ~10 11 Between 10 and 10 10 Between 10 2 ~10 10 Between 10 3 ~10 10 Between 10 4 ~10 10 Between 10 5 ~10 10 Between 10 6 ~10 10 Between 10 7 ~10 10 Between 10 8 ~10 10 Between 10 9 ~10 10 Between 10 and 10 9 Between 10 2 ~10 9 Between 10 3 ~10 9 Between 10 4 ~10 9 Between 10 5 ~10 9 Between 10 6 ~10 9 Between 10 7 ~10 9 Between 108 ~10 9 Between 10 and 10 8 Between 10 2 ~10 8 Between 10 3 ~10 8 Between 10 4 ~10 8 Between 10 5 ~10 8 Between 10 6 ~10 8 Between 10 7 ~10 8 Between 10 and 10 7 Between 10 2 ~10 7 Between 10 3 ~10 7 Between 10 4 ~10 7 Between 10 5 ~10 7 Between 10 6 ~10 7 Between 10 and 10 6 Between 10 2 ~10 6 Between 10 3 ~10 6 Between 10 4 ~10 6 Between 10 5 ~10 6 Between 10 and 10 5 Between 10 2 ~10 5 Between 10 3 ~10 5 Between 10 4 ~10 5 Between 10 and 10 4 Between 10 2 ~10 4 Between 10 3 ~10 4 Between 10 and 10 3 Between 10 2 ~10 3 Between or 10 and 10 2 In some embodiments, the compositions, including pharmaceutical compositions, contain between 10 and 10 per dosage. 13 Between 10 2 ~10 13 Between 103 ~10 13 Between 10 4 ~10 13 Between 10 5 ~10 13 Between 10 6 ~10 13 Between 10 7 ~10 13 Between 10 8 ~10 13 Between 10 9 ~10 13 Between 10 10 ~10 13 Between 10 11 ~10 13 Between 10 12 ~10 13 Between 10 and 10 12 Between 10 2 ~10 12 Between 10 3 ~10 12 Between 10 4 ~10 12 Between 10 5 ~10 12 Between 10 6 ~10 12 Between 10 7 ~10 12 Between 10 8 ~10 12 Between 10 9 ~10 12 Between 10 10 ~10 12 Between 10 11 ~10 12 Between 10 and 10 11 Between 10 2 ~10 11 Between 10 3 ~10 13 Between 10 4 ~10 13 Between 10 5 ~10 13 Between 10 6 ~10 13 Between 10 7 ~10 11 Between 10 8 ~10 11 Between 10 9 ~10 11 Between 1010 ~10 11 Between 10 and 10 10 Between 10 2 ~10 10 Between 10 3 ~10 10 Between 10 4 ~10 10 Between 10 5 ~10 10 Between 10 6 ~10 10 Between 10 7 ~10 10 Between 10 8 ~10 10 Between 10 9 ~10 10 Between 10 and 10 9 Between 10 2 ~10 9 Between 10 3 ~10 9 Between 10 4 ~10 9 Between 10 5 ~10 9 Between 10 6 ~10 9 Between 10 7 ~10 9 Between 10 8 ~10 9 Between 10 and 10 8 Between 10 2 ~10 8 Between 10 3 ~10 8 Between 10 4 ~10 8 Between 10 5 ~10 8 Between 10 6 ~10 8 Between 10 7 ~10 8 Between 10 and 10 7 Between 10 2 ~10 7 Between 10 3 ~10 7 Between 10 4 ~10 7 Between 10 5 ~10 7 Between 10 6 ~10 7Between 10 and 10 6 Between 10 2 ~10 6 Between 10 3 ~10 6 Between 10 4 ~10 6 Between 10 5 ~10 6 Between 10 and 10 5 Between 10 2 ~10 5 Between 10 3 ~10 5 Between 10 4 ~10 5 Between 10 and 10 4 Between 10 2 ~10 4 Between 10 3 ~10 4 Between 10 and 10 3 Between 10 2 ~10 3 Between or 10 and 10 2 Contains all bacteria between

[0178] In some embodiments, compositions, including pharmaceutical compositions, contain 10 to 10 13 Between 10 2 ~10 13 Between 10 3 ~10 13 Between 10 4 ~10 13 Between 10 5 ~10 13 Between 10 6 ~10 13 Between 10 7 ~10 13 Between 10 8 ~10 13 Between 10 9 ~10 13 Between 10 10 ~10 13 Between 10 11 ~10 13 Between 10 12 ~10 13 Between 10 and 10 12 Between 10 2 ~10 12 Between 10 3~10 12 Between 10 4 ~10 12 Between 10 5 ~10 12 Between 10 6 ~10 12 Between 10 7 ~10 12 Between 10 8 ~10 12 Between 10 9 ~10 12 Between 10 10 ~10 12 Between 10 11 ~10 12 Between 10 and 10 11 Between 10 2 ~10 11 Between 10 3 ~10 13 Between 10 4 ~10 13 Between 10 5 ~10 13 Between 10 6 ~10 13 Between 10 7 ~10 11 Between 10 8 ~10 11 Between 10 9 ~10 11 Between 10 10 ~10 11 Between 10 and 10 10 Between 10 2 ~10 10 Between 10 3 ~10 10 Between 10 4 ~10 10 Between 10 5 ~10 10 Between 10 6 ~10 10 Between 10 7 ~10 10 Between 10 8 ~10 10 Between 10 9 ~10 10 Between 10 and 10 9 Between 10 2 ~10 9 Between 10 3 ~10 9Between 10 4 ~10 9 Between 10 5 ~10 9 Between 10 6 ~10 9 Between 10 7 ~10 9 Between 10 8 ~10 9 Between 10 and 10 8 Between 10 2 ~10 8 Between 10 3 ~10 8 Between 10 4 ~10 8 Between 10 5 ~10 8 Between 10 6 ~10 8 Between 10 7 ~10 8 Between 10 and 10 7 Between 10 2 ~10 7 Between 10 3 ~10 7 Between 10 4 ~10 7 Between 10 5 ~10 7 Between 10 6 ~10 7 Between 10 and 10 6 Between 10 2 ~10 6 Between 10 3 ~10 6 Between 10 4 ~10 6 Between 10 5 ~10 6 Between 10 and 10 5 Between 10 2 ~10 5 Between 10 3 ~10 5 Between 10 4 ~10 5 Between 10 and 10 4 Between 10 2 ~10 4 Between 10 3 ~10 4 Between 10 and 10 3 Between 10 2 ~103 Between or 10 and 10 2 In some embodiments, the compositions, including pharmaceutical compositions, contain between 10 and 10 total CFU of each of the bacterial strains per dosage. 13 Between 10 2 ~10 13 Between 10 3 ~10 13 Between 10 4 ~10 13 Between 10 5 ~10 13 Between 10 6 ~10 13 Between 10 7 ~10 13 Between 10 8 ~10 13 Between 10 9 ~10 13 Between 10 10 ~10 13 Between 10 11 ~10 13 Between 10 12 ~10 13 Between 10 and 10 12 Between 10 2 ~10 12 Between 10 3 ~10 12 Between 10 4 ~10 12 Between 10 5 ~10 12 Between 10 6 ~10 12 Between 10 7 ~10 12 Between 10 8 ~10 12 Between 10 9 ~10 12 Between 10 10 ~10 12 Between 10 11 ~10 12 Between 10 and 10 11 Between 10 2 ~10 11 Between 10 3 ~10 13 Between 10 4 ~10 13 Between 10 5 ~10 13Between 10 6 ~10 13 Between 10 7 ~10 11 Between 10 8 ~10 11 Between 10 9 ~10 11 Between 10 10 ~10 11 Between 10 and 10 10 Between 10 2 ~10 10 Between 10 3 ~10 10 Between 10 4 ~10 10 Between 10 5 ~10 10 Between 10 6 ~10 10 Between 10 7 ~10 10 Between 10 8 ~10 10 Between 10 9 ~10 10 Between 10 and 10 9 Between 10 2 ~10 9 Between 10 3 ~10 9 Between 10 4 ~10 9 Between 10 5 ~10 9 Between 10 6 ~10 9 Between 10 7 ~10 9 Between 10 8 ~10 9 Between 10 and 10 8 Between 10 2 ~10 8 Between 10 3 ~10 8 Between 10 4 ~10 8 Between 10 5 ~10 8 Between 10 6 ~10 8 Between 10 7 ~10 8 Between 10 and 10 7 Between 10 2 ~10 7Between 10 3 ~10 7 Between 10 4 ~10 7 Between 10 5 ~10 7 Between 10 6 ~10 7 Between 10 and 10 6 Between 10 2 ~10 6 Between 10 3 ~10 6 Between 10 4 ~10 6 Between 10 5 ~10 6 Between 10 and 10 5 Between 10 2 ~10 5 Between 10 3 ~10 5 Between 10 4 ~10 5 Between 10 and 10 4 Between 10 2 ~10 4 Between 10 3 ~10 4 Between 10 and 10 3 Between 10 2 ~10 3 Between or 10 and 10 2 Contains between.

[0179] In some embodiments, compositions, including pharmaceutical compositions, contain 10 grams of bacteria of each of the bacterial strains in the composition per dosage. -7 ~10 -1 Between 10 -6 ~10 -1 Between 10 -5 ~10 -1 Between 10 -4 ~10 -1 Between 10 -3 ~10 -1 Between 10 -2 ~10 -1 Between 10 -7 ~10 -2 Between 10 -6 ~10 -2 Between 10 -5 ~10 -2 Between 10-4 ~10 -2 Between 10 -3 ~10 -2 Between 10 -7 ~10 -3 Between 10 -6 ~10 -3 Between 10 -5 ~10 -3 Between 10 -4 ~10 -3 Between 10 -7 ~10 -4 Between 10 -6 ~10 -4 Between 10 -5 ~10 -4 Between 10 -7 ~10 -5 Between 10 -6 ~10 -5 Between or 10 -7 ~10 -6 In some embodiments, compositions, including pharmaceutical compositions disclosed herein, contain between 10 and 100 grams of total combined (whole) bacteria per dosage. -7 ~10 -1 Between 10 -6 ~10 -1 Between 10 -5 ~10 -1 Between 10 -4 ~10 -1 Between 10 -3 ~10 -1 Between 10 -2 ~10 -1 Between 10 -7 ~10 -2 Between 10 -6 ~10 -2 Between 10 -5 ~10 -2 Between 10 -4 ~10 -2 Between 10 -3 ~10 -2 Between 10 -7 ~10 -3 Between 10 -6 ~10 -3 Between 10 -5 ~10 -3 Between 10 -4 ~10 -3 Between 10-7 ~10 -4 Between 10 -6 ~10 -4 Between 10 -5 ~10 -4 Between 10 -7 ~10 -5 Between 10 -6 ~10 -5 Between or 10 -7 ~10 -6 Contains between.

[0180] Aspects of the present disclosure also provide food products comprising any of the compositions provided herein and nutrients. Food products comprising any of the bacterial strains described herein and nutrients are also within the scope of the present disclosure. Food products are generally intended for human or animal consumption. Any of the compositions described herein may be formulated as a food product. In some embodiments, the bacterial strain is formulated as a food product in spore form. In some embodiments, the bacterial strain is formulated as a food product in vegetative form. In some embodiments, the food product contains both vegetative bacteria and spore form bacteria. The compositions disclosed herein can be used in foods or beverages such as health foods or beverages, foods or beverages for infants, foods or beverages for pregnant women, athletes, the elderly, or other specified groups, functional foods, beverages, foods or beverages for specified health uses, dietary supplements, foods or beverages for patients, or animal feed.

[0181] Non-limiting examples of foods and beverages include various beverages such as juices, soft drinks, teas, drink preparations, jelly drinks, and functional drinks; alcoholic beverages such as beer; carbohydrate-containing foods such as rice food products, noodles, bread, and pasta; paste products such as fish ham, sausage, and seafood paste products; retort pouch products such as curry, foods dressed with viscous starchy sauces, and soups; dairy products such as milk, dairy drinks, ice cream, cheese, and yogurt; fermented products such as miso paste, yogurt, fermented drinks, and pickles; soy products; Western confectionery products including biscuits, cookies, and the like; Japanese confectionery products including manju, mizu yokan, and the like; various confectionery products such as candy, chewing gum, gummies, and frozen desserts including jellies, creme caramel, and frozen desserts; instant foods such as instant soups and instant soybean soups; microwave foods; etc. Furthermore, examples also include health foods and beverages prepared in the form of powders, granules, tablets, capsules, liquids, pastes, and jellies.

[0182] Food products containing the bacterial strains described herein may be produced using methods known in the art and may contain the same amounts (e.g., by weight, amount, or CFU) of bacteria as the pharmaceutical compositions provided herein. Selecting the appropriate amount of bacteria in a food product will depend on various factors, including, for example, the serving size of the food product, the frequency of consumption of the food product, the particular bacterial strain contained in the food product, the amount of water in the food product, and / or additional conditions for the survival of the bacteria in the food product. Examples of food products that may be formulated to contain any of the bacterial strains described herein include, but are not limited to, beverages, drinks, bars, snacks, dairy products, confectionery products, cereal products, processed products, nutritional formulas such as dietary supplement formulas, and food or beverage additives.

[0183] The present invention is not limited in its application to the details of construction and the arrangement of components set forth in the following description or illustrated in the drawings. The invention is capable of other embodiments and of being practiced or carried out in various ways. Also, the phraseology and terminology used herein is for the purpose of description and should not be regarded as limiting. The use of "comprising," "including," "having," "containing," "relat- ing to," and variations thereof herein is meant to encompass the items listed thereafter and equivalents thereof as well as additional items.

[0184] Unless otherwise defined herein, scientific and technical terms used in connection with this disclosure will have the meanings commonly understood by those skilled in the art. Furthermore, unless otherwise required by context, singular terms will include pluralities, and plural terms will include the singular. The methods and techniques of the present disclosure are generally carried out in accordance with conventional methods well known in the art. In general, the techniques of biochemistry, enzymology, molecular and cell biology, microbiology, virology, cell or tissue culture, genetics, and protein and nucleic acid chemistry described herein, as well as the nomenclature used in connection therewith, are well known and commonly used in the art. The methods and techniques of the present disclosure are generally carried out in accordance with conventional methods well known in the art, and as described in the various general and more specific references cited and discussed throughout this specification, unless otherwise indicated.

[0185] SEQ ID NO: 1 strain 1 16S ribosomal RNA Clostridium bolteae

[0186] SEQ ID NO: 2 Strain 2 16S ribosomal RNA Anaerotruncus colihominis

[0187] SEQ ID NO: 3 strain 3 16S ribosomal RNA Ruminococcus torques

[0188] SEQ ID NO: 4 Strain 4 16S ribosomal RNA Clostridium symbiosum

[0189] SEQ ID NO: 5 strain 5 16S ribosomal RNA Blautia producta

[0190] SEQ ID NO: 6 Strain 6 16S ribosomal RNA Dorea Longicatena

[0191] SEQ ID NO: 7 Strain 7 16S ribosomal RNA Erysipelotrichaceae bacterium

[0192] SEQ ID NO: 8 Strain 8 16S ribosomal RNA Subdoligranulum spp.

[0193] Accession number 9, strain 9 VE202-4; Clostridium hathewayi GATGAACGCTGGCGGCGGTGCTTAACACATGCAAGTCGAGCGAAGCGGTTTCGAGTGAAGTTTTGGATGGAATTGAAATTGACTTAGCGGCGGACGGGTGAGTAACGCGTGGGTAACCTGCCTTACACTGGGGGATAACAGTTAGAAATGACTGCTAATACCGCATAAGCGCACAGGGCCGCATGGTCTGGTGCGAAAAACTCCGGTGGTGTAAGATGGACCCGCGTCTGATTAGGTAGTTGGTGGGGTAACGGCCCACCAAGCCGACGATCAGTAGCCGACCTGAGAGGGTGACCGGCCACATTGGGACTGAGACACGGCCCAA Accession number 10, strain 10 VE202-9 Clostridium indolis / Anaerostipes caccae GATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGCATTTTGGAAGGAAGTTTTCGGATGGAATTCCTTAATGACTGAGTGGCGGACGGGTGAGTAACGCGTGGGGAACCTGCCCTATACAGGGGGATAACAGCTGGAAACGGCTGCTAATACCGCATAAGCGCACAGAATCGCATGATTCGGTGTGAAAAGCTCCGGCAGTATAGGATGGTCCCGCGTCTGATTAGCTGGTTGGCGGGGTAACGGCCCACCAAGGCGACGATCAGTAGCCGGCTTGAGAGAGTGGACGGCCACATTGGGACTGAGACACGGCCCA Accession number 11, strain 11 VE202-27 Lachnospiraceae bacterium GATGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAACGGAGTTATGCAGAGGAAGTTTTCGGATGGAATCGGCGTAACTTAGTGGCGGACGGGTGAGTAACGCGTGGGAAACCTGCCCTGTACCGGGGGATAACACTTAGAAATAGGTGCTAATACCGCATAAGCGCACAGCTTCACATGAAGCAGTGTGAAAAACTCCGGTGGTACAGGATGGTCCCGCGTCTGATTAGCCAGTTGGCAGGGTAACGGCCTACCAAAGCGACGATCAGTAGCCGGCCTGAGAGGGTGAACGGCCACATTGGGACTGAGACACGGCCCA

[0194] Accession number 12 Strain 12 VE202-28 Clostridium species GATGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAACGAAGCATCCCATAGGAAGTTTTCGGATGGAATATGGGATGACTGAGTGGCGGACGGGTGAGTAACGCGTGGATAACCTGCCTCACACTGGGGGATAACAGTTAGAAATGGCTGCTAATACCGCATAAGCGCACAGTACCGCATGGTACGGTGTGAAAAACCCAGGTGGTGTGAGATGGATCCGCGTCTGATTAGCCAGTTGGCGGGGTAACGGCCCACCAAAGCGACGATCAGTAGCCGACCTGAGAGGGTGACCGGCCACATTGGGGACTGAGACACGGCCCA Accession number 13 Strain 13 VE202-29 Lachnospiraceae bacterium GATGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAACGAAGTTAGACAGAGGAAGTTTTCGGATGGAATCGGTATAACTTAGTGGCGGACGGGTGAGTAACGCGTGGGAAACCTGCCCTGTACCGGGGGATAACACTTAGAAATAGGTGCTAATACCG CATAAGCGCACGGAACCGCATGGGTTCTGTGTGAAAACTCCGGTGGTACAGGATGGTCCCGCGTCTGATTAGCCAGTTGGCAGGGTAACGGCCTACCAAAGCGACGATCAGTAGCCGGCCTGAGAGGGTGAACGGCCACATTGGGACTGAGACACGGCCCAA

[0195] The present invention is further illustrated by the following examples, which should not be construed as further limiting in any way. The entire contents of all references (including literature references, issued patents, published patent applications, and co-pending patent applications) cited throughout this application are hereby expressly incorporated by reference, particularly for the teachings referenced above. However, the citation of any reference is not intended as an admission that the reference is prior art.

[0196] example Example 1: Composition B induces regulatory T cells (Tregs) Each of the bacterial strains in Composition B was grown to logarithmic phase and combined to give approximately 10 8 The total dose was 1000 cfu. Germ-free mice were inoculated with Composition B or a negative control by oral gavage and sacrificed after 4 weeks of colonization. Lamina propria leukocytes were isolated from the colon tissue of each mouse by standard procedures and assessed by flow cytometry. Regulatory T cell content was assessed as the percentage of Foxp3-positive cells among CD4+ T cells. As shown in Figure 1, mice inoculated with Composition B were found to have significantly more regulatory T cells compared to mice inoculated with the control.

[0197] Example 2: Composition B suppresses the production of IgE antibodies Germ-free mice were inoculated with the test consortium as described in Example 1. Whole blood was collected into serum tubes at the time of mouse sacrifice and frozen until further analysis. Serum was then thawed, diluted 1:25, and total IgE in the serum was measured using standard ELISA methods. As shown in Figure 2, control germ-free (GF) mice had elevated serum IgE levels compared to specific pathogen-free (SPF) mice with normal commensal microbiota. Colonization with Composition B reduced serum IgE levels, indicating that the composition suppressed Th2-type inflammatory responses in inoculated germ-free mice.

[0198] Example 3: Compositions B, C, and D induce regulatory T cells and suppress IgE antibody production Selected bacterial strains from Composition B were selected to form Compositions C and D, as shown in Tables 2 and 3. Each of the bacterial strains was grown, combined into the indicated combinations, and used to inoculate germ-free mice by oral gavage. The mice were sacrificed, and lamina propria leukocytes were isolated and assessed as in Example 1. Whole blood at the time of sacrifice was collected into serum tubes and frozen until further analysis was performed.

[0199] [Table 2] [Table 3]

[0200] The content of regulatory T cells was assessed as the percentage of Foxp3-positive cells among CD4+ T cells. As shown in Figure 3, Compositions B, C, and D were found to have more regulatory T cells compared to control-inoculated mice. Serum samples were subsequently thawed and diluted, and total IgE in the serum was measured using standard ELISA methods. As shown in Figure 4, control germ-free (GF) mice had elevated serum IgE levels compared to specific pathogen-free (SPF) mice with normal commensal microbiota. Colonization with each of Compositions B, C, and D reduced serum IgE levels, indicating that the compositions suppressed Th2-type inflammatory responses in inoculated germ-free mice.

[0201] Example 3: Separation of regulatory T cell induction and butyrate production Both the induction of regulatory T cells and butyrate production have been proposed as mechanisms by which regulatory Clostridia may suppress inflammation (see, for example, Atarashi et al. (2013); Stefka et al. (2014)). To disentangle these potential mechanisms, bacterial consortia were identified that either (1) had little Treg-inducing activity but primarily produced butyrate, or (2) had no butyrate production but were highly Treg-inducing. These consortia were evaluated for their efficacy in protecting against experimental food allergies.

[0202] Induction of regulatory T cells (Treg) The amount of Treg induction (TrIS) for bacterial strains was given a score predicted by the mathematical model. Bacterial consortia predicted to induce high, intermediate, and low levels of Tregs were selected for experimental validation. Briefly, germ-free C57BL / 6 mice (5–6 weeks old) were inoculated with >=10 HIV-1 antibodies per mouse. 8 The bacterial composition was orally administered once at a dose of 100 CFU. Colonization was monitored for 4 weeks. At week 4, the mice were sacrificed and lamina propria leukocytes were isolated from the colon. The bacterial strains in the example bacterial composition, designated LBP1 and LBP2, are listed in Tables 4 and 5, respectively.

[0203] [Table 4] [Table 5] Tregs were quantified as Foxp3-positive CD4+ T cells, as shown in Figure 5. As expected, administration of LBP2 resulted in higher levels of Treg induction, while administration of LBP1 resulted in lower levels of Treg induction.

[0204] Short-chain fatty acid production Short-chain fatty acid (SCFA) production by the bacterial composition was assessed as described in Narushima et al. Gut Microbes (2014) 5(3): 333-339. Briefly, individual strains were grown to an OD of >0.3, supernatants were harvested, and colony-forming unit (CFU) counts were determined for each strain. The supernatants were subjected to targeted metabolomic profiling of seven short-chain fatty acids, and results were normalized to CFU. Figures 6A and 6B show the predicted levels of butyrate and acetate produced by LBP1 and LBP2 based on butyrate production by the individual strains of the composition. LBP1 was predicted to produce high levels of butyrate and low levels of acetate, while LBP2 was predicted to produce low levels of butyrate and high levels of acetate. SCFA production was also assessed in vivo in fecal samples from mice inoculated with LBP1 or LBP2. Fecal samples were collected on days 3, 7, 14, and 28 post-colonization. As expected, inoculation with LBP1 resulted in higher levels of butyrate and lower levels of acetate in fecal samples; and inoculation with LBP2 resulted in lower levels of butyrate and higher levels of acetate (Figures 6C and 6D).

[0205] Food allergy model The bacterial composition was evaluated in a mouse model of food allergy, as described, for example, in Mathias et al. JACI (2011) 127(3): 795-805. Briefly, IL4raF709 mice on a Balb / c background are hypersensitive to IL4R signaling and will be used as a model for food allergy. These mice are genetically prone to anaphylaxis in response to food allergen sensitization. As shown in Figure 7, mice were pretreated with antibiotics to create a niche for engraftment, followed by sensitization with OVA (ovalbumin) + SEB (staphylococcal enterotoxin B) for 8 weeks and inoculation with the bacterial composition. The mice were then challenged with OVA and evaluated.

[0206] To assess immune responses in the food allergy model, mice were bled at midpoint during week 4, and total serum IgE was measured. Challenge with OVA induced anaphylaxis and acute allergy in IL4raF709 mice, as measured by elevated serum total IgE, elevated serum OVA-specific IgE, elevated serum mMCP-1 (a signal for mast cell degranulation), increased Th2 cells in the MLN and small intestine (stained for IL4 and other cytokines / transcription factors), increased Th2-like regulatory T cells (stained for IL4 and other cytokines / transcription factors (Noval-Rivas et al., 2015)), and mast cell infiltration into the intestine (as measured by histology and cell isolation).

[0207] LBP1 and LBP2 were found to have protective effects in a mouse model of food allergy that were not specifically dependent on butyrate production. Inoculation with either LBP1 or LBP2 resulted in reduced levels of total IgE and OVA-specific IgE (Figures 8A and 8B). Additionally, mice administered LBP1 or LBP2 did not experience the reduction in temperature observed in mice that did not receive the bacterial composition (Figure 8C). Figure 8D shows representative photomicrographs of tissue samples from mice.

[0208] Mice inoculated with LBP1 or LBP2 were also found to have reduced allergy-related T cell responses. Notably, IL-4-producing Th2 cells were reduced in the small intestine of mice administered LBP1 or LBP2, whereas the total CD4+ T cell population was substantially unchanged (Figures 9A and 9B). Th2-phenotype regulatory T cells, including Foxp3+IL4+ cells and GATA3+ (GATA3-bright) cells, were also reduced in mice inoculated with LBP1 or LBP2 (Figures 9C and 9D). Mast cell and IgE responses were also assessed as a measure of protection from food allergy. As shown in Figures 10A-10D, mice inoculated with LBP1 or LBP2 were found to have reduced levels of mMCP-1, reduced numbers of mast cells, and reduced mast cell and B cell IgE. In summary, LBP1 and LBP2 were found to induce protection against food allergy, accompanied by a reduction in allergy-related T cell and granulocyte responses.

[0209] In a second experiment, we evaluated whether antibiotic pretreatment was necessary to create a niche to facilitate seed engraftment from LBP1 and LBP2 and allow them to modulate the allergic response. This experiment was performed as described above, except that antibiotic pretreatment was not performed (see Figure 32). Mice were bled 5 weeks after the start of bacterial dosing, and as shown in Figures 33A and 33B, both LBP1 and LBP2 reduced the rate of allergic sensitization, as measured by reduced total and OVA-specific IgE in serum. When anaphylactic responses were measured 8 weeks after sensitization and bacterial treatment, LBP1 and LBP2 treatment was insufficient to protect against experimental anaphylaxis, as measured by temperature drop (Figures 34A and 34B). However, measurements of allergy-associated T cell responses suggested that treatment with LBP1 and LBP2 had some immunomodulatory effects, with a reduction in Th2-phenotype regulatory T cells in the MLN and small intestine (Fig. 35A, Foxp3+IL4+ cells), and a reduction in Th2 cells in the spleen, MLN, and small intestine (Fig. 35B, Foxp3-IL4+ cells).

[0210] Evaluation of additional bacterial compositions Based on the results observed using LBP1 and LBP2, compositions B, C, and D, SCFA production, Treg induction, and protection from food allergies were also evaluated. As described above, bacterial strains from compositions B, C, and D were assessed for butyrate and acetate production in vitro. The levels of butyrate and acetate production for each composition were predicted based on the production of the individual strains. Compositions B, C, and D were predicted to have similar levels of butyrate production as LBP1 (Figures 11A and 11B). This was confirmed in vivo for compositions B and C (Figures 11C and 11D). Compositions B, C, and D were predicted to have higher levels of butyrate production than LBP2 (Figures 12A and 12B). This was confirmed in vivo for compositions B and C (Figures 12C and 12D). Inoculation of germ-free mice with the bacterial composition resulted in similar levels of Treg induction (Figure 13). IgE levels were found to be reduced to a similar extent in germ-free mice inoculated with the composition (Figure 14).

[0211] Compositions B and C were further evaluated in a mouse model of food allergy. Mice inoculated with Composition C did not experience the reduction in temperature observed in mice that did not receive the bacterial composition, suggesting that mice receiving Composition C were protected from anaphylaxis upon allergen challenge (Figures 15A, 17A, and 17B). Confirming this point, mice inoculated with Composition C were also found to have reduced levels of mMCP-1 compared to mice that did not receive the bacteria, as shown in Figures 15B, 17C, and 27A.

[0212] In one experiment, as shown in Figures 16A-D, treatment with Composition C led to increased numbers of total Tregs (CD4+Foxp3+) in the mesenteric lymph nodes, spleen, and small intestine, and reduced numbers of allergy-associated IL4-positive Th2 effectors (Foxp3-IL4+), Th2-like GATA3+ Tregs (Foxp3+GATA3+), and Th2 GATA3+ T effectors (Foxp3-GATA3+) in the small intestine. In another experiment, mice treated with Composition C showed a reduction in Th2-like Tregs (Foxp3+GATA3+) and Th2 effector cells (Foxp3-GATA3+) in the spleen (Figures 18A, 18B). In a separate experiment, mice treated with Compositions B and C showed a reduction in Th2-like Tregs (Foxp3+IL4+) in the small intestine and a reduction in Th2 effector cells (Foxp3-IL4+) in the mLN and small intestine. Levels of total IgE and OVA-specific IgE were also assessed, and Compositions B and C reduced OVA-specific IgE antibodies (Figures 27B and 27C and Figures 26A-28B).

[0213] In the experiments shown in Figures 16A-16D, 18A, and 18B, DNA was isolated from fecal pellets at various time points, and whole-genome shotgun sequencing was performed on an Illumina platform, followed by quality control and taxonomic assignment. Inoculation with Composition C was associated with a global shift in the gut microbiome (Figures 16E and 18E).

[0214] Additional characterization Samples obtained from mice inoculated with any of the compositions described herein may also be evaluated for levels of IL-33, IL25, TSLP (e.g., intestinal transcripts), TGFβ, and IL-10. Alternatively, or in addition, mice may be assessed for relative colonization (e.g., engraftment) of compositions comprising one or more strains of the composition. Samples obtained from mice may also be subjected to RNA sequencing or other expression analysis.

[0215] The effect of transplanted strains on the immune and biochemical response of host and the integrity of gastrointestinal barrier can also be assessed.The fecal fraction from mice inoculated with any of the compositions described herein can be analyzed to identify beneficial strains, which will undergo further characterization, including whole genome sequencing, metabolite production profiling, Treg induction ability, and the ability to enhance the integrity of gastrointestinal barrier.In addition, in silico analysis can be carried out to determine the abundance and prevalence of one or more strains in healthy subjects, co-occurrence network, and whether one or more bacterial strains are associated with favorable clinical response in subjects who have undergone oral immunotherapy.

[0216] Example 4: Evaluating Composition C and Composition B as treatments for food allergies The efficacy of compositions C and B as treatments for food allergies was evaluated. Bacterial compositions C and B were evaluated in a "curative" mouse model for treating food allergies, such as that described in PCT Publication WO2017 / 079450. Briefly, IL4raF709 mice on a Balb / c background are hypersensitive to IL4R signaling and will be used as a model for food allergies. These mice are genetically prone to anaphylaxis upon sensitization to food allergens. As shown in Figure 19, mice were sensitized with OVA (ovalbumin) + SEB (staphylococcal enterotoxin B) for 8 weeks. The mice were then pretreated with antibiotics to create a niche for engraftment, followed by twice-weekly inoculations of the bacterial composition for 4 weeks (total of 8 inoculations). During this period, mice continued to be sensitized with OVA + SEB. The mice were then challenged with OVA and evaluated.

[0217] Immune responses were assessed in a curative food allergy model following a full 12-week model. Challenge with OVA induced anaphylaxis and acute allergy in IL4raF709 mice, as measured by elevated serum total IgE, elevated serum OVA-specific IgE, elevated serum mMCP-1 (a signal for mast cell degranulation), and increased Th2 and Th2-like Treg cells in the mesenteric lymph nodes, small intestine, and spleen.

[0218] Compositions C and B were evaluated in a curative mouse model for treating food allergies. Mice inoculated with Composition C did not experience the reduction in temperature observed in mice inoculated with Composition B or mice that did not receive the bacterial composition, suggesting that mice receiving Composition C were protected from developing an allergic response to OVA challenge (Figures 20A, 20B, 23A, 23B). Notably, 7 of 14 mice administered Composition C showed no effect of exposure to the allergen, while all control mice experienced anaphylaxis (Figures 20B and 23B).

[0219] As shown in Figures 20C and 24A, mice inoculated with Composition C and protected from anaphylaxis were also found to have reduced levels of mMCP-1 compared with mice that did not receive the bacterial composition and experienced anaphylaxis. Furthermore, reduced numbers of allergy-associated Th2 effectors (CD4+FoxP3-GATA3+) and Th2-like Tregs (CD4+Foxp3+GATA3+) were observed in mice administered Composition C compared with mice administered Composition B or mice that did not receive the bacterial composition (Figures 21A-21D and Figures 25A-25D). Finally, mice inoculated with Composition C and protected from anaphylaxis had reduced levels of total IgE antibodies and antigen-specific OVA-IgE antibodies compared with mice that did not receive the bacterial composition and experienced anaphylaxis (Figures 22A, 22B, 24B, and 24C).

[0220] Example 5: Modulation of existing host microbiome and gut immunity by compositions B and C Germ-free mice, such as those used in Examples 1-3 herein, lack a resident microbiota and have an altered immune system compared to conventional mice, including a relative lack of intestinal regulatory T cells and elevated Th2-type immune responses. Having shown that Compositions B and C preferentially induce regulatory T cell responses in germ-free mice, we then investigated whether these bacterial compositions can induce immunomodulatory effects in mice with a resident microbiota and a normal immune system. We further explored whether pretreatment with antibiotics is necessary to create a niche that facilitates the engraftment of Compositions B and C species and allows them to modulate intestinal immunity, or whether the bacterial compositions can be effective in the absence of antibiotics.

[0221] Specific pathogen-free (SPF) mice (6-8 weeks old) that had reached immunological maturity were used to evaluate the effects of Compositions B and C. Mice were either treated or not with cefoperazone (5 mg / mouse) by oral gavage daily for 5 days, followed by a 3-day washout period (Figure 29). This is an adaptation of standard treatment methods to reduce the resident gut microbiota and facilitate bacterial engraftment (see, e.g., Schubert et al. (2015) mBio). Mice were then inoculated with Composition B, Composition C, or not treated. Mice receiving the bacterial compositions continued to be inoculated weekly.

[0222] A subset of mice from each experimental group was sacrificed at weeks 2 and 4, and leukocytes were isolated from colonic tissue to assess the induction of immunoregulatory responses. As shown in Figure 30A, in antibiotic-pretreated mice, Composition B induced colonic Tregs, defined as CD4+FoxP3+Helios- T cells, above a "no bacteria" baseline at weeks 2 and 4. When mice were not treated with antibiotics, Composition B induced colonic Tregs, but an increase above baseline was only observed 4 weeks after bacterial treatment. Similarly, as shown in Figure 30A, in antibiotic-pretreated mice, Composition C induced colonic Tregs above the "no bacteria" control baseline. In the absence of antibiotic treatment, both Compositions B and C showed a trend toward the induction of colonic Tregs 4 weeks after bacterial administration. These experiments suggest that compositions B and C are capable of inducing a regulatory immune response in the gut, even in the context of a replete host of microbiota with normal immune development.

[0223] Because Compositions B and C suggested that they had an effect on the intestine, even in mice with a resident microbiota, the intestinal microbial communities of experimental mice from Experiment 1 were examined (Figure 30A). Fecal pellets were sampled from mice not treated with antibiotics before bacterial administration (day 0), after the second bacterial dose (day 13), after the third bacterial dose (day 20), and after five doses (day 34) prior to sacrifice (Figure 31A). Principal component analysis (PCA) was performed on the composition of the microbiome population of each sample to examine microbiome variation during LBP treatment and allergic sensitization (see, for example, Zinkernagel, et al. (2017) Scientific Reports). PCA analysis revealed that the microbial communities of untreated mice (without bacteria) had similar profiles over the course of the experiment. However, for mice inoculated with Composition B ("LBP"), there was a shift in the microbiota over time compared to baseline, suggesting that inoculation with Composition B leads to changes in the resident microbiota even without antibiotic treatment. Similar results were observed in mice that received antibiotic pretreatment (Figure 31B).

[0224] For mice pretreated with antibiotics, fecal pellets were collected before antibiotic treatment (day 0), after antibiotics and prior to LBP inoculation (day 6), after two inoculations of the bacterial composition (day 13), after three inoculations of the bacterial composition (day 20), and after five inoculations of the bacterial composition and prior to sacrifice (day 34). In all mice, antibiotic treatment induced significant changes in the microbiota from baseline (day 0) to day 6. For mice not inoculated with Composition B, the gut dysbiosis remained dysbalanced, and the microbial profile was permanently altered and did not return to baseline. For mice inoculated with Composition B, the microbial profile began to return to the pre-antibiotic baseline over time, suggesting that Composition B leads to changes in the resident microbiota and that these changes may promote a return to healthy homeostasis.

Claims

1. 1. A method of treating a food allergy, comprising: administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains of a species selected from the group consisting of Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Dorea longicatena, Erysipelotrichaceae bacterium, and Subdolinogranulum spp.; The method comprising:

2. 1. A method of treating a food allergy, comprising: (a) administering an antibiotic to a subject in need thereof; and (b) administering to the subject a therapeutically effective amount of a composition comprising two or more purified bacterial strains of a species selected from the group consisting of Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Dorea longicatena, Erysipelotrichaceae bacterium, and Subdolinogranulum spp.; The method comprising:

3. 3. The method of claim 1 or 2, wherein the composition consists of purified bacterial strains Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Erysipelotrichaceae bacterium, and Subdolinogranulum spp.

4. 3. The method of claim 1 or 2, wherein the composition consists of purified bacterial strains of Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Dorea longicatena, and Subdolinogranulum spp.

5. 1. A method of treating a food allergy, comprising: administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains of a species selected from the group consisting of Clostridium indolis, Anaerostipes caccae, Lachnospiraceae bacterium, and Clostridium symbiosum; The method comprising:

6. 6. The method of claim 5, wherein the composition consists of purified bacterial strains Clostridium indolis, Anaerostipes caccae, Lachnospiraceae bacterium, and Clostridium symbiosum.

7. 1. A method of treating a food allergy, comprising: administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains of a species selected from the group consisting of Clostridium hathewayi, Clostridium bolteae, Sellimonas intestinalis, and Clostridium species; The method comprising:

8. 8. The method of claim 7, wherein the composition consists of purified bacterial strains Clostridium hathewayi, Clostridium bolteae, Sellimonas intestinalis, and Clostridium species.

9. 1. A method of treating a food allergy, comprising: administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 1-8; The method comprising:

10. 1. A method of treating a food allergy, comprising: (a) administering an antibiotic to a subject in need thereof; and (b) administering to the subject a therapeutically effective amount of a composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 1-8; The method comprising:

11. 11. The method of claim 9 or 10, wherein the composition consists of a purified bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleic acid sequences set forth as SEQ ID NOs: 1-5, 7, and 8.

12. 11. The method of claim 9 or 10, wherein the composition consists of a purified bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleic acid sequences set forth as SEQ ID NOs: 1-6 and 8.

13. 1. A method of treating a food allergy, comprising: administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO:10, SEQ ID NO:11; SEQ ID NO:13; and SEQ ID NO:4; The method comprising:

14. 14. The method of claim 13, wherein the composition consists of a purified bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleic acid sequences set forth as SEQ ID NO:10, SEQ ID NO:11; SEQ ID NO:13; and SEQ ID NO:

4.

15. 1. A method of treating a food allergy, comprising: administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO:9, SEQ ID NO:1; SEQ ID NO:3; and SEQ ID NO:12; The method comprising:

16. 16. The method of claim 15, wherein the composition consists of a purified bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleic acid sequences set forth as SEQ ID NO:9, SEQ ID NO:1; SEQ ID NO:3; and SEQ ID NO:

12.

17. The method of any one of claims 1 to 16, which results in the suppression of IgE antibody production.

18. The method of any one of claims 1 to 17, which results in the suppression of a Th2 immune response.

19. 19. The method of any one of claims 1 to 18, which results in suppression of the immune response associated with food allergy.

20. The method according to any one of claims 1 to 19, wherein the bacterial strain is freeze-dried.

21. The method of any one of claims 1 to 19, wherein the bacterial strain is spray dried.

22. 22. The method of any one of claims 1 to 21, wherein one or more of the bacterial strains is in spore form.

23. 23. The method of any one of claims 1 to 22, wherein each of the bacterial strains is in spore form.

24. The method of any one of claims 1 to 22, wherein one or more of the bacterial strains is in a vegetative form.

25. 25. The method of any one of claims 1 to 21 and 24, wherein each of the bacterial strains is in a vegetative form.

26. The method of any one of claims 1 to 25, wherein the administration is oral administration.

27. The method of any one of claims 1 to 26, wherein the composition is formulated for oral delivery.

28. The method of any one of claims 1 to 27, wherein the composition is formulated for rectal delivery.

29. The method of any one of claims 1 to 28, wherein the composition is formulated for delivery to the intestine.

30. 30. The method of any one of claims 1 to 29, wherein the composition is formulated for delivery to the colon.

31. 31. The method of any one of claims 1 to 30, wherein the food allergy is selected from the group consisting of nut allergy, fish allergy, wheat allergy, milk allergy, peanut allergy, tree nut allergy, shellfish allergy, soybean allergy, seed allergy, sesame seed allergy, and egg allergy.

32. The method of any one of claims 1 to 31, wherein the subject is a human.

33. The method of any one of claims 1 to 32, wherein the composition further comprises one or more adjuvants.

34. 34. The method of claim 33, wherein the adjuvant is associated with allergy treatment or immune tolerance.

35. 1. A method of modulating an immune response associated with food allergy, comprising: administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains of a species selected from the group consisting of Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Dorea longicatena, Erysipelotrichaceae bacterium, and Subdolinogranulum spp.; The method comprising:

36. 36. The method of claim 35, wherein the composition consists of purified bacterial strains of Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Erysipelotrichaceae bacterium, and Subdolinogranulum spp.

37. 36. The method of claim 35, wherein the composition consists of purified bacterial strains of Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Dorea longicatena, and Subdolinogranulum spp.

38. 1. A method of modulating an immune response associated with food allergy, comprising: administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains of a species selected from the group consisting of Clostridium indolis, Anaerostipes caccae, Lachnospiraceae bacterium, and Clostridium symbiosum; The method comprising:

39. 39. The method of claim 38, wherein the composition consists of purified bacterial strains Clostridium indolis, Anaerostipes caccae, Lachnospiraceae bacterium, and Clostridium symbiosum.

40. 1. A method of modulating an immune response associated with food allergy, comprising: administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains of a species selected from the group consisting of Clostridium hathewayi, Clostridium bolteae, Sellimonas intestinalis, and Clostridium species; The method comprising:

41. 41. The method of claim 40, wherein the composition consists of purified bacterial strains Clostridium hathewayi, Clostridium bolteae, Sellimonas intestinalis and Clostridium species.

42. 1. A method of modulating an immune response associated with food allergy, comprising: administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 1-8; The method comprising:

43. 43. The method of claim 42, wherein the composition consists of a purified bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleic acid sequence set forth as SEQ ID NOs: 1-5, 7, and 8.

44. 43. The method of claim 42, wherein the composition consists of a purified bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleic acid sequence set forth as SEQ ID NOs: 1-6 and 8.

45. 1. A method of modulating an immune response associated with food allergy, comprising: administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO:10, SEQ ID NO:11; SEQ ID NO:13; and SEQ ID NO:4; The method comprising:

46. 46. ​​The method of claim 45, wherein the composition consists of a purified bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleic acid sequences set forth as SEQ ID NO:10, SEQ ID NO:11; SEQ ID NO:13; and SEQ ID NO:

4.

47. Methods for modulating immune responses associated with food allergies, administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO:9, SEQ ID NO:1; SEQ ID NO:3; and SEQ ID NO:12; The method comprising:

48. 48. The method of claim 47, wherein the composition consists of a purified bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleic acid sequences set forth as SEQ ID NO:9, SEQ ID NO:1; SEQ ID NO:3; and SEQ ID NO:

12.

49. The method of any one of claims 35 to 48, which results in the induction of proliferation and / or accumulation of regulatory T cells.

50. 50. The method of any one of claims 35 to 49, which results in the suppression of IgE antibody production.

51. 51. The method of any one of claims 35 to 50, which results in the suppression of a Th2 immune response.

52. 52. The method of any one of claims 35 to 51, wherein the bacterial strain is freeze-dried.

53. 52. The method of any one of claims 35 to 51, wherein the bacterial strain is spray dried.

54. 54. The method of any one of claims 35 to 53, wherein one or more of the bacterial strains is in spore form.

55. 55. The method of any one of claims 35 to 54, wherein each of the bacterial strains is in spore form.

56. 55. The method of any one of claims 35 to 54, wherein one or more of the bacterial strains is in a vegetative form.

57. 57. The method of any one of claims 35 to 53 and 56, wherein each of the bacterial strains is in a vegetative form.

58. 58. The method of any one of claims 35 to 57, wherein the administration is oral administration.

59. 59. The method of any one of claims 35 to 58, wherein the composition is formulated for oral delivery.

60. 59. The method of any one of claims 35 to 58, wherein the composition is formulated for rectal delivery.

61. 61. The method of any one of claims 35 to 60, wherein the composition is formulated for delivery to the intestine.

62. 61. The method of any one of claims 35 to 60, wherein the composition is formulated for delivery to the colon.

63. 63. The method of any one of claims 35 to 62, wherein the food allergy is selected from the group consisting of nut allergy, fish allergy, wheat allergy, milk allergy, peanut allergy, tree nut allergy, shellfish allergy, soybean allergy, seed allergy, sesame seed allergy, and egg allergy.

64. The method of any one of claims 35 to 63, wherein the subject is a human.

65. The method of any one of claims 35 to 64, wherein the composition further comprises one or more adjuvants.

66. 66. The method of claim 65, wherein the adjuvant is associated with allergy treatment or immune tolerance.

67. 1. A method for inducing immune tolerance or hyposensitization to food allergy, comprising: administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains of a species selected from the group consisting of Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Dorea longicatena, Erysipelotrichaceae bacterium, and Subdolinogranulum spp.; The method comprising:

68. 68. The method of claim 67, wherein the composition consists of purified bacterial strains Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Erysipelotrichaceae bacterium, and Subdolinogranulum spp.

69. 68. The method of claim 67, wherein the composition consists of purified bacterial strains of Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Dorea longicatena, and Subdolinogranulum spp.

70. 1. A method for inducing immune tolerance or hyposensitization to food allergy, comprising: administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains of a species selected from the group consisting of Clostridium indolis, Anaerostipes caccae, Lachnospiraceae bacterium, and Clostridium symbiosum; The method comprising:

71. 71. The method of claim 70, wherein the composition consists of purified bacterial strains Clostridium indolis, Anaerostipes caccae, Lachnospiraceae bacterium, and Clostridium symbiosum.

72. 1. A method for inducing immune tolerance or hyposensitization to food allergy, comprising: administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains of a species selected from the group consisting of Clostridium hathewayi, Clostridium bolteae, Sellimonas intestinalis, and Clostridium species; The method comprising:

73. 73. The method of claim 72, wherein the composition consists of purified bacterial strains Clostridium hathewayi, Clostridium bolteae, Sellimonas intestinalis and Clostridium species.

74. 1. A method for inducing immune tolerance or hyposensitization to food allergy, comprising: administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 1-8; The method comprising:

75. 75. The method of claim 74, wherein the composition consists of a purified bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleic acid sequence set forth as SEQ ID NOs: 1-5, 7, and 8.

76. 75. The method of claim 74, wherein the composition consists of a purified bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleic acid sequence set forth as SEQ ID NOs: 1-6 and 8.

77. 1. A method for inducing immune tolerance or hyposensitization to food allergy, comprising: administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO:10, SEQ ID NO:11; SEQ ID NO:13; and SEQ ID NO:4; The method comprising:

78. 78. The method of claim 77, wherein the composition consists of a purified bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleic acid sequences set forth as SEQ ID NO:10, SEQ ID NO:11; SEQ ID NO:13; and SEQ ID NO:

4.

79. 1. A method for inducing immune tolerance or hyposensitization to food allergy, comprising: administering to a subject in need thereof a therapeutically effective amount of a composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO:9, SEQ ID NO:1; SEQ ID NO:3; and SEQ ID NO:12; The method comprising:

80. 80. The method of claim 79, wherein the composition consists of a purified bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to the nucleic acid sequences set forth as SEQ ID NO:9, SEQ ID NO:1; SEQ ID NO:3; and SEQ ID NO:

12.

81. The method of any one of claims 67 to 80, which results in the induction of proliferation and / or accumulation of regulatory T cells.

82. 82. The method of any one of claims 67 to 81, which results in the production of IgE antibodies.

83. 83. The method of any one of claims 67 to 82, which results in the suppression of a Th2 immune response.

84. 84. The method of any one of claims 67 to 83, wherein the bacterial strain is freeze-dried.

85. 84. The method of any one of claims 67 to 83, wherein the bacterial strain is spray dried.

86. 86. The method of any one of claims 67 to 85, wherein one or more of the bacterial strains is in spore form.

87. 87. The method of any one of claims 67 to 86, wherein each of the bacterial strains is in spore form.

88. 87. The method of any one of claims 67 to 86, wherein one or more of the bacterial strains is in a vegetative form.

89. 89. The method of any one of claims 67 to 85 and 88, wherein each of the bacterial strains is in a vegetative form.

90. 90. The method of any one of claims 67 to 89, wherein the administration is oral administration.

91. 91. The method of any one of claims 67 to 90, wherein the composition is formulated for oral delivery.

92. 91. The method of any one of claims 67 to 90, wherein the composition is formulated for rectal delivery.

93. 93. The method of any one of claims 67 to 92, wherein the composition is formulated for delivery to the intestine.

94. 93. The method of any one of claims 67 to 92, wherein the composition is formulated for delivery to the colon.

95. 95. The method of any one of claims 67 to 94, wherein the food allergy is selected from the group consisting of nut allergy, fish allergy, wheat allergy, milk allergy, peanut allergy, tree nut allergy, shellfish allergy, soybean allergy, seed allergy, sesame seed allergy, and egg allergy.

96. The method of any one of claims 67 to 95, wherein the subject is a human.

97. 97. The method of any one of claims 67 to 96, wherein the composition further comprises one or more adjuvants.

98. 98. The method of claim 97, wherein the adjuvant is associated with allergy treatment or immune tolerance.

99. 99. The method of any one of claims 35 to 98, wherein the subject is administered an antibiotic prior to administration of the composition.

100. A composition comprising two or more purified bacterial strains of species selected from the group consisting of Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Erysipelotrichaceae bacterium, and Subdolinogranulum spp., and wherein the composition does not contain Dorea longicatena.

101. A composition comprising two or more purified bacterial strains selected from the group consisting of Clostridium bolteae, Anaerotruncus colihominis, Sellimonas intestinales, Clostridium symbiosum, Blautia producta, Dorea longicatena, and Subdolinogranulum spp., and wherein the composition does not contain Erysipelotrichaceae bacterium.

102. A composition comprising two or more purified bacterial strains selected from the group consisting of Clostridium indolis, Anaerostipes caccae, Lachnospiraceae bacterium, and Clostridium symbiosum.

103. A composition comprising two or more purified bacterial strains selected from the group consisting of Clostridium hathewayi, Clostridium bolteae, Sellimonas intestinalis, and Clostridium species.

104. 1. A composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 1-5, 7, and 8, wherein the composition does not include a bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence provided by SEQ ID NO:

6.

105. 1. A composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NOs: 1-6 and 8, wherein the composition does not include a bacterial strain comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence provided by SEQ ID NO:

7.

106. A composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO:10, SEQ ID NO:11; SEQ ID NO:13; and SEQ ID NO:

4.

107. A composition comprising two or more purified bacterial strains comprising a 16S rDNA sequence having at least 97% sequence identity to a nucleic acid sequence selected from SEQ ID NO:9, SEQ ID NO:1; SEQ ID NO:3; and SEQ ID NO:

12.

108. The composition according to any one of claims 100 to 107, which induces proliferation and / or accumulation of regulatory T cells.

109. The composition according to any one of claims 100 to 108, which suppresses IgE antibody production.

110. The composition of any one of claims 100 to 109, which suppresses a Th2 immune response.

111. 111. The composition of any one of claims 100 to 110, further comprising one or more adjuvants.

112. 112. The composition of claim 111, wherein the adjuvant is associated with allergy treatment or immune tolerance.

113. 113. A pharmaceutical composition comprising the composition of any one of claims 100 to 112, further comprising a pharmaceutically acceptable excipient.

114. 114. The pharmaceutical composition of claim 113, formulated for oral delivery.

115. 114. The pharmaceutical composition of claim 113, formulated for rectal delivery.

116. 116. The pharmaceutical composition of any one of claims 113 to 115, formulated for intestinal delivery.

117. 116. The pharmaceutical composition of any one of claims 113 to 115, formulated for delivery to the colon.

118. 113. A food product comprising a composition according to any one of claims 100 to 112 and nutrients.

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