Methods and compositions relating to microbial treatment and diagnosis of disorders
The present disclosure provides methods, systems, compositions, and kits to address the need for microbiome-related treatment of health conditions and disease. The present disclosure provides for treatment of metabolic conditions using microbial compositions.
1. A composition comprising:
(a) a first microbe with a 16S ribosomal RNA (rRNA) sequence comprising at least about 97% sequence identity to a 16S rRNA sequence from Clostridium beijerinckii;
(b) a second microbe with a 16S rRNA sequence comprising at least about 97% sequence identity to a 16S rRNA sequence from Akkermansia muciniphila;
(c) a third microbe with a 16S rRNA sequence comprising at least about 97% sequence identity to a 16S rRNA sequence from Clostridium butyricum;
(d) a fourth microbe with a 16S rRNA sequence comprising at least about 97% sequence identity to a 16S rRNA sequence from Eubacterium hallii ; and
(e) an enteric coating.
2. The composition of claim 1 , wherein said composition is suitable for oral delivery.
3. The composition of claim 1 , wherein said enteric-coating dissolves at a pH greater than at least about pH 6.5.
4. The composition of claim 1 , wherein said composition is suitable for administration to a human subject.
5. The composition of claim 1 , wherein said composition further comprises a prebiotic.
6. The composition of claim 5 , wherein said prebiotic is selected from the group consisting of: a complex carbohydrate, a complex sugar, a resistant dextrin, a resistant starch, an amino acid, a peptide, biotin, polydextrose, a fructooligosaccharide (FOS), a galactooligosaccharide (GOS), inulin, a starch, lignin, psyllium, chitin, chitosan, gum, guar gum, high amylose cornstarch (HAS), cellulose, β-glucan, hemi-cellulose, lactulose, mannooligosaccharide, mannan oligosaccharide (MOS), oligofructose-enriched inulin, an oligofructose, an oligodextrose, a tagatose, a trans-galactooligosaccharide, pectin, a resistant starch, xylooligosaccharide (XOS), and any combination thereof.
7. The composition of claim 5 , wherein said prebiotic comprises inulin.
8. The composition of claim 5 , wherein said prebiotic comprises fructooligosaccharide.
9. The composition of claim 5 , wherein said prebiotic comprises fructooligosaccharide and inulin.
10. The composition of claim 1 , wherein said composition comprises at least about 10 5 colony forming units (CFU) of each of said first, second, third, and fourth microbes.
11. The composition of claim 1 , wherein said composition comprises at least about 10 7 CFUs of said first microbe, said second microbe, said third microbe, said fourth microbe, or a combination thereof.
12. The composition of claim 1 , wherein said composition further comprises a microbe with a 16S rRNA sequence comprising at least about 85% sequence identity to a 16S rRNA sequence of a microbe selected from the group consisting of: Anaerostipes caccae, Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium infantis, Bifidobacterium longum, Butyrivibrio fibrisolvens, Clostridium acetobutylicum, Clostridium aminophilum, Clostridium colinum, Clostridium indolis, Clostridium orbiscindens, Enterococcus faecium, Eubacterium rectale, Faecalibacterium prausnitzii, Fibrobacter succinogenes, Oscillospira guilliermondii, Roseburia cecicola, Roseburia inulinivorans, Ruminococcus flavefaciens, Ruminococcus gnavus, Ruminococcus obeum, Streptococcus cremoris, Streptococcus faecium, Streptococcus infantis, Streptococcus mutans, Streptococcus thermophilus, Anaerofustis stercorihominis, Anaerostipes hadrus, Anaerotruncus colihominis, Clostridium sporogenes, Clostridium tetani, Coprococcus, Coprococcus eutactus, Eubacterium cylindroides, Eubacterium dolichum, Eubacterium ventriosum, Roseburia faeccis, Roseburia hominis , and Roseburia intestinalis.
13. The composition of claim 1 , wherein said composition is suitable for delivery to a small intestine, a large intestine, an ileum, or a combination thereof of a subject.
14. The composition of claim 1 , wherein said first microbe is Clostridium beijerinckii.
15. The composition of claim 1 , wherein said second microbe is Akkermansia muciniphila.
16. The composition of claim 1 , wherein said third microbe is Clostridium butyricum.
17. The composition of claim 1 , wherein said fourth microbe is Eubacterium hallii.
18. The composition of claim 1 , wherein said composition further comprises a microbe with a 16S rRNA sequence comprising at least about 97% sequence identity to a 16S rRNA sequence from Bifidobacterium infantis.
19. The composition of claim 1 , wherein said composition further comprises Bifidobacterium infantis.
20. A composition comprising: Clostridium beijerinckii, Akkermansia muciniphila, Clostridium butyricum, Eubacterium hallii , and an enteric coating.
21. The composition of claim 20 , wherein said composition is suitable for oral delivery to a subject.
22. The composition of claim 20 , wherein said enteric-coating dissolves at a pH greater than at least about pH 6.5.
23. The composition of claim 20 , wherein said composition is suitable for administration to a human subject.
24. The composition of claim 20 , wherein said composition further comprises a prebiotic.
25. The composition of claim 24 , wherein said prebiotic is selected from the group consisting of: a complex carbohydrate, a complex sugar, a resistant dextrin, a resistant starch, an amino acid, a peptide, biotin, polydextrose, a fructooligosaccharide (FOS), a galactooligosaccharide (GOS), inulin, a starch, lignin, psyllium, chitin, chitosan, gum, guar gum, high amylose cornstarch (HAS), cellulose, β-glucan, hemi-cellulose, lactulose, mannooligosaccharide, mannan oligosaccharide (MOS), oligofructose-enriched inulin, an oligofructose, an oligodextrose, a tagatose, a trans-galactooligosaccharide, pectin, a resistant starch, xylooligosaccharide (XOS), and any combination thereof.
26. The composition of claim 24 , wherein said prebiotic comprises inulin.
27. The composition of claim 24 , wherein said prebiotic comprises fructooligosaccharide.
28. The composition of claim 24 , wherein said prebiotic comprises inulin and fructooligosaccharide.
29. The composition of claim 20 , wherein said composition comprises at least about 10 5 colony forming units (CFU) of each of said Clostridium beijerinckii , said Akkermansia muciniphila , said Clostridium butyricum , and said Eubacterium hallii.
30. The composition of claim 20 , wherein said composition comprises at least about 10 7 colony forming units (CFU) of each of said Clostridium beijerinckii , said Akkermansia muciniphila , said Clostridium butyricum , and said Eubacterium hallii.
31. The composition of claim 20 , wherein said composition further comprises a microbe with a 16S rRNA sequence comprising at least about 85% sequence identity to a 16S rRNA sequence of a microbe selected from the group consisting of: Anaerostipes caccae, Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium infantis, Bifidobacterium longum, Butyrivibrio fibrisolvens, Clostridium acetobutylicum, Clostridium aminophilum, Clostridium colinum, Clostridium indolis, Clostridium orbiscindens, Enterococcus faecium, Eubacterium rectale, Faecalibacterium prausnitzii, Fibrobacter succinogenes, Oscillospira guilliermondii, Roseburia cecicola, Roseburia inulinivorans, Ruminococcus flavefaciens, Ruminococcus gnavus, Ruminococcus obeum, Streptococcus cremoris, Streptococcus faecium, Streptococcus infantis, Streptococcus mutans, Streptococcus thermophilus, Anaerofustis stercorihominis, Anaerostipes hadrus, Anaerotruncus colihominis, Clostridium sporogenes, Clostridium tetani, Coprococcus, Coprococcus eutactus, Eubacterium cylindroides, Eubacterium dolichum, Eubacterium ventriosum, Roseburia faeccis, Roseburia hominis , and Roseburia intestinalis.
32. The composition of claim 20 , wherein said composition is suitable for delivery to a small intestine, a large intestine, an ileum, or a combination thereof of a subject.
33. The composition of claim 20 , wherein said composition further comprises a microbe with a 16S rRNA sequence comprising at least about 97% sequence identity to a 16S rRNA sequence from Bifidobacterium infantis.
34. The composition of claim 20 , wherein said composition further comprises Bifidobacterium infantis.