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Intestine Offers Board and Lodging for Intestinal Microbes on a Short- or Long-Term Stay

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Metabolism of Alimentary Compounds by the Intestinal Microbiota and Health
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Abstract

The gut microbiota is a complex mixture of bacteria, archaea, viruses, and fungi. Approximately 150 different bacterial species can be identified at the individual level, but the heterogeneity of composition is important when comparing individuals between them. Ecological basis for such many species corresponds likely to the large number of substrates that are available for the global bacterial metabolic activity. Most studies have been performed using fecal samples, thus representing the microbiota composition representative of the distal part of the large intestine, and only a few analyses have been performed in the different parts of the intestinal tract. In the small intestine, the transit of the luminal fluid is rapid, and the concentration of bacteria is low and progressively increases from the duodenum to the ileum. In contrast, in the large intestine, the transit is considerably slowed down and the bacteria concentration is much higher. The intestinal tract is rapidly colonized after birth, and the intestinal microbiota composition found in neonates moves progressively within the first 3 years to the adult composition. Thereafter, the bacterial composition stays relatively stable. Interestingly, the composition of milk has an impact on the metabolic activity of intestinal bacteria in infants. The microbiota composition and metabolic activity depend mainly on environmental parameters, including alimentary parameters. The intestinal microbiota evolves in very old individuals, and the reasons for such changes are likely multifactorial.

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References

  1. Lighthart K, Belzer C, de Vos WM, Tytgat HLP. Bridging bacteria and the gut: functional aspects of type IV pili. Trends Microbiol. 2020;28(5):340–8.

    Article  Google Scholar 

  2. Palmela C, Chevarin C, Xu Z, Torres J, Sevrin G, Hirten R, Barnich N, Ng SC, Colombel JF. Adherent-invasive Escherichia coli in inflammarory bowel disease. Gut. 2018;67(3):574–87.

    Article  CAS  PubMed  Google Scholar 

  3. Rolhion N, Darfeuille-Michaud A. Adherent-invasive Escherichia coli in inflammatory bowel disease. Inflamm Bowel Dis. 2007;13(10):1277–83.

    Article  PubMed  Google Scholar 

  4. Matijasic M, Mestrovic T, Paljetak HC, Peric M, Baresic A, Verbanac D. Gut microbiota beyond bacteria-mycobiome, virome, archeome, and eukaryotic parasites in IBD. Int J Mol Sci. 2020;21(8):2668.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Valentine DL. Adaptations to energy stress dictate the ecology and evolution of Archea. Nat Rev Microbiol. 2007;5(4):316–23.

    Article  CAS  PubMed  Google Scholar 

  6. Janssen PH, Kirs M. Structure of the archeal community of the rumen. Appl Env Microbiol. 2008;74(12):3619–25.

    Article  CAS  Google Scholar 

  7. Raymann K, Moeller AH, Goodman AL, Ochman H. Unexplored archeal diversity in the great ape gut microbiome. mSphere. 2017;2(1):00026–17.

    Article  Google Scholar 

  8. Gaci N, Borrel G, Tottey W, O’Toole PW, Brugère JF. Archaea and the human gut: new beginning of an old story. World J Gastroenterol. 2014;20(43):16062–78.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Wanpach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanamasy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C, Wilmes P. Colonization and succession within the human gut microbiome by archea, bacteria, and microeukaryotes during the first year of life. Front Microbiol. 2017;8:738.

    Article  Google Scholar 

  10. Samuel BS, Gordon JI. A humanized gnotobiotic mouse model of host-archeal-bacterial mutualism. Proc Natl Acad Sci U S A. 2006;103(26):10011–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Dridi B, Henry M, El Khéchine A, Raoult D, Drancourt M. High prevalence of Methanobrevibacter smithii and methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol. PLoS One. 2009;4(9):e7063.

    Article  PubMed  PubMed Central  Google Scholar 

  12. Carding SR, Davis N, Hoyles L. Review article: the human intestine virome in health and disease. Aliment Pharmacol Ther. 2017;46(9):800–15.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Sausset R, Petit MA, Gaboriau-Routhiau V, De Paepe M. New insights into intestinal phages. Mucosal Immunol. 2020;13(2):205–15.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Balfour Sartor R, Wu GD. Roles for intestinal bacteria, viruses, and fungi in pathogenesis of inflammatory bowel diseases and therapeutic approaches. Gastroenterology. 2017;152(2):327–39.

    Article  PubMed  Google Scholar 

  15. Hallen Adams HE, Suhr MJ. Fungi in the healthy human gastrointestinal tract. Virulence. 2017;8(3):352–8.

    Article  CAS  PubMed  Google Scholar 

  16. Mukherjee PK, Sendid B, Hoarau G, Colombel JF, Poulain D, Ghannoum MA. Mycobiota in gastrointestinal diseases. Nat Rev Gastroenterol Hepatol. 2015;12(2):77–87.

    Article  PubMed  Google Scholar 

  17. Paterson MJ, Oh S, Underhill DM. Host-microbe interactions: commensal fungi in the gut. Curr Opin Microbiol. 2017;40:131–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Lacour M, Zunder T, Huber R, Sander A, Daschner F, Frank U. The pathogenic significance of intestinal Candida colonization. A systematic review from an interdisciplinary and environmental medical point of view. Int J Hyg Environ Health. 2002;205(4):257–68.

    Article  PubMed  Google Scholar 

  19. Burgess SL, Gilchrist CA, Lynn TC, Petri WA Jr. Parasitic protozoan and interactions with the host intestinal microbiota. Infect Immunol. 2017;85(8):e00101–17.

    Article  CAS  Google Scholar 

  20. Salazar N, Valdés-Varela L, Gonzalez S, Gueimonde M, de Los Reyes-Gavilan CG. Nutrition and the gut microbiome in the elderly. Gut Microbes. 2017;8(2):82–97.

    Article  CAS  PubMed  Google Scholar 

  21. Ley RE, Peterson DA, Gordon JI. Ecological and evolutionary forcers shaping microbial diversity in the human intestine. Cell. 2006;124(4):837–48.

    Article  CAS  PubMed  Google Scholar 

  22. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA. Diversity of the human intestinal microbial flora. Science. 2005;308(5728):1635–8.

    Article  PubMed  PubMed Central  Google Scholar 

  23. Sender R, Fuchs S, Milo R. Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell. 2016;164(3):337–40.

    Article  CAS  PubMed  Google Scholar 

  24. Calvez J, Benoit S, Piedcoq J, Khodorova N, Azzout-Marniche D, Tomé D, Benamouzig R, Airinei G, Gaudichon C. Very low ileal nitrogen and amino acid digestibility of zein compared to whey protein isolate in healthy volunteers. Am J Clin Nutr. 2021;113(1):70–82.

    Article  PubMed  Google Scholar 

  25. Chacko A, Cummings JH. Nitrogen losses from the human small bowel: obligatory losses and the effect of physical form of food. Gut. 1988;29(6):809–15.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Jimenez E, Marin ML, Martin R, Odriozola JM, Olivares M, Xaus J, Fernandez L, Rodriguez JM. Is meconium from healthy newborns really sterile? Res Microbiol. 2008;159(3):187–93.

    Article  CAS  PubMed  Google Scholar 

  27. Aagaard K, Ma J, Antony KM, Ganu R, Petrosino J, Versalovic J. The placenta harbors a unique microbiome. Sci Transl Med. 2014;6(237):237ra65.

    Article  PubMed  PubMed Central  Google Scholar 

  28. Di Giulio DB, Romero R, Amogan HP, Kusanovic JP, Bik EM, Gotsch F, Kim CJ, Erez O, Edwin S, Relman DA. Microbial prevalence, diversity and abundance in amniotic fluid during preterm labor: a molecular and culture-based investigation. PLoS One. 2008;3(8):e3056.

    Article  Google Scholar 

  29. Ardissone AN, de la Cruz DM, Davis-Richardson AG, Rechcigl KT, Li N, Drew JC, Murgas-Torrazza R, Sharma R, Hudak ML, Triplett EW, Neu J. Meconium microbiome analysis identifies bacteria correlated with premature birth. PLoS One. 2014;9(3):e90784.

    Article  PubMed  PubMed Central  Google Scholar 

  30. Moles L, Gomez M, Heilig H, Bustos G, Fuentes S, de Vos W, Fernandez L, Rodriguez JM, Jimenez E. Bacterial diversity in meconium of preterm neonates and evolution of their fecal microbiota during the first month of life. PLoS One. 2013;8(6):e66986.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Milani C, Duranti S, Bottacini F, Casey E, Turroni F, Mahony J, Belzer C, Delgado Palacio S, Arboleya Montes S, Mancabelli L, Lugli GA, Rodriguez JM, Bode L, de Vos W, Geuimonde M, Margolles A, van Sinderen D, Ventura M. The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota. Microbiol Mol Biol Rev. 2017;81(4):e00036–17.

    Article  PubMed  PubMed Central  Google Scholar 

  32. Palmer C, Bik EM, Di Giulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. PLoS Biol. 2007;5(7):e177.

    Article  PubMed  PubMed Central  Google Scholar 

  33. Healey GR, Murphy R, Brough L, Butts CA, Coad J. Interindividual variability in gut microbiota and host response to dietary interventions. Nutr Rev. 2017;75(12):1059–80.

    Article  PubMed  Google Scholar 

  34. Houghteling PD, Walker WA. Why is initial bacterial colonization of the intestine important to infants’ and children’ health? J Pediatr Gastroenterol Nutr. 2015;60(3):294–307.

    Article  PubMed  PubMed Central  Google Scholar 

  35. Matamoros S, Gras-Leguen C, Le Vacon F, Potel G, de La Cochetiere MF. Development of intestinal microbiota in infants and its impact on health. Trends Microbiol. 2013;21(4):167–73.

    Article  CAS  PubMed  Google Scholar 

  36. Rodriguez JM, Murphy K, Stanton C, Ross RP, Kober OI, Juge N, Avershina E, Rudi K, Narbad A, Jenmalm MC, Marchesi JR, Collado MC. The composition of the gut microbiota throughout life, with an emphasis on early life. Microbiol Ecol Health Dis. 2015;26:26050.

    Google Scholar 

  37. Yassour M, Vatanen T, Siljander H, Hämäläinen AM, Härkönen T, Ryhänen SJ, Franzoca EA, Vlamakis H, Huttenhower C, Gevers D, Lander ES, Knip M, DIABIMMUNE study Group, Xavier RJ. Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Sci Transl Med. 2016;8(343):343ra81.

    Article  PubMed  PubMed Central  Google Scholar 

  38. Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, Knight R. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A. 2010;107(26):11971–5.

    Article  PubMed  PubMed Central  Google Scholar 

  39. Chu DM, Ma J, Prince AL, Antony KM, Seferovic MD, Aagaard KM. Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Nat Med. 2017;23(3):314–26.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, Tito RY, Chaffron S, Rymenans L, Verspecht C, De Sutter L, Lima-Mendez G, D’Hoe K, Jonckeere K, Homola D, Garcia R, Tigchelaar EF, Eeckhaudt L, Fu J, Henckaerts L, Zhernakova A, Wijmenga C, Raes J. Population-level analysis of gut microbiome variation. Science. 2016;352(6285):560–4.

    Article  CAS  PubMed  Google Scholar 

  41. Bezirtzoglou E, Tsiotsias A, Welling GW. Microbiota profile in feces of breast- and formula- fed newborns by using in situ hybridization (FISH). Anaerobe. 2011;17(6):478–82.

    Article  PubMed  Google Scholar 

  42. He X, Parenti M, Grip T, Lönnerdal B, Timby N, Domelöff M, Hernell O, Slupsky CM. Fecal microbiome and metabolome of infants fed bovine MFGM supplemented formula or standard formula with breast-fed infants as reference: a randomized controlled study. Sci Rep. 2019;9(1):11589.

    Article  PubMed  PubMed Central  Google Scholar 

  43. Bode L. Human milk oligosachharides: prebiotics and beyond. Nutr Rev. 2009;67(S2):S183–91.

    Article  PubMed  Google Scholar 

  44. Smilowitz JT, Lebrilla CB, Mills DA, Bruce German J, Freeman SL. Breast milk oligosaccharides: structure-function relationships in the neonate. Annu Rev Nutr. 2014;34:143–69.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Andreas NJ, Kampmann B, Mehring Le-Doare K. Human breast milk: a review on its composition and bioactivity. Early Hum Dev. 2015;91(11):629–35.

    Article  CAS  PubMed  Google Scholar 

  46. Moubareck CA. Human milk microbiota and oligosaccharides: a glimpse into benefits, diversity, and correlations. Nutrients. 2021;13(4):1123.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Morrow AL, Ruiz-Palacios GM, Altaye M, Jiang X, Guerrero ML, Meinzen-Derr JK, Farkas T, Chaturvedi P, Pickering LK, Newburg DS. Human milk oligosachharide blood group epitopes and innate immune protection against campylobacter and calicivirus diarrhea in breastfed infants. Adv Exp Med Biol. 2004;554:443–6.

    Article  CAS  PubMed  Google Scholar 

  48. Davis MY, Zhang H, Brannan LE, Carman LJ, Boone JH. Rapid change of fecal microbiome and disappearance of Clostridium difficile in a colonized infant after transition from breast milk to cow milk. Microbiome. 2016;4(1):53.

    Article  PubMed  PubMed Central  Google Scholar 

  49. Fallami M, Amarri S, Uusijarvi A, Adam R, Khanna S, Aguilera M, Gil A, Vieites JM, Norin E, Young D, Scott JA, Doré J, Edwards CA, The Infabio Team. Determinants of the human infant intestinal microbiota after the introduction of first complementary foods in infant samples from five European centers. Microbiology (Reading). 2011;157(5):1385–92.

    Article  Google Scholar 

  50. Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, Angenent LT, Ley RE. Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci. 2011;108(S1):4578–85.

    Article  CAS  PubMed  Google Scholar 

  51. Tanaka S, Kobayashi T, Songjinda P, Tateyama A, Tsubouchi M, Kiyohara C, Shirakawa T, Sonomoto K, Kakayama J. Influence of antibiotic exposure in the early postnatal period on the development of intestinal microbiota. FEMS Immunol Med Microbiol. 2009;56(1):80–7.

    Article  CAS  PubMed  Google Scholar 

  52. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota. Nature. 2012;489(7415):220–30.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Valdes AM, Walter J, Segal E, Spector TD. Role of the gut microbiota in nutrition and health. BMJ. 2018;361:k2179.

    Article  PubMed  PubMed Central  Google Scholar 

  54. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. Bacterial community variation in human body habitats across space and time. Science. 2009;326(5960):1694–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Health AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI. Human gut microbiome viewed across age and geography. Nature. 2012;486(7402):222–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Biagi E, Nylund L, Candela M, Ostan R, Bucci L, Pini E, Nikkïla J, Monti D, Satokari R, Franceschi C, Brigidi P, De Vos W. Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians. PLoS One. 2010;5(5):e10667.

    Article  PubMed  PubMed Central  Google Scholar 

  57. Claesson MJ, Cusack S, O’Sullivan O, Greene-Diniz R, de Weerd H, Flannery E, Marchesi JR, Falush D, Dinan T, Fitzgerald G, Stanton C, van Sinderen D, O’Connor M, Harnedy N, O’Connor K, Henry C, O’Mahony D, Fitzgerald AP, Shanahan F, Twomey C, Hill C, Ross RP, O’Toole PW. Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc Natl Acad Sci U S A. 2011;108(S1):4586–91.

    Article  CAS  PubMed  Google Scholar 

  58. O’Toole PW, Jeffery IB. Gut microbiota and aging. Science. 2015;350(6265):1214–5.

    Article  PubMed  Google Scholar 

  59. Odamaki T, Kato K, Sugahara H, Hashikura N, Takahashi S, Xiao JZ, Abe F, Osawa R. Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study. BMC Microbiol. 2016;16:90.

    Article  PubMed  PubMed Central  Google Scholar 

  60. Govindaraju T, Sahle BW, McCaffrey TA, McNeil JJ, Owen AJ. Dietary patterns and quality of life in older adults. Nutrients. 2018;10(8):971.

    Article  PubMed  PubMed Central  Google Scholar 

  61. Grassi M, Petraccia L, Mennumi G, Fontana M, Scarno A, Sabetta S, Fraioli A. Changes, functional disorders, and diseases in the gastrointestinal tract of the elderly. Nutr Hosp. 2011;26(4):659–68.

    CAS  PubMed  Google Scholar 

  62. Drozdowski L, Thomson AB. Aging and the intestine. World J Gastroenterol. 2006;12(47):7578–84.

    Article  PubMed  PubMed Central  Google Scholar 

  63. Soenen S, Rayner CK, Jones KL, Horowitz M. The ageing gastrointestinal tract. Curr Opin Clin Nutr Metab Care. 2016;19(1):12–8.

    Article  PubMed  Google Scholar 

  64. Salazar N, Gonzales S, Nogacka AM, Rios-Covian D, Arboleya S, Guemonde M, de Los Reyes-Gavilan CG. Microbiome: effects of ageing and diet. Curr Issues Mol Biol. 2020;36:33–62.

    Article  PubMed  Google Scholar 

  65. Woodmansey EJ, McMurdo MET, Macfarlane GT, Macfarlane S. 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. 2004;70(10):6113–22.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Gibson PR, Barrett JS. The concept of small intestine bacterial overgrowth in relation to functional gastrointestinal disorders. Nutrition. 2010;26(11–12):1038–43.

    Article  CAS  PubMed  Google Scholar 

  67. Gorbach SL. Population control in the small intestine. Gut. 1967;8(6):530–2.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Stephen AM, Cummings JH. The microbial contribution to human fecal mass. J Med Microbiol. 1980;13(1):45–56.

    Article  CAS  PubMed  Google Scholar 

  69. Stephen AM, Wiggins HS, Cummings JM. Effects of changing transit time on colonic microbial metabolism in man. Gut. 1987;28(5):601–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Bharucha AE, Anderson A, Bouchoucha M. More movement with evaluating colonic transit in humans. Neurogastroenterol Motil. 2019;31(2):e13541.

    Article  PubMed  PubMed Central  Google Scholar 

  71. Miller LE, Ibarra A, Ouwehand AC. Normative values for colonic transit time and patient assessment of constipation in adults with functional constipation: systematic review with meta-analysis. Clin Med Insights Gastroenterol. 2017;11:1–8.

    Google Scholar 

  72. Wilson CG. The transit of dosage form through the colon. Int J Pharm. 2010;395(1–2):17–25.

    Article  CAS  PubMed  Google Scholar 

  73. Roager HM, Hansen LBS, Bahl MI, Frandsen HL, Carvalho V, Gobel RJ, Dalgaard MD, Plichta DR, Sparholt MH, Vestergaard H, Hansen T, Sicheritz-Ponten T, Bjorn Nielsen H, Pedersen O, Lauritzen L, Kristensen M, Gupta R, Licht TR. Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut. Nature Microbiol. 2016;1(9):16093.

    Article  CAS  Google Scholar 

  74. Rigottier-Gois L. Dysbiosis in inflammatory bowel diseases: the oxygen hypothesis. ISME J. 2013;7(7):1256–61.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Macfarlane GT, Cummings JH. The colonic flora, fermentation, and large bowel digestive function. In: Phillips SF, Pemberton JH, Shorter RG, editors. The large intestine: physiology, pathophysiology, and disease. New York: Raven Press; 1991.

    Google Scholar 

  76. Rutayisire E, Huang K, Liu Y, Tao F. The mode of delivery affects the diversity and colonization pattern of the gut microbiota during the first year of infants’ life: a systematic review. BMC Gastroenterol. 2016;16(1):86.

    Article  PubMed  PubMed Central  Google Scholar 

  77. Borenstein E, Kupiec M, Feldman MW, Ruppin E. Large-scale reconstruction and phylogenetic analysis of metabolic environments. Proc Natl Acad Sci U S A. 2008;105(38):14482–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PT. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505(7484):559–63.

    Article  CAS  PubMed  Google Scholar 

  79. De Filippo C, Di Paola M, Ramazzotti M, Albanese D, Pieraccini G, Banci E, Miglietta F, Cavalieri D, Lionetti P. Diet, environment, and gut microbiota. A preliminary investigation in children living in rural and urban Burkina Faso and Italy. Front Microbiol. 2017;8:1979.

    Article  PubMed  PubMed Central  Google Scholar 

  80. Freilich S, Goldovsky L, Gottlieb A, Blanc E, Tsoka S, Ouzounis CA. Stratification of co-evolving genomic groups using ranked phylogenetic profiles. BMC Bioinformatics. 2009;10:355.

    Article  PubMed  PubMed Central  Google Scholar 

  81. Gomez A, Petrzelkova KJ, Burns MB, Yeoman CJ, Amato KR, Vlckova K, Modry D, Todd A, Jost Robinson CA, Remis MJ, Torralba MG, Morton E, Umana JD, Carbonero F, Rex Gaskins H, Nelson KE, Wilson BA, Stumpf RM, White BA, Leigh SR, Blekhman R. Gut microbiome of coexisting BaAka pygmies and Bantu reflects gradients of traditional subsistence patterns. Cell Rep. 2016;14(9):2142–53.

    Article  CAS  PubMed  Google Scholar 

  82. Martinez I, Stegen JC, Maldonado-Gomez MX, Murat Eren A, Siba PM, Greenhill AR, Walter J. The gut microbiota of rural Papua new Guineans: composition, diversity patterns, and ecological processes. Cell Rep. 2015;11(4):527–38.

    Article  CAS  PubMed  Google Scholar 

  83. Salonen A, de Vos WM. Impact of diet on human intestinal microbiota and health. Annu Rev Food Sci Technol. 2014;5:239–62.

    Article  CAS  PubMed  Google Scholar 

  84. Schnorr SL, Candela M, Rampelli S, Centanni M, Consolandi C, Basaglia G, Turroni S, Biagi E, Peano C, Severgnini M, Fiori J, Gotti R, De Bellis G, Luiselli D, Brigidi P, Mabulla A, Marlowe F, Henry AG, Crittenden AN. Gut microbiome of the Hadza hunter-gatherers. Nat Commun. 2014;5:3654.

    Article  CAS  PubMed  Google Scholar 

  85. Moya A, Ferrer M. Functional redundancy-induced stability of gut microbiota subjected to disturbance. Trends Microbiol. 2016;24(5):402–13.

    Article  CAS  PubMed  Google Scholar 

  86. Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J. 2017;474(11):1823–36.

    Article  CAS  PubMed  Google Scholar 

  87. Fassarella M, Blaak EE, Penders J, Nauta A, Smidt H, Zoedental EG. Gut microbiome stability and resilience: elucidating the response to perturbations in order to modulate gut health. Gut. 2021;70(3):595–605.

    Article  CAS  PubMed  Google Scholar 

  88. Sommer F, Moltzau Anderson J, Bharti R, Raes J, Rosenthal P. The resilience of the intestinal microbiota influences health and disease. Nat Rev Microbiol. 2017;15(10):630–8.

    Article  CAS  PubMed  Google Scholar 

  89. Marietta E, Rishi A, Taneja V. Immunogenetic control of the intestinal microbiota. Immunology. 2015;145(3):313–22.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Spor A, Koren O, Ley R. Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol. 2011;9(4):279–90.

    Article  CAS  PubMed  Google Scholar 

  91. De Palma G, Capilla A, Nova E, Castillejo G, Varea V, Pozo T, Garrote JA, Polanco I, Lopez A, Ribes-Koninckx C, Marcos A, Garcia-Novo MD, Calvo C, Ortigosa L, Pena-Quintana L, Palau F, Sang Y. Influence of milk-feeding type and genetic risk of developing coeliac disease on intestinal microbiota of infants: the PROFICIEL study. PLoS One. 2012;7(2):e30791.

    Article  PubMed  PubMed Central  Google Scholar 

  92. Madden K, Chabot-Richards D. HLA testing in the molecular diagnostic laboratory. Virchows Arch. 2019;474(2):139–47.

    Article  PubMed  Google Scholar 

  93. Benson AK, Kelly SA, Legge R, Ma F, Low SJ, Kim J, Zhang M, Oh PL, Nehrenberg D, Hua K, Kachman SD, Moriyama EN, Walter J, Peterson DA, Pomp D. Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc Natl Acad Sci U S A. 2010;107(44):18933–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, Beaumont M, van Treuren W, Knight R, Bell JT, Spector TD, Clark AG, Ley RE. Human genetics shape the gut microbiome. Cell. 2014;159(4):789–99.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Rothschild D, Kurilshikov A, Korem T, Zeevi D, Costea PI, Godneva A, Kalka IN, Bar N, Shilo S, Lador D, Vila AV, Zmora N, Pevsner-Fischer M, Israeli D, Kosower N, Malka G, Wolf BC, Avnit-Sagi T, Lotan-Pompan M, Weinberger C, Zhernakova A, Elinav E, Segal E. Environment dominates over host genetics in shaping the human gut microbiota. Nature. 2018;555(7695):210–5.

    Article  CAS  PubMed  Google Scholar 

  96. Weersma RH, Zhernakova A, Fu J. Interactions between drugs and the gut microbiome. Gut. 2020;69(8):1510–9.

    Article  CAS  PubMed  Google Scholar 

  97. Koppel N, Maini Redkal V, Balskus EP. Chemical transformation of xenobiotics by the human microbiota. Science. 2017;356(6344):eaag2770.

    Article  PubMed  Google Scholar 

  98. Clayton TA, Baker D, Lindon JC, Everett JR, Nicholson JK. Pharmacometabonomic identification of a significant host-microbiome interaction affecting human drug metabolism. Proc Natl Acad Sci U S A. 2009;106(34):14728–33.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Tan E, Braithwaite I, McKinley CJD, Dalziel SR. Comparison of acetaminophen (paracetamol) with ibuprofen for tnt of fever or pain in children younger than 2 years: a systematic review and meta-analysis. JAMA Netw Open. 2020;3(10):e2022398.

    Article  PubMed  PubMed Central  Google Scholar 

  100. Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL. Mapping human microbiome drug metabolism by gut bacteria and their genes. Nature. 2019;570(7762):462–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Sousa T, Patterson R, Moore V, Carlsson A, Abrahamsson B, Basit AW. The gastrointestinal microbiota as a site for the biotransformation of drugs. Int J Pharm. 2008;363(1–2):1–25.

    Article  CAS  PubMed  Google Scholar 

  102. El Kaoutari A, Armougom F, Gordon JI, Raoult D, Henrissat B. The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nat Rev Microbiol. 2013;11(7):497–504.

    Article  PubMed  Google Scholar 

  103. Levin BJ, Huang YY, Peck SC, Wei Y, Martinez-Del Campo A, Marks JA, Franzosa EA, Huttenhower C, Balskus EP. A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans4-hydroxl-l-proline. Science. 2017;355(6325):eaai8386.

    Article  PubMed  PubMed Central  Google Scholar 

  104. Ryan A, Kaplan E, Nebel JC, Polycarpon E, Crescente V, Lowe E, Preston GM, Sim E. Identification of NAD(P)H quinone oxidoreductase activity in azoreductases from P. aeruginosa: azoreductases and NAD(P)H quinone oxidoreductases belong to the same FMN-dependent superfamily of enzymes. PLoS One. 2014;9(6):e98551.

    Article  PubMed  PubMed Central  Google Scholar 

  105. Spanogiannopoulos P, Bess EN, Carmody RN, Turnbaugh PJ. The microbial pharmacists within us: a metagenomics view of xenobiotic metabolism. Nat Rev Microbiol. 2016;14(5):273–87.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Damiao AOMC, de Azevedo MFC, Carlos AS, Wada MY, Silva TVM, Feitosa FC. Conventional therapy for moderate to severe inflammatory bowel disease: a systematic literature review. World J Gastroenterol. 2019;25(9):1142–57.

    Article  PubMed  PubMed Central  Google Scholar 

  107. Azadkhan AK, Truelove SC, Aronson JK. The disposition and metabolism of sulphasalazine in man. Br J Clin Pharmacol. 1982;13:523–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Barberio B, Segal JP, Quraishi MN, Black CJ, Savarino EV, Ford AC. Efficacy of oral, topical, or combined oral and topical 5-aminosalicylates, in ulcerative colitis: systematic review and network meta-analysis. J Crohns Colitis. 2021;15(7):1184–96.

    Article  PubMed  Google Scholar 

  109. van Hogezand RA, Kennis HM, van Schaik A, Koopman JP, van Hees PA, van Tongeren JH. Bacterial acetylation of 5-aminosalicylic acid in fecal suspensions cultured under aerobic and anaerobic conditions. Eur J Clin Pharmacol. 1992;43(2):189–92.

    Article  PubMed  Google Scholar 

  110. Deloménie C, Fouix S, Longuemaux S, Brahimi N, Bizet C, Picard B, Denamur E, Dupret JM. Identification and functional characterization of arylamine N-acetyltransferases in Eubacteria: evidence for highly selective acetylation of 5-aminosalicylic acid. J Bacteriol. 2001;183(11):3417–27.

    Article  PubMed  PubMed Central  Google Scholar 

  111. Sandberg-Gertzen H, Kjellander J, Sundberg-Gilla B, Järnerot G. In vitro effects of sulphasalazine, azodisal sodium, and their metabolites on Clostridium difficile and some other fecal bacteria. Scand J Gastroenterol. 1985;20(5):607–12.

    Article  CAS  PubMed  Google Scholar 

  112. Harris G, KuoLee R, Chen W. Role of toll-like receptors in health and diseases of gastrointestinal tract. World J Gastroenterol. 2006;12(14):2149–60.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Hayashi F, Smith KD, Ozinski A, Hawn TR, Yi EC, Goodlett DR, Eng JK, Akira S, Underhill DM, Aderem A. The innate immune response to bacterial flagellin is mediated by toll-like receptor 5. Nature. 2001;410(6832):1099–103.

    Article  CAS  PubMed  Google Scholar 

  114. Hemmi H, Takeuchi O, Kawai T, Kaisho T, Sato S, Sanjo H, Matsumoto M, Hoshino K, Wagner H, Takeda K, Akira S. A toll-like receptor recognizes bacterial DNA. Nature. 2000;408(6813):740–5.

    Article  CAS  PubMed  Google Scholar 

  115. Takeuchi O, Hoshino K, Kawai T, Sanjo H, Takada H, Ogawa T, Takeda K, Akira S. Differential roles of TLR2 and TLR4 in recognition of gram-negative and gram-positive bacterial cell wall components. Immunity. 1999;11(4):443–51.

    Article  CAS  PubMed  Google Scholar 

  116. Underhill DM, Ozinsky A, Smith KD, Aderem A. Toll-like receptor-2 mediates mycobacteria-induced proinflammatory signaling in macrophages. Proc Natl Acad Sci U S A. 1999;96(25):14459–63.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Burgueno JF, Abreu MT. Epithelial toll-like receptors and their role in gut homeostasis and disease. Nat Rev Gastroenterol Hepatol. 2020;17(5):263–78.

    Article  CAS  PubMed  Google Scholar 

  118. Frosali S, Pagliari D, Gambassi G, Landolfi R, Pandolfi F, Cianci R. How the intricate interaction among toll-like receptors, microbiota, and intestinal immunity can influence gastrointestinal physiology. J Immunol Res. 2015;2015:489821.

    Article  PubMed  PubMed Central  Google Scholar 

  119. Doxey AC, Mansfield MJ, Montecucco C. Discovery of novel bacterial toxins by genomics and computational biology. Toxicon. 2018;147:2–12.

    Article  CAS  PubMed  Google Scholar 

  120. Chandrasekaran R, Lacy DB. The role of toxins in Clostridium difficile infection. FEMS Microbiol Rev. 2017;41(6):723–50.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Abt MC, McKenney PT, Palmer EG. Clostridium difficile colitis: pathogenesis and host defense. Nat Rev Microbiol. 2016;4(10):609–20.

    Article  Google Scholar 

  122. Sorg JA, Sonenhein AL. Bile salts and glycine as cogerminants for Clostridium difficile spores. J Bacteriol. 2008;190(7):255–2512.

    Article  Google Scholar 

  123. Dubinski V, Dotan I, Gophna U. Carriage of colibactin-producing bacteria and colorectal cancer risk. Trends Microbiol. 2020;28(11):874–6.

    Article  Google Scholar 

  124. Faïs T, Delmas J, Barnich N, Bonnet R, Delmasso G. Colibactin: more than a new bacterial toxin. Toxins (Basel). 2018;10(4):151.

    Article  PubMed  Google Scholar 

  125. Wami H, Wallenstein A, Sauer D, Stoll M, von Bünau R, Oswald E, Müller R, Dobrindt U. Insights into evolution and coexistence of the colibactin- and yersiniabactin secondary metabolite determinants in enterobacterial populations. Microb Genom. 2021;7(6):000577.

    CAS  PubMed  PubMed Central  Google Scholar 

  126. Wilson MR, Jiang Y, Villalta PW, Stornetta A, Boudreau PD, Carra A, Brennan CA, Chun E, Ngo L, Samson LD, Engelward BP, Garrett WS, Balbo S, Balskus EP. The human gut bacterial genotoxin colibactin alkylates DNA. Science. 2019;363(6428):eaar7785.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Blachier, F. (2023). Intestine Offers Board and Lodging for Intestinal Microbes on a Short- or Long-Term Stay. In: Metabolism of Alimentary Compounds by the Intestinal Microbiota and Health. Springer, Cham. https://doi.org/10.1007/978-3-031-26322-4_2

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