The human gut microbiome and its dysfunctions

Digestive Diseases

Volumn 31, Issue 3-4, 2013, Pages 278-285

  Mondot, Stanislas ^a   De Wouters, Tomas ^b   Doré, Joël ^b   Lepage, Patricia ^b  

^a PSL RESEARCH UNIVERSITY   (France)

^b UMR1319 MICALIS   (France)

Author keywords

Gut ecosystem; Inflammatory bowel disease; Microbiota; Resilience

Indexed keywords

ANTIBIOTIC AGENT; FATTY ACID; IMMUNOGLOBULIN A; OLIGOSACCHARIDE; POLYPEPTIDE ANTIBIOTIC AGENT; PREBIOTIC AGENT; PROBIOTIC AGENT;

ANAEROBIC BACTERIUM; BACTERIAL COLONIZATION; BACTEROIDES; BACTEROIDETES; BIFIDOBACTERIACEAE; BIFIDOBACTERIUM; CLOSTRIDIUM; CONFERENCE PAPER; CORYNEBACTERIUM; CROHN DISEASE; DIGESTIVE SYSTEM FUNCTION DISORDER; ECOSYSTEM RESILIENCE; ECOSYSTEM RESTORATION; ENTERITIS; ENTEROBACTERIACEAE; ESCHERICHIA COLI; FAECALIBACTERIUM PRAUSNITZII; FECES MICROFLORA; FIRMICUTES; HUMAN; INTESTINE FLORA; LACTOBACILLUS; MICROBIAL DIVERSITY; MICROBIOME; NONHUMAN; OBESITY; PEDIOCOCCUS; POPULATION; PREVOTELLA; PRIORITY JOURNAL; PROPIONIBACTERIUM; RUMINOCOCCUS; STAPHYLOCOCCUS; STREPTOCOCCUS; ULCERATIVE COLITIS; VEILLONELLA; ADULT; ANTIBIOTIC THERAPY; BIRTH; DIET; DYSBIOSIS; ECOSYSTEM; HOMEOSTASIS; INFLAMMATORY BOWEL DISEASE; METAGENOMICS; SYMBIOSIS; BIODIVERSITY; GASTROINTESTINAL TRACT; MICROBIOLOGY; MICROFLORA; PATHOLOGY; PHYSIOLOGY;

BIODIVERSITY; GASTROINTESTINAL TRACT; HUMANS; MICROBIOTA; OBESITY;

EID: 84888221261     PISSN: 02572753     EISSN: 14219875     Source Type: Journal    
DOI: 10.1159/000354678     Document Type: Conference Paper

References (79)

1. Dethlefsen L, McFall-Ngai M, Relman DA: An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature 2007; 449: 811-818.
2. Walter J, Ley RE: The human gut microbiome: ecology and recent evolutionary changes. Annu Rev Microbiol 2011; 65: 411-429.
3. Stecher B, Hardt W-D: The role of microbiota in infectious disease. Trends Microbiol 2008; 16: 107-114.
4. Round JL, Mazmanian SK: The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol 2009; 9: 313-323.
5. Guarner F: Enteric flora in health and disease. Digestion 2006; 73(suppl 1):5-12.
6. Tamboli CP, Neut C, Desreumaux P, Colombel JF: Dysbiosis in inflammatory bowel disease. Gut 2004; 53: 1-4.
7. Collins SM, Denou E, Verdu EF, Bercik P: The putative role of the intestinal microbiota in the irritable bowel syndrome. Dig Liver Dis 2009; 41: 850-853.
8. Sartor RB: Microbial influences in inflammatory bowel diseases. Gastroenterology 2008; 134: 577-594.
9. Manson JM, Rauch M, Gilmore MS: The commensal microbiology of the gastrointestinal tract. Adv Exp Med Biol 2008; 635: 15-28.
10. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, et al: Diversity of the human intestinal microbial flora. Science 2005; 308: 1635-1638.
11. Rajili-Stojanovi M, Smidt H, De Vos WM: Diversity of the human gastrointestinal tract microbiota revisited. Environ Microbiol 2007; 9: 2125-2136.
12. Tap J, Mondot S, Levenez F, Pelletier E, Caron C, Furet J, et al: Towards the human intestinal microbiota phylogenetic core. Environ Microbiol 2009; 11: 2574-2584.
13. Rajili-Stojanovi M, Heilig HG, Molenaar D, Kajander K, Surakka A, Smidt H, et al: Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults. Environ Microbiol 2009; 11: 1736-1751.
14. DiGiulio DB, Romero R, Amogan HP, Kusanovic JP, Bik EM, Gotsch F, et al: Microbial prevalence, diversity and abundance in amniotic fluid during preterm labor: a molecular and culture-based investigation. PloS One 2008; 3:e3056.
15. Jiménez E, Fernández L, Marín ML, Martín R, Odriozola JM, Nueno-Palop C, et al: Isolation of commensal bacteria from umbilical cord blood of healthy neonates born by cesarean section. Curr Microbiol 2005; 51: 270-274.
16. Penders J, Thijs C, Vink C, Stelma FF, Snijders B, Kummeling I, et al: Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics 2006; 118: 511-521.
17. Mackie RI, Sghir A, Gaskins HR: Developmental microbial ecology of the neonatal gastrointestinal tract. Am J Clin Nutr 1999; 69: 1035S-1045S.
18. Matamoros S, Gras-Leguen C, Le Vacon F, Potel G, De La Cochetiere M-F: Development of intestinal microbiota in infants and its impact on health. Trends Microbiol 2013; 21: 167-173.
19. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO: Development of the human infant intestinal microbiota. PLoS Biol 2007; 5:e177.
20. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al: Human gut microbiome viewed across age and geography. Nature 2012; 486: 222-227.
21. Vaishampayan PA, Kuehl J V, Froula JL, Morgan JL, Ochman H, Francino MP: Comparative metagenomics and population dynamics of the gut microbiota in mother and infant. Genome Biol Evol 2010; 2: 53-66.
22. Madan JC, Salari RC, Saxena D, Davidson L, O'Toole GA, Moore JH, et al: Gut microbial colonisation in premature neonates predicts neonatal sepsis. Arch Dis Child Fetal Neonatal Ed 2012; 97:F456-F462.
23. Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, et al: Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci USA 2010; 107: 11971-11975.
24. Donnet-Hughes A, Perez PF, Doré J, Leclerc M, Levenez F, Benyacoub J, et al: Potential role of the intestinal microbiota of the mother in neonatal immune education. Proc Nutr Soc 2010; 69: 407-415.
25. Jost T, Lacroix C, Braegger C, Chassard C: Assessment of bacterial diversity in breast milk using culture-dependent and culture-independent approaches. Br J Nutr 2013; 14: 1-10.
26. Ward TL, Hosid S, Ioshikhes I, Altosaar I: Human milk metagenome: a functional capacity analysis. BMC Microbiol 2013; 13: 116.
27. Fernández L, Langa S, Martín V, Maldonado A, Jiménez E, Martín R, et al: The human milk microbiota: origin and potential roles in health and disease. Pharmacol Res 2013; 69: 1-10.
28. O'Hara AM, Shanahan F: The gut flora as a forgotten organ. EMBO Rep 2006; 7: 688-693.
29. Blottiere HM, Buecher B, Galmiche J-P, Cherbut C: Molecular analysis of the effect of short-chain fatty acids on intestinal cell proliferation. Proc Nutr Soc 2003; 62: 101-106.
30. Gaudier E, Jarry A, Blottiere HM, De Coppet P, Buisine MP, Aubert JP, et al: Butyrate specifically modulates MUC gene expression in intestinal epithelial goblet cells deprived of glucose. Am J Physiol Gastrointest Liver Physiol 2004; 287:G1168-G1174.
31. Cherbut C, Aubé AC, Blottiere HM, Galmiche JP: Effects of short-chain fatty acids on gastrointestinal motility. Scand J Gastroenterol 1997; 222(suppl):58-61.
32. Flint HJ, Scott KP, Louis P, Duncan SH: The role of the gut microbiota in nutrition and health. Nat Rev Gastroenterol Hepatol 2012; 9: 577-589.
33. Ge H, Li X, Weiszmann J, Wang P, Baribault H, Chen J-L, et al: Activation of G-proteincoupled receptor 43 in adipocytes leads to inhibition of lipolysis and suppression of plasma-free fatty acids. Endocrinology 2008; 149: 4519-4526.
34. Leblanc JG, Milani C, De Giori GS, Sesma F, Van Sinderen D, Ventura M: Bacteria as vitamin suppliers to their host: a gut microbiota perspective. Curr Opin Biotechnol 2013; 24: 160-168.
35. Druart C, Neyrinck AM, Dewulf EM, De Backer FC, Possemiers S, Van de Wiele T, et al: Implication of fermentable carbohydrates targeting the gut microbiota on conjugated linoleic acid production in high-fat-fed mice. Br J Nutr 2013, E-pub ahead of print.
36. Macpherson AJ, Geuking MB, McCoy KD: Immunoglobulin A: a bridge between innate and adaptive immunity. Curr Opin Gastroenterol 2011; 27: 529-533.
37. Tschöp MH, Hugenholtz P, Karp CL: Getting to the core of the gut microbiome. Nat Biotechnol 2009; 27: 344-346.
38. Shade A, Peter H, Allison SD, Baho DL, Berga M, Bürgmann H, et al: Fundamentals of microbial community resistance and resilience. Front Microbiol 2012; 3: 417.
39. Cani PD, Neyrinck AM, Fava F, Knauf C, Burcelin RG, Tuohy KM, et al: Selective increases of Bifidobacteria in gut microflora improve high-fat-diet-induced diabetes in mice through a mechanism associated with endotoxaemia. Diabetologia 2007; 50: 2374-2383.
40. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, et al: Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci USA 2010; 107: 14691-14696.
41. Rigottier-Gois L: Dysbiosis in inflammatory bowel diseases: the oxygen hypothesis. ISME J 2013; 7: 1256-1261.
42. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, et al: Evolution of mammals and their gut microbes. Science 2008; 777: 1647-1651.
43. Ley RE, Peterson DA, Gordon JI: Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 2006; 124: 837-848.
44. Lepage P, Häsler R, Spehlmann ME, Rehman A, Zvirbliene A, Begun A, et al: Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. Gastroenterology 2011; 141: 227-236.
45. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, et al: A core gut microbiome in obese and lean twins. Nature 2009; 457: 480-484.
46. Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI: Host-bacterial mutualism in the human intestine. Science 2005; 307: 1915-1920.
47. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al: A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010; 464: 59-65.
48. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, et al: Enterotypes of the human gut microbiome. Nature 2011; 473: 174-180.
49. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen Y-Y, Keilbaugh SA, et al: Linking longterm dietary patterns with gut microbial enterotypes. Science 2011; 334: 105-108.
50. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R: Diversity, stability and resilience of the human gut microbiota. Nature 2012; 489: 220-230.
51. Seksik P, Rigottier-Gois L, Gramet G, Sutren M, Pochart P, Marteau P, et al: Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon. Gut 2003; 52: 237-242.
52. Seksik P, Lepage P, De la Cochetiere M-F, Bourreille A, Sutren M, Galmiche J, et al: Search for localized dysbiosis in Crohn's disease ulcerations by temporal temperature gradient gel electrophoresis of 16S rRNA. J Clin Microbiol 2005; 43: 4654-4658.
53. Dicksved J, Halfvarson J, Rosenquist M, Järnerot G, Tysk C, Apajalahti J, et al: Molecular analysis of the gut microbiota of identical twins with Crohn's disease. ISME J 2008; 2: 716-727.
54. Willing BP, Dicksved J, Halfvarson J, Andersson AF, Lucio M, Zheng Z, et al: A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology 2010; 139: 1844-1854.e1.
55. Sokol H, Seksik P, Furet JP, Firmesse O, Nion-Larmurier I, Beaugerie L, et al: Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm Bowel Dis 2009; 15: 1183-1189.
56. Sokol H, Seksik P, Rigottier-Gois L, Lay C, Lepage P, Podglajen I, et al: Specificities of the fecal microbiota in inflammatory bowel disease. Inflamm Bowel Dis 2006; 12: 106-111.
57. Joossens M, Huys G, Cnockaert M, De Preter V, Verbeke K, Rutgeerts P, et al: Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives. Gut 2011; 60: 631-637.
58. Darfeuille-Michaud A, Neut C, Barnich N, Lederman E, Di Martino P, Desreumaux P, et al: Presence of adherent Escherichia coli strains in ileal mucosa of patients with Crohn's disease. Gastroenterology 1998; 115: 1405-1413.
59. Darfeuille-Michaud A, Boudeau J, Bulois P, Neut C, Glasser A-L, Barnich N, et al: High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease. Gastroenterology 2004; 127: 412-421.
60. Mondot S, Kang S, Furet JP, Aguirre de Carcer D, McSweeney C, Morrison M, et al: Highlighting new phylogenetic specificities of Crohn's disease microbiota. Inflamm Bowel Dis 2011; 17: 185-192.
61. Pitcher MC, Beatty ER, Cummings JH: The contribution of sulphate reducing bacteria and 5-aminosalicylic acid to faecal sulphide in patients with ulcerative colitis. Gut 2000; 46: 64-72.
62. Erickson AR, Cantarel BL, Lamendella R, Darzi Y, Mongodin EF, Pan C, et al: Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease. PloS One 2012; 7:e49138.
63. Marchesi JR, Holmes E, Khan F, Kochhar S, Scanlan P, Shanahan F, et al: Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J Proteome Res 2007; 6: 546-551.
64. Jansson J, Willing B, Lucio M, Fekete A, Dicksved J, Halfvarson J, et al: Metabolomics reveals metabolic biomarkers of Crohn's disease. PloS One 2009; 4:e6386.
65. Le Gall G, Noor SO, Ridgway K, Scovell L, Jamieson C, Johnson IT, et al: Metabolomics of fecal extracts detects altered metabolic activity of gut microbiota in ulcerative colitis and irritable bowel syndrome. J Proteome Res 2011; 10: 4208-4218.
66. Rausch P, Rehman A, Künzel S, Häsler R, Ott SJ, Schreiber S, et al: Colonic mucosa-associated microbiota is influenced by an interaction of Crohn disease and FUT2 (Secretor) genotype. Proc Natl Acad Sci USA 2011; 108: 19030-19035.
67. Frank DN, Robertson CE, Hamm CM, Kpadeh Z, Zhang T, Chen H, et al: Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases. Inflamm Bowel Dis 2011; 17: 179-184.
68. Greenblum S, Turnbaugh PJ, Borenstein E: Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease. Proc Natl Acad Sci USA 2012; 109: 594-599.
69. Bäckhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, et al: The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci USA 2004; 101: 15718-15723.
70. Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI: Obesity alters gut microbial ecology. Proc Natl Acad Sci USA 2005; 102: 11070-11075.
71. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI: An obesityassociated gut microbiome with increased capacity for energy harvest. Nature 2006; 444: 1027-1031.
72. Turnbaugh PJ, Bäckhed F, Fulton L, Gordon JI, Ba F: Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 2008; 3: 213-223.
73. Samuel BS, Shaito A, Motoike T, Rey FE, Backhed F, Manchester JK, et al: Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding Gprotein-coupled receptor, Gpr41. Proc Natl Acad Sci USA 2008; 105: 16767-16772.
74. Furet J-P, Kong L-C, Tap J, Poitou C, Basdevant A, Bouillot J-L, et al: Differential adaptation of human gut microbiota to bariatric surgery-induced weight loss: links with metabolic and low-grade inflammation markers. Diabetes 2010; 59: 3049-3057.
75. Kruis W, Fric P, Pokrotnieks J, Lukás M, Fixa B, Kascák M, et al: Maintaining remission of ulcerative colitis with the probiotic Escherichia coli Nissle 1917 is as effective as with standard mesalazine. Gut 2004; 53: 1617-1623.
76. Tursi A, Brandimarte G, Papa A, Giglio A, Elisei W, Giorgetti GM, et al: Treatment of relapsing mild-to-moderate ulcerative colitis with the probiotic VSL#3 as adjunctive to a standard pharmaceutical treatment: a doubleblind, randomized, placebo-controlled study. Am J Gastroenterol 2010; 105: 2218-2227.
77. Kelly CP: Fecal microbiota transplantation-an old therapy comes of age. N Engl J Med 2013; 368: 474-475.
78. Van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, De Vos WM, et al: Duodenal infusion of donor feces for recurrent Clostridium difficile . N Engl J Med 2013; 368: 407-415.
79. Vrieze A, Van Nood E, Holleman F, Salojärvi J, Kootte RS, Bartelsman JF, et al: Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome. Gastroenterology 2012; 143: 913-916.e7.