What are friendly bacteria that aid with the bodys biological functions such as digestion resident bacteria protozoans viruses fungi?

1. Bengmark S. (1998) Ecological control of the gastrointestinal tract. The role of probiotic flora. Gut 42, 2–7 doi: 10.1136/gut.42.1.2 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

2. Backhed F. (2005) Host-bacterial mutualism in the human intestine. Science 307, 1915–1920 doi: 10.1126/science.1104816 [PubMed] [CrossRef] [Google Scholar]

3. Neish A.S. (2009) Microbes in gastrointestinal health and disease. Gastroenterology 136, 65–80 doi: 10.1053/j.gastro.2008.10.080 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

4. Gill S.R., Pop M., DeBoy R.T., Eckburg P.B., Turnbaugh P.J., Samuel B.S. et al. (2006) Metagenomic analysis of the human distal gut microbiome. Science 312, 1355–1359 doi: 10.1126/science.1124234 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

5. Sender R., Fuchs S. and Milo R. (2016) Revised estimates for the number of human and bacteria cells in the body. bioRxiv [PMC free article] [PubMed] [Google Scholar]

6. Luckey T.D. (1972) Introduction to intestinal microecology. Am. J. Clin. Nutr. 25, 1292–1294 [PubMed] [Google Scholar]

7. Natividad J.M.M. and Verdu E.F. (2013) Modulation of intestinal barrier by intestinal microbiota: Pathological and therapeutic implications. Pharmacol. Res. 69, 42–51 doi: 10.1016/j.phrs.2012.10.007 [PubMed] [CrossRef] [Google Scholar]

8. den Besten G., van Eunen K., Groen A.K., Venema K., Reijngoud D.-J., Bakker B.M. (2013) The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. J. Lipid Res. 54, 2325–2340 doi: 10.1194/jlr.R036012 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

9. Bäumler A.J. and Sperandio V. (2016) Interactions between the microbiota and pathogenic bacteria in the gut. Nature 535, 85–93 doi: 10.1038/nature18849 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

10. Gensollen T., Iyer S.S., Kasper D.L., Blumberg R.S. (2016) How colonization by microbiota in early life shapes the immune system. Science 352, 539–544 doi: 10.1126/science.aad9378 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

11. Chang C. and Lin H. (2016) Dysbiosis in gastrointestinal disorders. Best Pract. Res. Clin. Gastroenterol. 30, 3–15 doi: 10.1016/j.bpg.2016.02.001 [PubMed] [CrossRef] [Google Scholar]

12. Schroeder B.O. and Bäckhed F. (2016) Signals from the gut microbiota to distant organs in physiology and disease. Nat. Med. 22, 1079–1089 doi: 10.1038/nm.4185 [PubMed] [CrossRef] [Google Scholar]

13. Moore W.E.C. and Holdeman L.V. (1974) Human fecal flora - normal flora of 20 Japanese-hawaiians. Appl. Microbiol. 27, 961–979 [PMC free article] [PubMed] [Google Scholar]

14. Poretsky R., Rodriguez-R L.M., Luo C., Tsementzi D., Konstantinidis K.T., Rodriguez-Valera F. (2014) Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics. PLoS ONE 9, e93827 doi: 10.1371/journal.pone.0093827 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

15. Mizrahi-Man O., Davenport E.R., Gilad Y., and White B.A. (2013) Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs. PLoS ONE 8, e53608 doi: 10.1371/journal.pone.0053608 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

16. Suau A., et al. (1999) Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl. Environ. Microbiol. 65, 4799–4807 [PMC free article] [PubMed] [Google Scholar]

17. Hugon P., Dufour J.-C., Colson P., Fournier P.-E., Sallah K., Raoult D. (2015) A comprehensive repertoire of prokaryotic species identified in human beings. Lancet Infect. Dis. 15, 1211–1219 doi: 10.1016/S1473-3099(15)00293-5 [PubMed] [CrossRef] [Google Scholar]

18. Li J., Jia H., Cai X., Zhong H., Feng Q., Sunagawa S. et al. (2014) An integrated catalog of reference genes in the human gut microbiome. Nat. Biotechnol. 32, 834–841 doi: 10.1038/nbt.2942 [PubMed] [CrossRef] [Google Scholar]

19. Schluter J., Foster K.R., Ellner S.P. (2012) The evolution of mutualism in gut microbiota via host epithelial selection. PLoS Biol. 10, e1001424 doi: 10.1371/journal.pbio.1001424 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

20. Costello E.K., Lauber C.L., Hamady M., Fierer N., Gordon J.I., Knight R. (2009) Bacterial community variation in human body habitats across space and time. Science 326, 1694–1697 doi: 10.1126/science.1177486 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

21. Pérez-Cobas A.E., Gosalbes M.J., Friedrichs A., Knecht H., Artacho A., Eismann K. et al. (2013) Gut microbiota disturbance during antibiotic therapy: a multi-omic approach. Gut 62, 1591–1601 doi: 10.1136/gutjnl-2012-303184 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

22. Moya A. and Ferrer M. (2016) Functional redundancy-Induced stability of Gut microbiota subjected to disturbance. Trends Microbiol. 24, 402–413 doi: 10.1016/j.tim.2016.02.002 [PubMed] [CrossRef] [Google Scholar]

23. Aagaard K., Ma J., Antony K.M., Ganu R., Petrosino J., Versalovic J. (2014) The placenta harbors a unique microbiome. Sci. Transl. Med. 6, 237ra65 doi: 10.1126/scitranslmed.3008599 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

24. Rodriguez J.M., et al. (2015) The composition of the gut microbiota throughout life, with an emphasis on early life. Microb. Ecol. Health Dis. 26, 26050. [PMC free article] [PubMed] [Google Scholar]

25. Koenig J.E., Spor A., Scalfone N., Fricker A.D., Stombaugh J., Knight R. et al. (2011) Succession of microbial consortia in the developing infant gut microbiome. Proc. Natl. Acad. Sci. U.S.A. 108(Suppl 1), 4578–4585 doi: 10.1073/pnas.1000081107 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

26. Avershina E., Storrø O., Øien T., Johnsen R., Pope P., Rudi K. (2014) Major faecal microbiota shifts in composition and diversity with age in a geographically restricted cohort of mothers and their children. FEMS Microbiol. Ecol. 87, 280–290 doi: 10.1111/1574-6941.12223 [PubMed] [CrossRef] [Google Scholar]

27. Aagaard K., Riehle K., Ma J., Segata N., Mistretta T.-A., Coarfa C. et al. (2012) A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. PLoS ONE 7, e36466 doi: 10.1371/journal.pone.0036466 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

28. Jakobsson H.E., Abrahamsson T.R., Jenmalm M.C., Harris K., Quince C., Jernberg C. et al. (2014) Decreased gut microbiota diversity, delayed Bacteroidetes colonisation and reduced Th2 responses in infants delivered by caesarean section. Gut 63, 559–566 doi: 10.1136/gutjnl-2012-303249 [PubMed] [CrossRef] [Google Scholar]

29. Salminen S. (2004) Influence of mode of delivery on gut microbiota composition in seven year old children. Gut 53, 1388–1389 doi: 10.1136/gut.2004.041640 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

30. Backhed F., Roswall J., Peng Y., Feng Q., Jia H., Kovatcheva-Datchary P. et al. (2015) Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe 17, 852 doi: 10.1016/j.chom.2015.05.012 [PubMed] [CrossRef] [Google Scholar]

31. Bäckhed F. (2011) Programming of host metabolism by the gut microbiota. Ann. Nutr. Metab. 58(Suppl 2), 44–52 doi: 10.1159/000328042 [PubMed] [CrossRef] [Google Scholar]

32. Palmer C., Bik E.M., DiGiulio D.B., Relman D.A., Brown P.O., Ruan Y. (2007) Development of the human infant intestinal microbiota. PLoS Biol. 5, e177 doi: 10.1371/journal.pbio.0050177 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

33. Dethlefsen L. and Relman D.A. (2011) Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc. Natl. Acad. Sci. U.S.A. 108, 4554–4561 doi: 10.1073/pnas.1000087107 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

34. Claesson M.J., Cusack S., O'Sullivan O., Greene-Diniz R., de Weerd H., Flannery E. et al. (2011) Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc. Natl. Acad. Sci. U.S.A. 108(Supplement 1), 4586–4591 doi: 10.1073/pnas.1000097107 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

35. Biagi E., Nylund L., Candela M., Ostan R., Bucci L., Pini E. et al. (2010) Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians. PLoS ONE 5, e10667 doi: 10.1371/journal.pone.0010667 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

36. Claesson M.J., et al. (2012) Gut microbiota composition correlates with diet and health in the elderly. Nature 488, 178–+ [PubMed] [Google Scholar]

37. Woodmansey E.J., McMurdo M.E.T., Macfarlane G.T., Macfarlane S. (2004) Comparison of compositions and metabolic activities of fecal microbiotas in young adults and in antibiotic-treated and non-antibiotic-treated elderly subjects. Appl. Environ. Microbiol. 70, 6113–6122 doi: 10.1128/AEM.70.10.6113-6122.2004 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

38. Biagi E., Candela M., Turroni S., Garagnani P., Franceschi C., Brigidi P. (2013) Ageing and gut microbes: perspectives for health maintenance and longevity. Pharmacol. Res. 69, 11–20 doi: 10.1016/j.phrs.2012.10.005 [PubMed] [CrossRef] [Google Scholar]

39. Macpherson A.J. and McCoy K.D. (2013) Stratification and compartmentalisation of immunoglobulin responses to commensal intestinal microbes. Semin. Immunol. 25, 358–363 doi: 10.1016/j.smim.2013.09.004 [PubMed] [CrossRef] [Google Scholar]

40. Donaldson G.P., Lee S.M. and Mazmanian S.K. (2015) Gut biogeography of the bacterial microbiota. Nat. Rev. Microbiol. 14, 20–32 doi: 10.1038/nrmicro3552 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

41. Gu S., Chen D., Zhang J.-N., Lv X., Wang K., Duan L.-P. et al. (2013) Bacterial community mapping of the mouse gastrointestinal tract. PLoS ONE 8, e74957 doi: 10.1371/journal.pone.0074957 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

42. Eckburg P.B. (2005) Diversity of the human intestinal microbial flora. Science 308, 1635–1638 doi: 10.1126/science.1110591 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

43. Lavelle A., et al. (2015) Spatial variation of the colonic microbiota in patients with ulcerative colitis and control volunteers. Gut [PMC free article] [PubMed] [Google Scholar]

44. Van den Abbeele P., Belzer C., Goossens M., Kleerebezem M., De Vos W.M., Thas O. et al. (2013) Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model. ISME J. 7, 949–961 doi: 10.1038/ismej.2012.158 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

45. Li H., Limenitakis J.P., Fuhrer T., Geuking M.B., Lawson M.A., Wyss M. et al. (2015) The outer mucus layer hosts a distinct intestinal microbial niche. Nat. Commun. 6, 8292 doi: 10.1038/ncomms9292 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

46. Turnbaugh P.J., Hamady M., Yatsunenko T., Cantarel B.L., Duncan A., Ley R.E. et al. (2009) A core gut microbiome in obese and lean twins. Nature 457, 480–484 doi: 10.1038/nature07540 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

47. Jakobsson H.E., Jernberg C., Andersson A.F., Sjölund-Karlsson M., Jansson J.K., Engstrand L. et al. (2010) Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS ONE 5 doi: 10.1371/journal.pone.0009836 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

48. Ding T. and Schloss P.D. (2014) Dynamics and associations of microbial community types across the human body. Nature 509, 357–360 doi: 10.1038/nature13178 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

49. Arumugam M., Raes J., Pelletier E., Le Paslier D., Yamada T., Mende D.R. et al. (2011) Enterotypes of the human gut microbiome. Nature 473, 174–180 doi: 10.1038/nature09944 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

50. Jeffery I.B., Claesson M.J., O'Toole P.W., Shanahan F. (2012) Categorization of the gut microbiota: enterotypes or gradients? Nat. Rev. Microbiol. 10, 591–592 doi: 10.1038/nrmicro2859 [PubMed] [CrossRef] [Google Scholar]

51. Hooper L.V. and Macpherson A.J. (2010) Immune adaptations that maintain homeostasis with the intestinal microbiota. Nat. Rev. Immunol. 10, 159–169 doi: 10.1038/nri2710 [PubMed] [CrossRef] [Google Scholar]

52. Ley R.E., Peterson D.A. and Gordon J.I. (2006) Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124, 837–848 doi: 10.1016/j.cell.2006.02.017 [PubMed] [CrossRef] [Google Scholar]

53. Travisano M. and Velicer G.J. (2004) Strategies of microbial cheater control. Trends Microbiol. 12, 72–78 doi: 10.1016/j.tim.2003.12.009 [PubMed] [CrossRef] [Google Scholar]

54. Zoetendal E.G. Raes J., van den Bogert B., Arumugam M., Booijink C.C.G.M., Troost F.J. et al. (2012) The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. ISME J. 6, 1415–1426 doi: 10.1038/ismej.2011.212 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

55. David L.A., Maurice C.F., Carmody R.N., Gootenberg D.B., Button J.E., Wolfe B.E. et al. (2013) Diet rapidly and reproducibly alters the human gut microbiome. Nature 505, 559–563 doi: 10.1038/nature12820 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

56. Walker A.W., Ince J., Duncan S.H., Webster L.M., Holtrop G., Ze X. et al. (2011) Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J. 5, 220–230 doi: 10.1038/ismej.2010.118 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

57. Yu Z.T., Chen C., Kling D.E., Liu B., McCoy J.M., Merighi M. et al. (2013) The principal fucosylated oligosaccharides of human milk exhibit prebiotic properties on cultured infant microbiota. Glycobiology 23, 169–177 doi: 10.1093/glycob/cws138 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

58. Marcobal A., Barboza M., Sonnenburg E.D., Pudlo N., Martens E.C., Desai P. et al. (2011) Bacteroides in the infant gut consume milk oligosaccharides via mucus-utilization pathways. Cell Host Microbe 10, 507–514 doi: 10.1016/j.chom.2011.10.007 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

59. Bezirtzoglou E., Tsiotsias A. and Welling G.W. (2011) Microbiota profile in feces of breast- and formula-fed newborns by using fluorescence in situ hybridization (FISH). Anaerobe 17, 478–482 doi: 10.1016/j.anaerobe.2011.03.009 [PubMed] [CrossRef] [Google Scholar]

60. Penders J., Thijs C., Vink C., Stelma F.F., Snijders B., Kummeling I. et al. (2006) Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics 118, 511–521 doi: 10.1542/peds.2005-2824 [PubMed] [CrossRef] [Google Scholar]

61. Favier C.F., Vaughan E.E., De Vos W.M., Akkermans A.D.L. (2002) Molecular monitoring of succession of bacterial communities in human neonates. Appl. Environ. Microbiol. 68, 219–226 doi: 10.1128/AEM.68.1.219-226.2002 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

62. Kau A.L., et al. (2015) Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy. Sci. Transl. Med. 7, 276ra24 [PMC free article] [PubMed] [Google Scholar]

63. De Filippo C., Cavalieri D., Di Paola M., Ramazzotti M., Poullet J.B., Massart S. et al. (2010) Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl. Acad. Sci. U.S.A. 107, 14691–14696 doi: 10.1073/pnas.1005963107 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

64. Wu G.D., Chen J., Hoffmann C., Bittinger K., Chen Y.-Y., Keilbaugh S.A. et al. (2011) Linking long-term dietary patterns with gut microbial enterotypes. Science 334, 105–108 doi: 10.1126/science.1208344 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

65. Sonnenburg E.D. and Sonnenburg J.L. (2014) Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates. Cell Metab. 20, 779–786 doi: 10.1016/j.cmet.2014.07.003 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

66. Sonnenburg E.D., Smits S.A., Tikhonov M., Higginbottom S.K., Wingreen N.S., Sonnenburg J.L. (2016) Diet-induced extinctions in the gut microbiota compound over generations. Nature 529, 212–215 doi: 10.1038/nature16504 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

67. Blanton L.V., Charbonneau M.R., Salih T., Barratt M.J., Venkatesh S., Ilkaveya O. et al. (2016) Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children. Science 351, aad3311 doi: 10.1126/science.aad3311 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

68. Charbonneau M.R., O'Donnell D., Blanton L.V., Totten S.M., Davis J.C.C., Barratt M.J. et al. (2016) Sialylated milk oligosaccharides promote microbiota-Dependent growth in models of infant undernutrition. Cell 164, 859–871 doi: 10.1016/j.cell.2016.01.024 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

69. Schwarzer M., Makki K., Storelli G., Machuca-Gayet I., Srutkova D., Hermanova P. et al. (2016) Lactobacillus plantarum strain maintains growth of infant mice during chronic undernutrition. Science 351, 854–857 doi: 10.1126/science.aad8588 [PubMed] [CrossRef] [Google Scholar]

70. Tailford L.E., Owen C.D., Walshaw J., Crost E.H., Hardy-Goddard J., Le Gall G. et al. (2015) Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation. Nat. Commun. 6, 7624 doi: 10.1038/ncomms8624 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

71. Arike L. and Hansson G.C. (2016) The densely O-glycosylated MUC2 mucin protects the intestine and provides food for the commensal bacteria. J. Mol. Biol [PMC free article] [PubMed] [Google Scholar]

72. Ouwerkerk J.P., de Vos W.M., Belzer B. (2013) Glycobiome: Bacteria and mucus at the epithelial interface. Best Pract. Res. Clin. Gastroenterol. 27, 25–38 doi: 10.1016/j.bpg.2013.03.001 [PubMed] [CrossRef] [Google Scholar]

73. Johansson M.E.V., Larsson J.M.H. and Hansson G.C. (2011) The two mucus layers of colon are organized by the MUC2 mucin, whereas the outer layer is a legislator of host-microbial interactions. Proc. Natl. Acad. Sci. U.S.A. 108(Suppl 1), 4659–4665 doi: 10.1073/pnas.1006451107 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

74. Gustafsson J.K., Ermund A., Johansson M.E.V., Schutte A., Hansson G.C., Sjovall H. (2012) An ex vivo method for studying mucus formation, properties, and thickness in human colonic biopsies and mouse small and large intestinal explants. Am. J. Physiol. Gastrointest. Liver Physiol. 302, G430–G438 doi: 10.1152/ajpgi.00405.2011 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

75. Johansson M.E., Jakobsson H.E., Holmén-Larsson J., Schütte A., Ermund A., Rodríguez-Piñeiro A.M. et al. (2015) Normalization of host intestinal mucus layers requires long-Term microbial colonization. Cell Host Microbe 18, 582–592 doi: 10.1016/j.chom.2015.10.007 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

76. Juge N. (2012) Microbial adhesins to gastrointestinal mucus. Trends Microbiol. 20, 30–39 doi: 10.1016/j.tim.2011.10.001 [PubMed] [CrossRef] [Google Scholar]

77. Tailford L.E., Crost E.H., Kavanaugh D., Juge N. (2015) Mucin glycan foraging in the human gut microbiome. Frontiers in Genetics. 6, 131 doi: 10.3389/fgene.2015.00081 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

78. Rausch P., Rehman A., Kunzel S., Hasler R., Ott S.J., Schreiber S. et al. (2011) Colonic mucosa-associated microbiota is influenced by an interaction of crohn disease and FUT2 (Secretor) genotype. Proc Natl Acad Sci U.S.A. 108, 19030–19035 doi: 10.1073/pnas.1106408108 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

79. Arpaia N., Campbell C., Fan X., Dikiy S., van der Veeken J., deRoos P. et al. (2013) Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature. 504, 451–455 doi: 10.1038/nature12726 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

80. Furusawa Y., Obata Y., Fukuda S., Endo T.A., Nakato G., Takahashi D. et al. (2013) Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature. 504, 446–450 doi: 10.1038/nature12721 [PubMed] [CrossRef] [Google Scholar]

81. Zarepour M., Bhullar K., Montero M., Ma C., Huang T., Velcich A. et al. (2013) The mucin MUC2 limits pathogen burdens and epithelial barrier dysfunction during salmonella enterica serovar typhimurium colitis. Infect Immun. 81, 3672–3683 doi: 10.1128/IAI.00854-13 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

82. Earle K.A., Billings G., Sigal M., Lichtman J.S., Hansson G.C., Elias J.E. et al. (2015) Quantitative imaging of gut microbiota spatial organization. Cell Host Microbe 18, 478–488 doi: 10.1016/j.chom.2015.09.002 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

83. Desai M.S., Seekatz A.M., Koropatkin N.M., Kamada N., Hickey C.A., Wolter M. et al. (2016) A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell. 167, 1339–1353.e21 doi: 10.1016/j.cell.2016.10.043 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

84. Everard A., Belzer C., Geurts L., Ouwerkerk J.P., Druart C., Bindels L.B. et al. (2013) Cross-talk between akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc Natl Acad Sci U.S.A. 110, 9066–9071 doi: 10.1073/pnas.1219451110 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

85. Li J., Lin S., Vanhoutte P.M., Woo C.W., Xu A. (2016) Akkermansia muciniphila protects against atherosclerosis by preventing metabolic endotoxemia-induced inflammation in apoe-/- mice. Circulation. 133, 2434–2446 doi: 10.1161/CIRCULATIONAHA.115.019645 [PubMed] [CrossRef] [Google Scholar]

86. Plovier H., Everard A., Druart C., Depommier C., Van Hul M., Geurts L. et al. (2016) A purified membrane protein from akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice. Nat Med. 23, 107–113 doi: 10.1038/nm.4236 [PubMed] [CrossRef] [Google Scholar]

87. Zhao S., Liu W., Wang J., Shi J., Sun Y., Wang W. et al. (2017) Akkermansia muciniphila improves metabolic profiles by reducing inflammation in chow diet-fed mice. J Mol Endocrinol. 58, 1–14 doi: 10.1530/JME-16-0054 [PubMed] [CrossRef] [Google Scholar]

88. Cockburn D.W. and Koropatkin N.M. (2016) Polysaccharide degradation by the intestinal microbiota and its influence on human health and disease. J Mol Biol. 428, 3230–3252 doi: 10.1016/j.jmb.2016.06.021 [PubMed] [CrossRef] [Google Scholar]

89. El Kaoutari A., Armougom F., Gordon J.I., Raoult D., Henrissat B. (2013) The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nat Rev Microbiol. 11, 497–504 doi: 10.1038/nrmicro3050 [PubMed] [CrossRef] [Google Scholar]

90. Cantarel B.L., Lombard V., Henrissat B. and Appanna V.D. (2012) Complex carbohydrate utilization by the healthy human microbiome. PLoS One. 7, e28742 doi: 10.1371/journal.pone.0028742 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

91. Larsbrink J., Rogers T.E., Hemsworth G.R., McKee L.S., Tauzin A.S., Spadiut O. et al. (2014) A discrete genetic locus confers xyloglucan metabolism in select human gut bacteroidetes. Nature. 506, 498–502 doi: 10.1038/nature12907 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

92. Rogowski A., Briggs J.A., Mortimer J.C., Tryfona T., Terrapon N., Lowe E.C. et al. (2015) Glycan complexity dictates microbial resource allocation in the large intestine. Nat Commun. 6, 7481 doi: 10.1038/ncomms8481 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

93. Cuskin F., Lowe E.C., Temple M.J., Zhu Y., Cameron E.A., Pudlo N.A. et al. (2015) Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism. Nature. 517, 165–169 doi: 10.1038/nature13995 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

94. Tauzin A.S., Kwiatkowski K.J., Orlovsky N.I., Smith C.J., Creagh A.L., Haynes C.A. et al. (2016) Molecular dissection of xyloglucan recognition in a prominent human Gut symbiont. MBio. 7, e02134–15 doi: 10.1128/mBio.02134-15 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

95. Foley M.H., Cockburn D.W. and Koropatkin N.M. (2016) The Sus operon: a model system for starch uptake by the human gut bacteroidetes. Cell Mol Life Sci. 73, 2603–2617 doi: 10.1007/s00018-016-2242-x [PMC free article] [PubMed] [CrossRef] [Google Scholar]

96. Glenwright A.J., Pothula K.R., Bhamidimarri S.P., Chorev D.S., Baslé A., Firbank S.J. et al. (2017) Structural basis for nutrient acquisition by dominant members of the human gut microbiota. Nature. 541, 407–411 doi: 10.1038/nature20828 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

97. Ze X., et al. (2015) Unique organization of extracellular amylases into amylosomes in the resistant starch-utilizing human colonic firmicutes bacterium Ruminococcus bromii. MBio. 6, e01058–15 [PMC free article] [PubMed] [Google Scholar]

98. Bjedov I. (2003) Stress-induced mutagenesis in bacteria. Science. 300, 1404–1409 doi: 10.1126/science.1082240 [PubMed] [CrossRef] [Google Scholar]

99. Xu J., et al. (2007) Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol. 5, 1574–1586 [Google Scholar]

100. Svanback R. and Bolnick D.I. (2007) Intraspecific competition drives increased resource use diversity within a natural population. Proceedings of the Royal Society B-Biological Sciences. 274, 839–844 doi: 10.1098/rspb.2006.0198 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

101. Emerson B.C. and Kolm N. (2005) Species diversity can drive speciation. Nature 434, 1015–1017 doi: 10.1038/nature03450 [PubMed] [CrossRef] [Google Scholar]

102. Louis P. and Flint H.J. (2016) Formation of propionate and butyrate by the human colonic microbiota. Environ Microbiol [Google Scholar]

103. Ze X., Duncan S.H., Louis P., Flint H.J. (2012) Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. ISME J 6, 1535–1543 doi: 10.1038/ismej.2012.4 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

104. Louis P., Scott K.P., Duncan S.H. and Flint H.J. (2007) Understanding the effects of diet on bacterial metabolism in the large intestine. Journal of Applied Microbiology 102, 1197–1208 doi: 10.1111/j.1365-2672.2007.03322.x [PubMed] [CrossRef] [Google Scholar]

105. Duncan S.H., Louis P. and Flint H.J. (2004) Lactate-utilizing bacteria, isolated from human feces, that produce butyrate as a major fermentation product. Appl Environ Microbiol 70, 5810–5817 doi: 10.1128/AEM.70.10.5810-5817.2004 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

106. Rakoff-Nahoum S., Foster K.R. and Comstock L.E. (2016) The evolution of cooperation within the gut microbiota. Nature 533, 255–259 doi: 10.1038/nature17626 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

107. Juge N., Tailford L. and Owen C.D. (2016) Sialidases from gut bacteria: a mini-review. Biochem Soc Trans 44, 166–175 doi: 10.1042/BST20150226 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

108. Crost E.H., Tailford L.E., Le Gall G., Fons M., Henrissat B., Juge N. et al. (2013) Utilisation of mucin glycans by the human Gut symbiont ruminococcus gnavus Is strain-Dependent. PLoS One 8, e76341 doi: 10.1371/journal.pone.0076341 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

109. Crost E.H., et al. (2016) The mucin-degradation strategy of ruminococcus gnavus: The importance of intramolecular trans-sialidases. Gut Microbes 1–11 [PMC free article] [PubMed] [Google Scholar]

110. Larsson J.M.H., Karlsson H., Crespo J.G., Johansson M.E.V., Eklund L., Sjövall H. et al. (2011) Altered o-glycosylation profile of MUC2 mucin occurs in active ulcerative colitis and is associated with increased inflammation. Inflamm Bowel Dis 17, 2299–2307 doi: 10.1002/ibd.21625 [PubMed] [CrossRef] [Google Scholar]

111. Carbonero F., Benefiel A.C., Alizadeh-Ghamsari A.H., Gaskins H.R. (2012) Microbial pathways in colonic sulfur metabolism and links with health and disease. Front Physiol 3, 448 doi: 10.3389/fphys.2012.00448 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

112. Ridlon J.M., Kang D.J., Hylemon P.B., Bajaj J.S. (2014) Bile acids and the gut microbiome. Curr Opin Gastroenterol 30, 332–338 doi: 10.1097/MOG.0000000000000057 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

113. Staley C., Weingarden A.R., Khoruts A., Sadowsky M.J. (2017) Interaction of gut microbiota with bile acid metabolism and its influence on disease states. Appl Microbiol Biotechnol 101, 47–64 doi: 10.1007/s00253-016-8006-6 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

114. Browne H.P., Forster S.C., Anonye B.O., Kumar N., Neville B.A., Stares M.D. et al. (2016) Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation. Nature 533, 543–546 doi: 10.1038/nature17645 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

115. Kakiyama G., Pandak W.M., Gillevet P.M., Hylemon P.B., Heuman D.M., Daita K. et al. (2013) Modulation of the fecal bile acid profile by gut microbiota in cirrhosis. J Hepatol 58, 949–955 doi: 10.1016/j.jhep.2013.01.003 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

116. Hooper L.V., Littman D.R. and Macpherson A.J. (2012) Interactions between the microbiota and the immune system. Science 336, 1268–1273 doi: 10.1126/science.1223490 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

117. Macpherson A.J. (2000) A primitive T cell-independent mechanism of intestinal mucosal IgA responses to commensal bacteria. Science 288, 2222–2226 doi: 10.1126/science.288.5474.2222 [PubMed] [CrossRef] [Google Scholar]

118. Macpherson A.J. and Uhr T. (2004) Induction of protective IgA by intestinal dendritic cells carrying commensal bacteria. Science 303, 1662–1665 doi: 10.1126/science.1091334 [PubMed] [CrossRef] [Google Scholar]

119. Cash H.L. (2006) Symbiotic bacteria direct expression of an intestinal bactericidal lectin. Science 313, 1126–1130 doi: 10.1126/science.1127119 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

120. McGuckin M.A., Lindén S.K., Sutton P. and Florin T.H. (2011) Mucin dynamics and enteric pathogens. Nat Rev Microbiol 9, 265–278 doi: 10.1038/nrmicro2538 [PubMed] [CrossRef] [Google Scholar]

121. Meyer-Hoffert U., Hornef M.W., Henriques-Normark B., Axelsson L.-G., Midtvedt T., Putsep K. et al. (2008) Secreted enteric antimicrobial activity localises to the mucus surface layer. Gut 57, 764–771 doi: 10.1136/gut.2007.141481 [PubMed] [CrossRef] [Google Scholar]

122. Wehkamp J. (2004) NOD2 (CARD15) mutations in crohn's disease are associated with diminished mucosal alpha-defensin expression. Gut 53, 1658–1664 doi: 10.1136/gut.2003.032805 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

123. Wehkamp J., Salzman N.H., Porter E., Nuding S., Weichenthal M., Petras R.E. et al. (2005) Reduced paneth cell alpha-defensins in ileal crohn's disease. Proc Natl Acad Sci U.S.A 102, 18129–18134 doi: 10.1073/pnas.0505256102 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

124. Rogier E.W., Frantz A., Bruno M. and Kaetzel C. (2014) Secretory IgA is concentrated in the outer layer of colonic mucus along with gut bacteria. Pathogens 3, 390–403 doi: 10.3390/pathogens3020390 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

125. Bollinger R.R.., Everett M.L., Palestrant D., Love S.D., Lin S.S. and Parker W. (2003) Human secretory immunoglobulin A May contribute to biofilm formation in the gut. Immunology 109, 580–587 doi: 10.1046/j.1365-2567.2003.01700.x [PMC free article] [PubMed] [CrossRef] [Google Scholar]

126. Friman V., et al. (1996) Decreased expression of mannose-specific adhesins by Escherichia coli in the colonic microflora of immunoglobulin A-deficient individuals. Infect Immun 64, 2794–2798 [PMC free article] [PubMed] [Google Scholar]

127. Suzuki K., Meek B., Doi Y., Muramatsu M., Chiba T., Honjo T. et al. (2004) Aberrant expansion of segmented filamentous bacteria in IgA-deficient gut. Proc Natl Acad Sci U.S.A. 101, 1981–1986 doi: 10.1073/pnas.0307317101 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

128. Biedermann L., Zeitz J., Mwinyi J., Sutter-Minder E., Rehman A., Ott S.J. et al. (2013) Smoking cessation induces profound changes in the composition of the intestinal microbiota in humans. PLoS One 8, e59260 doi: 10.1371/journal.pone.0059260 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

129. Jiang H., Ling Z., Zhang Y., Mao H., Ma Z., Yin Y. et al. (2015) Altered fecal microbiota composition in patients with major depressive disorder. Brain Behavior and Immunity 48, 186–194 doi: 10.1016/j.bbi.2015.03.016 [PubMed] [CrossRef] [Google Scholar]

130. Tyakht A.V., Kostryukova E.S., Popenko A.S., Belenikin M.S., Pavlenko A.V., Larin A.K. et al. (2013) Human gut microbiota community structures in urban and rural populations in russia. Nature Commun 4, 2469 doi: 10.1038/ncomms3469 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

131. Maurice C.F., Haiser H.J. and Turnbaugh P.J. (2013) Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 152, 39–50 doi: 10.1016/j.cell.2012.10.052 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

132. Jernberg C., Löfmark S., Edlund C. and Jansson J.K. (2007) Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J 1, 56–66 doi: 10.1038/ismej.2007.3 [PubMed] [CrossRef] [Google Scholar]

133. Ferrer M., Martins dos Santos V.A.P., Ott S.J. and Moya A. (2014) Gut microbiota disturbance during antibiotic therapy: a multi-omic approach. Gut Microbes 5, 64–70 doi: 10.4161/gmic.27128 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

134. Ge X., Ding C., Zhao W., Xu L., Tian H., Gong J. et al. (2017) Antibiotics-induced depletion of mice microbiota induces changes in host serotonin biosynthesis and intestinal motility. J Transl Med 15, 13 doi: 10.1186/s12967-016-1105-4 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

135. Ng K.M., Ferreyra J.A., Higginbottom S.K., Lynch J.B., Kashyap P.C., Gopinath S. et al. (2013) Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens. Nature 502, 96–99 doi: 10.1038/nature12503 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

136. Musso G., Gambino R. and Cassader M. (2010) Obesity, diabetes, and gut microbiota: The hygiene hypothesis expanded? Diabetes Care 33, 2277–2284 doi: 10.2337/dc10-0556 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

137. Louis P., Hold G.L. and Flint H.J. (2014) The gut microbiota, bacterial metabolites and colorectal cancer. Nat Rev Microbiol 12, 661–672 doi: 10.1038/nrmicro3344 [PubMed] [CrossRef] [Google Scholar]

138. Corrêa-Oliveira R., Fachi J.L., Vieira A., Sato F.T. and Vinolo M.A.R. (2016) Regulation of immune cell function by short-chain fatty acids. Clin Transl Immunol 5, e73 doi: 10.1038/cti.2016.17 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

139. Macfarlane S. and Macfarlane G.T. (2003) Regulation of short-chain fatty acid production. Proc Nutr Soc 62, 67–72 doi: 10.1079/PNS2002207 [PubMed] [CrossRef] [Google Scholar]

140. Morrison D.J. and Preston T. (2016) Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism. Gut Microbes 7, 189–200 doi: 10.1080/19490976.2015.1134082 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

141. Derrien M. (2004) Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. Int J Syst Evol Microbiol 54(Pt 5), 1469–1476 doi: 10.1099/ijs.0.02873-0 [PubMed] [CrossRef] [Google Scholar]

142. Guarner F. and Malagelada J.R. (2003) Gut flora in health and disease. Lancet 361, 512–519 doi: 10.1016/S0140-6736(03)12489-0 [PubMed] [CrossRef] [Google Scholar]

143. Lin L. and Zhang J. (2017) Role of intestinal microbiota and metabolites on gut homeostasis and human diseases. BMC Immunol. 18 [PMC free article] [PubMed] [Google Scholar]

144. Donohoe D.R., Collins L.B., Wali A., Bigler R., Sun W. and Bultman S.J. (2012) The warburg effect dictates the mechanism of butyrate-mediated histone acetylation and cell proliferation. Mol Cell. 48, 612–626 doi: 10.1016/j.molcel.2012.08.033 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

145. Chambers E.S., Morrison D.J. and Frost G. (2015) Control of appetite and energy intake by SCFA: what are the potential underlying mechanisms? Proc Nutr Soc. 74, 328–336 doi: 10.1017/S0029665114001657 [PubMed] [CrossRef] [Google Scholar]

146. Pingitore A., et al. (2016) The diet-derived short chain fatty acid propionate improves beta-cell function in humans and stimulates insulin secretion from human islets in vitro. Diabetes Obes. Metab. 19, 257–265 doi: 10.1111/dom.12811 [PubMed] [CrossRef] [Google Scholar]

147. Byrne C.S., Chambers E.S., Alhabeeb H., Chhina N., Morrison D.J., Preston T. et al. (2016) Increased colonic propionate reduces anticipatory reward responses in the human striatum to high-energy foods. Am J Clin Nutr. 104, 5–14 doi: 10.3945/ajcn.115.126706 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

148. Nagai M., Obata Y., Takahashi D. and Hase K. (2016) Fine-tuning of the mucosal barrier and metabolic systems using the diet-microbial metabolite axis. Int Immunopharmacol. 37, 79–86 doi: 10.1016/j.intimp.2016.04.001 [PubMed] [CrossRef] [Google Scholar]

149. LeBlanc J.G., Milani C., de Giori G.S., Sesma F., van Sinderen D. and Ventura M. (2013) Bacteria as vitamin suppliers to their host: a gut microbiota perspective. Current Opinion in Biotechnology. 24, 160–168 doi: 10.1016/j.copbio.2012.08.005 [PubMed] [CrossRef] [Google Scholar]

150. Martens J.H., Barg H., Warren M. and Jahn D. (2002) Microbial production of vitamin B-12. Applied Microbiology and Biotechnology. 58, 275–285 doi: 10.1007/s00253-001-0902-7 [PubMed] [CrossRef] [Google Scholar]

151. Pompei A., Cordisco L., Amaretti A., Zanoni S., Matteuzzi D. and Rossi M. (2007) Folate production by bifidobacteria as a potential probiotic property. Appl Environ Microbiol. 73, 179–185 doi: 10.1128/AEM.01763-06 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

152. Hill M.J. (1997) Intestinal flora and endogenous vitamin synthesis. European Journal of Cancer Prevention. 6, S43–S45 doi: 10.1097/00008469-199703001-00009 [PubMed] [CrossRef] [Google Scholar]

153. Palau-Rodriguez M., Tulipani S., Isabel Queipo-Ortuño M., Urpi-Sarda M., Tinahones F.J. and Andres-Lacueva C. (2015) Metabolomic insights into the intricate gut microbial-host interaction in the development of obesity and type 2 diabetes. Front Microbiol. 6, 1151 doi: 10.3389/fmicb.2015.01151 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

154. Smith K., McCoy K.D. and Macpherson A.J. (2007) Use of axenic animals in studying the adaptation of mammals to their commensal intestinal microbiota. Seminars in Immunology. 19, 59–69 doi: 10.1016/j.smim.2006.10.002 [PubMed] [CrossRef] [Google Scholar]

155. Swanson P.A. II, Kumar A., Samarin S., Vijay-Kumar M., Kundu K., Murthy N. et al. (2011) Enteric commensal bacteria potentiate epithelial restitution via reactive oxygen species-mediated inactivation of focal adhesion kinase phosphatases. Proc Natl Acad Sci U.S.A. 108, 8803–8808 doi: 10.1073/pnas.1010042108 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

156. Reunanen J., et al. (2015) Akkermansia muciniphila adheres to enterocytes and strengthens the integrity of epithelial cell layer. Appl Environ Microbiol [PMC free article] [PubMed] [Google Scholar]

157. Chen H.Q., Yang J., Zhang M., Zhou Y.-K., Shen T.-Y., Chu Z.-X. et al. (2010) Lactobacillus plantarum ameliorates colonic epithelial barrier dysfunction by modulating the apical junctional complex and PepT1 in IL-10 knockout mice. Am J Physiol Gastrointest Liver Physiol. 299, G1287–G1297 doi: 10.1152/ajpgi.00196.2010 [PubMed] [CrossRef] [Google Scholar]

158. Petersson J., Schreiber O., Hansson G.C., Gendler S.J., Velcich A., Lundberg J.O. et al. (2011) Importance and regulation of the colonic mucus barrier in a mouse model of colitis. Am J Physiol Gastrointest Liver Physiol. 300, G327–G333 doi: 10.1152/ajpgi.00422.2010 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

159. Wrzosek L., Miquel S., Noordine M.-L., Bouet S., Chevalier-Curt M., Robert V. et al. (2013) Bacteroides thetaiotaomicron and faecalibacterium prausnitzii influence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent. BMC Biol. 11, 61 doi: 10.1186/1741-7007-11-61 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

160. Graziani F., Pujol A., Nicoletti C., Dou S., Maresca M., Giardina T. et al. (2016) Ruminococcus gnavus E1 modulates mucin expression and intestinal glycosylation. J Appl Microbiol. 120, 1403–1417 doi: 10.1111/jam.13095 [PubMed] [CrossRef] [Google Scholar]

161. Varyukhina S., Freitas M., Bardin S., Robillard E., Tavan E., Sapin C. et al. (2012) Glycan-modifying bacteria-derived soluble factors from bacteroides thetaiotaomicron and lactobacillus casei inhibit rotavirus infection in human intestinal cells. Microbes Infect. 14, 273–278 doi: 10.1016/j.micinf.2011.10.007 [PubMed] [CrossRef] [Google Scholar]

162. Freitas M., Cayuela C., Antoine J.-M., Piller F., Sapin C. and Trugnan G. (2001) A heat labile soluble factor from bacteroides thetaiotaomicron VPI-5482 specifically increases the galactosylation pattern of HT29-MTX cells. Cell Microbiol. 3, 289–300 doi: 10.1046/j.1462-5822.2001.00113.x [PubMed] [CrossRef] [Google Scholar]

163. Mazmanian S.K., Liu C.H., Tzianabos A.O. and Kasper D.L. (2005) An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell. 122, 107–118 doi: 10.1016/j.cell.2005.05.007 [PubMed] [CrossRef] [Google Scholar]

164. Hevia A., Delgado S., Sánchez B. and Margolles A. (2015) Molecular players involved in the interaction between beneficial bacteria and the immune system. Front Microbiol. 6, 1285 doi: 10.3389/fmicb.2015.01285 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

165. Schnupf P., Gaboriau-Routhiau V., Gros M., Friedman R., Moya-Nilges M., Nigro G. et al. (2015) Growth and host interaction of mouse segmented filamentous bacteria in vitro. Nature. 520, 99–103 doi: 10.1038/nature14027 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

166. Candela M., Biagi E., Maccaferri S., Turroni S. and Brigidi P. (2012) Intestinal microbiota is a plastic factor responding to environmental changes. Trends Microbiol. 20, 385–391 doi: 10.1016/j.tim.2012.05.003 [PubMed] [CrossRef] [Google Scholar]

167. Ellekilde M., Krych L., Hansen C.H.F., Hufeldt M.R., Dahl K., Hansen L.H. et al. (2014) Characterization of the gut microbiota in leptin deficient obese mice - correlation to inflammatory and diabetic parameters. Res Vet Sci. 96, 241–250 doi: 10.1016/j.rvsc.2014.01.007 [PubMed] [CrossRef] [Google Scholar]

168. Hansen C.H., Krych L., Nielsen D.S., Vogensen F.K., Hansen L.H., Sørensen S.J. et al. (2012) Early life treatment with vancomycin propagates akkermansia muciniphila and reduces diabetes incidence in the NOD mouse. Diabetologia. 55, 2285–2294 doi: 10.1007/s00125-012-2564-7 [PubMed] [CrossRef] [Google Scholar]

169. Le Chatelier E., Nielsen T., Qin J., Prifti E., Hildebrand F., Falony G. et al. (2013) Richness of human gut microbiome correlates with metabolic markers. Nature. 500, 541–546 doi: 10.1038/nature12506 [PubMed] [CrossRef] [Google Scholar]

170. Wang L., Christophersen C.T., Sorich M.J., Gerber J.P., Angley M.T. and Conlon M.A. (2011) Low relative abundances of the mucolytic bacterium akkermansia muciniphila and bifidobacterium spp. in feces of children with autism. Appl Environ Microbiol. 77, 6718–6721 doi: 10.1128/AEM.05212-11 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

171. Derrien M., Belzer C. and de Vos W.M. (2016) Akkermansia muciniphila and its role in regulating host functions. Microb. Pathog. doi: 10.1016/j.micpath.2016.02.005 [PubMed] [CrossRef] [Google Scholar]

172. Sokol H., Seksik P., Furet J.P., Firmesse O., Nion-Larmurier I., Beaugerie L. et al. (2009) Low counts of faecalibacterium prausnitzii in colitis microbiota. Inflamm Bowel Dis. 15, 1183–1189 doi: 10.1002/ibd.20903 [PubMed] [CrossRef] [Google Scholar]

173. Lopez-Siles M., et al. (2017) Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics. ISME J. doi: 10.1038/ismej.2016.176 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

174. Quévrain E., Maubert M.A., Michon C., Chain F., Marquant R., Tailhades J. et al. (2016) Identification of an anti-inflammatory protein from faecalibacterium prausnitzii, a commensal bacterium deficient in crohn's disease. Gut. 65, 415–425 doi: 10.1136/gutjnl-2014-307649 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

175. Ferreyra J.A., Wu K.J., Hryckowian A.J., Bouley D.M., Weimer B.C., Sonnenburg J.L. et al. (2014) Gut microbiota-produced succinate promotes C. difficile infection after antibiotic treatment or motility disturbance. Cell Host Microbe 16, 770–777 doi: 10.1016/j.chom.2014.11.003 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

176. Huang Y.L., Chassard C., Hausmann M., von Itzstein M. and Hennet T. (2015) Sialic acid catabolism drives intestinal inflammation and microbial dysbiosis in mice. Nat Commun. 6, 8141 doi: 10.1038/ncomms9141 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

177. Mathias A., Pais B., Favre L., Benyacoub J. and Corthésy B. (2014) Role of secretory IgA in the mucosal sensing of commensal bacteria. Gut Microbes. 5, 688–695 doi: 10.4161/19490976.2014.983763 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

178. Rios D., Wood M.B., Li J., Chassaing B., Gewirtz A.T. and Williams I.R. (2016) Antigen sampling by intestinal M cells is the principal pathway initiating mucosal IgA production to commensal enteric bacteria. Mucosal Immunol. 9, 907–916 doi: 10.1038/mi.2015.121 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

179. Jandhyala S.M. (2015) Role of the normal gut microbiota. World J Gastroenterol. 21, 8787–8803 doi: 10.3748/wjg.v21.i29.8787 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

180. Guinane C.M. and Cotter P.D. (2013) Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ. Therap Adv Gastroenterol. 6, 295–308 doi: 10.1177/1756283X13482996 [PMC free article] [PubMed] [CrossRef] [Google Scholar]

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