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Since human microbiota study’s still in its infancy, strong, conclusive proof of symbiotic associations aren’t yet available. Rather, strong correlations are. Proof of symbiosis requires

  1. A specific bacterial species consistently associated with several humans across time.
  2. Abundance in health versus reduction in disease.
  3. Successful re-planting of such a species into a diseased body should fully or partially restore health.

Further, being genetically diverse, geographically widespread, and having extremely varied diets, human-microbe symbioses are probably redundant between bacterial species and even across genera. This makes the 3rd proposition difficult to prove. Decisive proof becomes even more difficult given bacterial species associated with humans are being identified at exponential pace. For e.g., in the GI tract alone, bacterial species identified have increased from ~300 in 1980 to ~1000 by 2010 due to molecular technologies  (see figure below from 1).

Substantial data supports at least the first two conditions in the example of Faecalibacterium (formerly Fusobacterium) prausnitzii, associated with the colon.

  • Presence confirmed by both culture (2) and 16SrRNA (3, 4, 5, 6), F. prausnitzii is one of the most abundant anaerobic bacteria in human colon and feces.
  • Possible symbiotic function? One of the main sources of colonic butyrate (3, 7), generally considered beneficial to intestinal health as well as a preferred energy source for colonic epithelial cells, the colonocytes (8, 9, 10).
  • Reduced presence in a variety of inflammatory bowel diseases (11, 12, 13, 14) including Crohn’s disease (15, 16, 17) and colorectal cancer (18, 19).

Bibliography

1. Rajilić-Stojanović, Mirjana, and Willem M. de Vos. “The first 1000 cultured species of the human gastrointestinal microbiota.” FEMS microbiology reviews 38.5 (2014): 996-1047. http://femsre.oxfordjournals.org…

2. Moore, W. E., and Lillian H. Moore. “Intestinal floras of populations that have a high risk of colon cancer.” Applied and environmental microbiology 61.9 (1995): 3202-3207. Intestinal floras of populations that have a high risk of colon cancer.

3. Hold, Georgina L., et al. “Oligonucleotide probes that detect quantitatively significant groups of butyrate-producing bacteria in human feces.” Applied and environmental microbiology 69.7 (2003): 4320-4324. Oligonucleotide Probes That Detect Quantitatively Significant Groups of Butyrate-Producing Bacteria in Human Feces

4. Suau, Antonia, et al. “Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut.” Applied and environmental microbiology 65.11 (1999): 4799-4807. Direct Analysis of Genes Encoding 16S rRNA from Complex Communities Reveals Many Novel Molecular Species within the Human Gut

5. Suau, Antonia, et al. “Fusobacterium prausnitzii and related species represent a dominant group within the human fecal flora.” Systematic and Applied Microbiology 24.1 (2001): 139-145. https://www.researchgate.net/pro…

6. Walker, Alan W., et al. “Dominant and diet-responsive groups of bacteria within the human colonic microbiota.” The ISME journal 5.2 (2011): 220-230. http://www.nature.com/ismej/jour…

7. Barcenilla, Adela, et al. “Phylogenetic relationships of butyrate-producing bacteria from the human gut.” Applied and environmental microbiology 66.4 (2000): 1654-1661. Phylogenetic Relationships of Butyrate-Producing Bacteria from the Human Gut

8. Hamer, Henrike M., et al. “Review article: the role of butyrate on colonic function.” Alimentary pharmacology & therapeutics 27.2 (2008): 104-119. http://onlinelibrary.wiley.com/d…

9. Pryde, Susan E., et al. “The microbiology of butyrate formation in the human colon.” FEMS microbiology letters 217.2 (2002): 133-139. http://femsle.oxfordjournals.org…

10. Roediger, W. E. W. “The colonic epithelium in ulcerative colitis: an energy-deficiency disease?.” The Lancet 316.8197 (1980): 712-715.

11. Sartor, R. Balfour. “Therapeutic correction of bacterial dysbiosis discovered by molecular techniques.” Proceedings of the National Academy of Sciences 105.43 (2008): 16413-16414. http://www.pnas.org/content/105/…

12. Cucchiara, Salvatore, et al. “The microbiota in inflammatory bowel disease in different age groups.” Digestive Diseases 27.3 (2009): 252-258.

13. Sokol, H., et al. “Low counts of Faecalibacterium prausnitzii in colitis microbiota.” Inflammatory bowel diseases 15.8 (2009): 1183-1189. https://www.researchgate.net/pro…

14. Schwiertz, Andreas, et al. “Microbiota in pediatric inflammatory bowel disease.” The Journal of pediatrics 157.2 (2010): 240-244. https://www.researchgate.net/pro…

15. Sokol, Harry, et al. “Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients.” Proceedings of the National Academy of Sciences 105.43 (2008): 16731-16736. http://www.pnas.org/content/105/…

16. Willing, Ben, et al. “Twin studies reveal specific imbalances in the mucosa‐associated microbiota of patients with ileal Crohn’s disease.” Inflammatory bowel diseases 15.5 (2009): 653-660. https://www.researchgate.net/pro…

17. Kang, Seungha, et al. “Dysbiosis of fecal microbiota in Crohn’s disease patients as revealed by a custom phylogenetic microarray.” Inflammatory bowel diseases 16.12 (2010): 2034-2042. https://www.researchgate.net/pro…

18. Balamurugan, Ramadass, et al. “Real‐time polymerase chain reaction quantification of specific butyrate‐producing bacteria, Desulfovibrio and Enterococcus faecalis in the feces of patients with colorectal cancer.” Journal of gastroenterology and hepatology 23.8pt1 (2008): 1298-1303. https://www.researchgate.net/pro…

19. Chen, Weiguang, et al. “Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer.” PloS one 7.6 (2012): e39743. http://www.plosone.org/article/f…

https://www.quora.com/Microbiology-What-different-kinds-of-symbioses-do-humans-have-with-bacteria/answer/Tirumalai-Kamala

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