Microbial consortia

Abstract

Provided herein are microbial strains isolated de novo. In some instances, the bacterial strains include genera, species, and/or strains of Lactobacillus johnsonii, Lactobacillus crispatus, Faecalibacterium prausnitzii, Akkermansia muciniphila, Bifidobacterium longum , and/or Bifidobacterium longum infantis strains. These bacterial strains can be used in the treatment of dysbiosis, inflammation, and other disorders.

1 .- 72 . (canceled) 
     
     
         73 . A pharmaceutical composition, wherein said pharmaceutical composition comprises at most about 50% of  Akkermansia muciniphila  DSM 33213 by weight of said pharmaceutical composition, and wherein said pharmaceutical composition is formulated as an oral dosage. 
     
     
         74 . The pharmaceutical composition of  claim 73 , wherein said oral dosage form comprises a liquid dosage form. 
     
     
         75 . The pharmaceutical composition of  claim 73 , wherein said pharmaceutical composition is lyophilized or frozen. 
     
     
         76 . The pharmaceutical composition of  claim 75 , wherein said pharmaceutical composition is lyophilized. 
     
     
         77 . The pharmaceutical composition of  claim 75 , wherein said pharmaceutical composition is frozen. 
     
     
         78 . The pharmaceutical composition of  claim 73 , further comprising  Lactobacillus  sp. or  Faecalibacterium  sp. 
     
     
         79 . The pharmaceutical composition of  claim 78 , further comprising said  Lactobacillus  sp. and said  Faecalibacterium  sp. 
     
     
         80 . The pharmaceutical composition of  claim 78 , further comprising  Lactobacillus  crispatus or  Faecalibacterium prausnitzii.    
     
     
         81 . The pharmaceutical composition of  claim 78 , further comprising  Lactobacillus  crispatus and  Faecalibacterium prausnitzii.    
     
     
         82 . A method for modulating an immune response in a subject, comprising administering to said subject a composition comprising (1)  Akkermansia  sp. that produces a phospholipid or (2) said phospholipid,
 wherein in said phospholipid, an amine group is attached to an oxygen atom of a phosphate group via an ethyl group, and   wherein, when assayed from 7 days to 28 days subsequent to said administering:   (1) a fecal sample of said subject has an increased level of said phospholipid, relative to a level of said phospholipid in a fecal sample of a subject not administered with said composition; or (2) a blood sample of said subject has an increased level of said phospholipid, relative to a level of said phospholipid in a blood sample of said subject not administered with said composition.   
     
     
         83 . The method of  claim 82 , wherein, when assayed at 7 days, 14 days, 21 days, or 28 days subsequent to said administering,
 (1) said fecal sample of said subject has said increased level of said phospholipid, relative to said level of said phospholipid in said fecal sample of said subject not administered with said composition; or   (2) said blood sample of said subject has said increased level of said phospholipid, relative to said level of said phospholipid in said blood sample of said subject not administered with said composition.   
     
     
         84 . The method of  claim 82 , wherein, when assayed from 7 days to 28 days using mass spectroscopy subsequent to said administering:
 (1) said fecal sample of said subject has said increased level of said phospholipid, relative to said level of said phospholipid in said fecal sample of said subject not administered with said composition; or   (2) said blood sample of said subject has said increased level of said phospholipid, relative to said level of said phospholipid in said blood sample of said subject not administered with said composition.   
     
     
         85 . The method of  claim 82 , wherein said composition is administered to said subject as an oral dosage form. 
     
     
         86 . The method of  claim 82 , wherein said subject is less than about 24 months old. 
     
     
         87 . The method of  claim 86 , wherein said subject is a neonate. 
     
     
         88 . The method of  claim 82 , wherein said subject has a disease or a risk of said disease, wherein said disease comprises dysbiosis, inflammatory disease, autoimmune disorder, infection, cancer, or any combination thereof. 
     
     
         89 . The method of  claim 88 , wherein said disease comprises said inflammatory disease. 
     
     
         90 . The method of  claim 89 , wherein said inflammatory disease comprises an acne vulgaris, an Addison's disease, an allergic asthma, an allergy, an ankylosing spondylitis, an arthritis, an asthma, an atherosclerosis, an atopic dermatitis, an atopy, an autoimmune disease, an auto-immune thyroiditis, an autoinflammatory disease, a Behcet's disease, a bullous pemphigoid, a Celiac disease, a chronic persistent diarrhea, a chronic prostatitis, a colitis, a collagenous colitis, a Crohn's disease, a diabetes mellitus type 1, a diverticulitis, an erythema nodosum, a glomerulonephritis, a Graves ophthalmopathy, a Guillain-Barre syndrome, a Hashimoto's encephalitis, a Hashimoto's thyroiditis, a hypersensitivity, an ichthyosis, an immunoproliferative small intestinal disease, an inflammatory bowel disease, an interstitial cystitis, an intractable diarrhea of infancy, an irritable bowel syndrome, a juvenile idiopathic arthritis, a juvenile onset diabetes, a lymphocytic colitis, a multiple sclerosis, a myasthenia gravis, a pediatric allergic asthma, a pelvic inflammatory disease, a postenteritis syndrome, a psoriasis, a psoriatic arthritis, a pyoderma gangrenosum, a reperfusion injury, a rheumatoid arthritis, a sarcoidosis, a sarcoidosis, a short bowel syndrome, a Sjogren's syndrome, a stagnant loop syndrome, a systemic lupus erythematosus (SLE), a transplant rejection, a traumatic brain injury, a Traveler's diarrhea, a tropical sprue, an ulcerative colitis, an uveitis, a vasculitis, a Vitiligo, a Whipple's disease, or a Wolman disease. 
     
     
         91 . The method of  claim 82 , wherein said composition is lyophilized or frozen. 
     
     
         92 . The method of  claim 82 , wherein said composition further comprises  Lactobacillus  sp. or  Faecalibacterium  sp.