Microbial consortium and uses thereof

Abstract

Provided herein are, inter alia, microbial compositions and methods of using the same. The microbial compositions provided include, inter alia, therapeutically effective amounts of Lactobacillus johnsonii, Faecalibacterium prausnitzii, Akkermansia muciniphila, Myxococcus xanthus and Pediococcus pentosaceus and are particularly useful for methods of treating and preventing inflammatory diseases.

What is claimed is: 
     
         1 . A pharmaceutical composition, comprising:
 a purified bacterial population comprising at least one strain of  Lactobacillus  sp., at least one strain of  Faecalibacterium  sp., and at least one strain of  Akkermansia  sp.,   wherein the at least one strain of  Lactobacillus  sp., the at least one strain of  Faecalibacterium  sp., and the at least one strain of  Akkermansia  sp. are at least 80% of the bacteria in the purified bacterial population,   wherein the purified bacterial population is present in an effective amount for reducing the incidence of allergic inflammation in a subject in need thereof, and   wherein the pharmaceutical composition is formulated as an oral dosage form for delivery to the gastrointestinal tract.   
     
     
         2 . The pharmaceutical composition of  claim 1 , wherein the at least one strain of  Lactobacillus  sp., the at least one strain of  Faecalibacterium  sp., and the at least one strain of  Akkermansia  sp. are at least 90% of the bacteria in the purified bacterial population. 
     
     
         3 . The pharmaceutical composition of  claim 1 , wherein the at least one strain of  Lactobacillus  sp., the at least one strain of  Faecalibacterium  sp., and the at least one strain of  Akkermansia  sp. are at least 95% of the bacteria in the purified bacterial population. 
     
     
         4 . The pharmaceutical composition of  claim 1 , wherein the at least one strain of  Lactobacillus  sp., the at least one strain of  Faecalibacterium  sp., and the at least one strain of  Akkermansia  sp. are at least 98% of the bacteria in the purified bacterial population. 
     
     
         5 . The pharmaceutical composition of  claim 1 , wherein the oral dosage form is in the form of a liquid, an emulsion or a powder. 
     
     
         6 . The pharmaceutical composition of  claim 1 , wherein the at least one strain of  Lactobacillus  sp. comprises  Lactobacillus johnsonii  or  Lactobacillus crispatus,  wherein the at least one strain of  Faecalibacterium  sp. comprises  Faecalibacterium prausnitzii,  and wherein the at least one strain of  Akkermansia  sp. comprises  Akkermansia muciniphila.    
     
     
         7 . The pharmaceutical composition of  claim 1 , wherein the at least one strain of  Lactobacillus  sp. comprises  Lactobacillus johnsonii  or  Lactobacillus crispatus.    
     
     
         8 . The pharmaceutical composition of  claim 1 , wherein the at least one strain of  Faecalibacterium  sp. comprises  Faecalibacterium prausnitzii.    
     
     
         9 . The pharmaceutical composition of  claim 1 , wherein the at least one strain of  Akkermansia  sp. comprises  Akkermansia muciniphila.    
     
     
         10 . The pharmaceutical composition of  claim 1 , wherein each member of the purified bacterial population is present in an amount of 10 3  to 10 15  colony forming units (cfu). 
     
     
         11 . A method of treating a subject that has or is at risk for developing an inflammatory disease, said method comprising:
 (i) obtaining a first biological sample from the subject;   (ii) measuring a first proportion of  Bifidobacteria  sp.,  Lactobacillus  sp.,  Faecalibacterium  sp. or  Akkermansia  sp. in the biological sample, wherein the first proportion of  Bifidobacteria  sp.,  Lactobacillus  sp.,  Faecalibacterium  sp. or  Akkermansia  sp. is reduced compared to a healthy or general population; and   (iii) administering to the subject an effective amount of a bacterial population comprising  Bifidobacteria  sp.  Lactobacillus  sp.,  Faecalibacterium  sp. or  Akkermansia  sp.   
     
     
         12 . The method of  claim 11 , wherein the biological sample is a bodily fluid. 
     
     
         13 . The method of  claim 12 , wherein the bodily fluid is blood, plasma, serum, fecal water, or a brancheoaleolar lavage. 
     
     
         14 . The method of  claim 13 , wherein the bodily fluid is fecal water. 
     
     
         15 . The method of  claim 11 , wherein the method further comprises
 (i) obtaining a second biological sample from the subject;   (ii) measuring a second proportion of  Bifidobacteria  sp.,  Lactobacillus  sp.,  Faecalibacterium  sp. or  Akkermansia  sp. in the second biological sample;   (iii) comparing the second proportion to the first proportion, thereby determining the effect of treatment.   
     
     
         16 . The method of  claim 11 , wherein the effective amount is effective to
 (i) increase the level of a  Bifidobacteria  sp.,  Lactobacillus  sp.,  Faecalibacterium  sp. or  Akkermansia  sp. in the subject;   (ii) lower the pH in the feces of the subject;   (iii) increase the level of lactic acid in the feces of the subject;   (iv) increase the level of circulating itaconate in the subject;   (v) treat, reduce, or reduce the incidence of allergic inflammation in the subject;   (vi) reduce an adaptive immune response in an airway of the subject;   (vii) reduce dendritic cell activation in a gastrointestinal-associated mesenteric lymph node;   (viii) increase the level of repair macrophages in the lungs, blood, serum, or plasma of the subject;   (ix) increase the level of an anti-inflammatory compound in the subject;   (x) decrease the level of a pro-inflammatory compound in the subject;   (xi) decrease the level of eotaxin expression and/or secretion in the subject; and/or   (xii) decrease the level of mucin expression and/or secretion in the subject.   
     
     
         17 . A method of treating a subject that has or is at risk for developing an inflammatory disease, said method comprising:
 (i) obtaining a biological sample from the subject;   (ii) measuring the level of a pro-inflammatory compound or an anti-inflammatory compound in the biological sample, wherein (a) the level of the anti-inflammatory compound is reduced compared to a healthy or general population, or (b) the level of the pro-inflammatory compound is increased compared to a healthy or general population; and   (iii) administering to the subject an effective amount of a bacterial population comprising  Bifidobacteria  sp.  Lactobacillus  sp.,  Faecalibacterium  sp. or  Akkermansia  sp.   
     
     
         18 . The method of  claim 17 , wherein the biological sample is a bodily fluid. 
     
     
         19 . The method of  claim 18 , wherein the bodily fluid is blood, plasma, serum, fecal water, or a brancheoaleolar lavage. 
     
     
         20 . The method of  claim 19 , wherein the bodily fluid is fecal water. 
     
     
         21 . The method of  claim 17 , wherein the effective amount is effective to
 (i) increase the level of a  Bifidobacteria  sp.,  Lactobacillus  sp.,  Faecalibacterium  sp. or  Akkermansia  sp. in the subject;   (ii) lower the pH in the feces of the subject;   (iii) increase the level of lactic acid in the feces of the subject;   (iv) increase the level of circulating itaconate in the subject;   (v) treat, reduce, or reduce the incidence of allergic inflammation in the subject;   (vi) reduce an adaptive immune response in an airway of the subject;   (vii) reduce dendritic cell activation in a gastrointestinal-associated mesenteric lymph node;   (viii) increase the level of repair macrophages in the lungs, blood, serum, or plasma of the subject;   (ix) increase the level of an anti-inflammatory compound in the subject;   (x) decrease the level of a pro-inflammatory compound in the subject;   (xi) decrease the level of eotaxin expression and/or secretion in the subject; and/or   (xii) decrease the level of mucin expression and/or secretion in the subject.   
     
     
         22 . The method of  claim 17 , wherein the measuring of the level of the proinflammatory or anti-inflammatory compound in the biological sample further comprises contacting an antigen presenting cell with the biological sample. 
     
     
         23 . The method of  claim 22 , wherein the antigen presenting cell is a dendritic cell. 
     
     
         24 . The method of  claim 22 , wherein the detecting of the level of a proinflammatory or anti-inflammatory compound in the biological sample further comprises contacting a naive T cell with the antigen presenting cell to produce a contacted T cell. 
     
     
         25 . The method of  claim 24 , further comprising detecting a cytokine produced by the contacted T cell or the progeny of the contacted T cell.