The small intestine microbiota, nutritional modulation and relevance for health

Current Opinion in Biotechnology

Volumn 32, Issue , 2015, Pages 14-20

  Aidy, Sahar E1 ^a,b,c   van den Bogert, Bartho1omeus ^a,d   Kleerebezem, Michiel ^a,d,e  

^a TOP INSTITUTE FOOD AND NUTRITION   (Netherlands)

^b UNIVERSITY COLLEGE CORK   (Ireland)

^c UNIVERSITY OF SADAT CITY   (Egypt)

^d WAGENINGEN UNIVERSITY   (Netherlands)

^e NIZO FOOD RESEARCH   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

MICROBIOTAS; SMALL INTESTINE;

DISEASE PREDISPOSITION; ESCHERICHIA; HOST PATHOGEN INTERACTION; HUMAN; IMMUNE RESPONSE; IMMUNOMODULATION; INFLAMMATION; INTESTINE FLORA; METABOLIC REGULATION; MICROBIAL COLONIZATION; MICROBIAL COMMUNITY; MICROBIAL POPULATION DYNAMICS; MUCOSAL IMMUNITY; NON INSULIN DEPENDENT DIABETES MELLITUS; NONHUMAN; NUTRITION; PERIPHERAL BLOOD MONONUCLEAR CELL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; SMALL INTESTINE; STREPTOCOCCUS; VEILLONELLA; ANIMAL; METABOLIC SYNDROME X; METABOLISM; MICROBIOLOGY; MICROFLORA;

AMIDASE; CHOLOYLGLYCINE HYDROLASE; PROBIOTIC AGENT;

AMIDOHYDROLASES; ANIMALS; HUMANS; INTESTINE, SMALL; METABOLIC SYNDROME X; MICROBIOTA; PROBIOTICS;

EID: 84908093485     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2014.09.005     Document Type: Review

References (57)

1. Van den Bogert B., Leimena M.M., De Vos W.M., Zoetendal E.G., Kleerebezem M. Functional intestinal metagenomics. Handbook of Molecular Microbial Ecology 2011, 170-190. Wiley-Blackwell. F.J. De Bruin (Ed.).
2. de Vos W.M., de Vos E.A. Role of the intestinal microbiome in health and disease: from correlation to causation. Nutr Rev 2012, 70(Suppl. 1):S45-S56.
3. Leser T.D., Molbak L. Better living through microbial action: the benefits of the mammalian gastrointestinal microbiota on the host. Environ Microbiol 2009, 11:2194-2206.
4. Sekirov I., Russell S.L., Antunes L.C., Finlay B.B. Gut microbiota in health and disease. Physiol Rev 2010, 90:859-904.
5. Ermund A., Schutte A., Johansson M.E., Gustafsson J.K., Hansson G.C. Studies of mucus in mouse stomach, small intestine, and colon. I. Gastrointestinal mucus layers have different properties depending on location as well as over the Peyer's patches. Am J Physiol Gastrointest Liver Physiol 2013, 305:G341-G347.
6. Cotter P.D. Small intestine and microbiota. Curr Opin Gastroenterol 2011, 27:99-105.
7. Raoult D., Henrissat B. Are stool samples suitable for studying the link between gut microbiota and obesity?. Eur J Epidemiol 2014, 29:307-309.
8. Booijink C.C., Zoetendal E.G., Kleerebezem M., de Vos W.M. Microbial communities in the human small intestine: coupling diversity to metagenomics. Fut Microbiol 2007, 2:285-295.
9. Gevers D., Kugathasan S., Denson L.A., Vazquez-Baeza Y., Van Treuren W., Ren B., Schwager E., Knights D., Song S.J., Yassour M., et al. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe 2014, 15:382-392.
10. Vrieze A., Van Nood E., Holleman F., Salojarvi J., Kootte R.S., Bartelsman J.F., Dallinga-Thie G.M., Ackermans M.T., Serlie M.J., Oozeer R., et al. Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome. Gastroenterology 2012, 143. 913-916 e917.
11. Zoetendal E.G., Raes J., van den Bogert B., Arumugam M., Booijink C.C., Troost F.J., Bork P., Wels M., de Vos W.M., Kleerebezem M. The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. ISME J 2012, 6:1415-1426.
12. van der Schaar P.J., Dijksman J.F., Broekhuizen-de Gast H., Shimizu J., van Lelyveld N., Zou H., Iordanov V., Wanke C., Siersema P.D. A novel ingestible electronic drug delivery and monitoring device. Gastrointest Endosc 2013, 78:520-528.
13. Booijink C.C., El-Aidy S., Rajilić-Stojanović M., Heilig H.G., Troost F.J., Smidt H., Kleerebezem M., De Vos W.M., Zoetendal E.G. High temporal and inter-individual variation detected in the human ileal microbiota. Environ Microbiol 2010, 12:3213-3227.
14. van den Bogert B., Erkus O., Boekhorst J., de Goffau M., Smid E.J., Zoetendal E.G., Kleerebezem M. Diversity of human small intestinal Streptococcus and Veillonella populations. FEMS Microbiol Ecol 2013, 85:376-388.
15. Rajilić-Stojanović M., Heilig H.G., Molenaar D., Kajander K., Surakka A., Smidt H., de Vos W.M. 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.
16. Salonen A., Lahti L., Salojarvi J., Holtrop G., Korpela K., Duncan S.H., Date P., Farquharson F., Johnstone A.M., Lobley G.E., et al. Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men. ISME J 2014, http://dx.doi.org/10.1038/ismej.2014.63.
17. Van den Bogert B., Boekhorst J., Herrmann R., Smid E.J., Zoetendal E.G., Kleerebezem M. Comparative genomics analysis of streptococcus isolates from the human small intestine reveals their adaptation to a highly dynamic ecosystem. PLoS ONE 2013, 8:e83418.
18. van den Bogert B., Boekhorst J., Smid E.J., Zoetendal E.G., Kleerebezem M. Draft genome sequence of Veillonella parvula HSIVP1, isolated from the human small intestine. Genome Announc 2013, 1.
19. Kostic A.D., Howitt M.R., Garrett W.S. Exploring host-microbiota interactions in animal models and humans. Genes Dev 2013, 27:701-718.
20. El Aidy S., van Baarlen P., Derrien M., Lindenbergh-Kortleve D.J., Hooiveld G., Levenez F., Doré J., Dekker J., Samsom J.N., Nieuwenhuis E.E., Kleerebezem M. Temporal and spatial interplay of microbiota and intestinal mucosa drive establishment of immune homeostasis in conventionalized mice. Mucosal Immunol 2012, 5:567-579.
21. Nicholson J.K., Holmes E., Kinross J., Burcelin R., Gibson G., Jia W., Pettersson S. Host-gut microbiota metabolic interactions. Science 2012, 336:1262-1267.
22. Lozupone C.A., Stombaugh J.I., Gordon J.I., Jansson J.K., Knight R. Diversity, stability and resilience of the human gut microbiota. Nature 2012, 489:220-230.
23. Belkaid Y., Hand T.W. Role of the microbiota in immunity and inflammation. Cell 2014, 157:121-141.
24. Wagner R.D. Effects of microbiota on GI health: gnotobiotic research. GI Microbiota and Regulation of the Immune System 2008, 41-56. Landies Biosciences and Springer Science + Bussiness Media. B. Huffnagle, C. Maisi, Noverr (Eds.).
25. Chung H1, Pamp S.J., Hill J.A., Surana N.K., Edelman S.M., Troy E.B., Reading N.C., Villablanca E.J., Wang S., Mora J.R., et al. Gut immune maturation depends on colonization with a host-specific microbiota. Cell 2012, 149:1578-1593.
26. Sommer F., Bäckhed F. The gut microbiota - masters of host development and physiology. Nat Rev Microbiol 2013, 11:227-238.
27. Hsiao E.Y., McBride S.W., Hsien S., Sharon G., Hyde E.R., McCue T., Codelli J.A., Chow J., Reisman S.E., Petrosino J.F., et al. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell 2013, 155:1451-1463.
28. El Aidy S., Merrifield C.A., Derrien M., van Baarlen P., Hooiveld G., Levenez F., Doré J., Dekker J., Holmes E., Claus S.P., et al. The gut microbiota elicits a profound metabolic reorientation in the mouse jejunal mucosa during conventionalisation. Gut 2013, 62:1306-1314.
29. Hansen C.H., Nielsen D.S., Kverka M., Zakostelska Z., Klimesova K., Hudcovic T., Tlaskalova-Hogenova H., Hansen A.K. Patterns of early gut colonization shape future immune responses of the host. PLoS ONE 2012, 7:e34043.
30. El Aidy S., Derrien M., Aardema R., Hooiveld G., Richards S.E., Dane A., Dekker J., Vreeken R., Levenez F., Doré J., et al. Transient inflammatory-like state and microbial dysbiosis are pivotal in establishment of mucosal homeostasis during colonisation of germ-free mice. Benef Microbes 2014, 5:67-77.
31. Menckeberg C.L., Hol J., de Ruiter H., Raatgeep H.C., Simons-Oosterhuis Y., Lindenbergh-Kortleve D., Korteland-van Male A., El Aidy S., van Lierop P.E., et al. Human buccal epithelium acquires microbial hyporesponsiveness at birth, a role for secretory leukocyte protease inhibitor. Gut 2014, pii: gutjnl-2013-306149, http://dx.doi.org/10.1136/gutjnl-2013-306149.
32. Brugman S., Schneeberger K., Witte M., Klein M.R., van den Bogert B., Boekhorst J., Timmerman H.M., Boes M., Kleerebezem M., Nieuwenhuis E.E.S. T lymphocytes control microbial composition by actively repressing overgrowth of pathogenic bacteria in the zebrafish gut. Gut Microbes 2014, (in press).
33. Lécuyer E., Rakotobe S., Lengliné-Garnier H., Lebreton C., Picard M., Juste C., Fritzen R., Eberl G., McCoy K.D., Macpherson A.J., et al. Segmented filamentous bacterium uses secondary and tertiary lymphoid tissues to induce gut IgA and specific T helper 17 cell responses. Immunity 2014, 40:608-620.
34. Rescigno M., Di Sabatino A. Dendritic cells in intestinal homeostasis and disease. J Clin Invest 2009, 119:2441-2450.
35. Corthésy B. Multi-faceted functions of secretory IgA at mucosal surfaces. Front Immunol 2013, 4:185.
36. Olszak T., An D., Zeissig S., Vera M.P., Richter J., Franke A., Glickman J.N., Siebert R., Baron R.M., Kasper D.L., Blumberg R.S. Microbial exposure during early life has persistent effects on natural killer T cell function. Science 2012, 336:489-493.
37. Atarashi K., Tanoue T., Shima T., Imaoka A., Kuwahara T., Momose Y., Cheng G., Yamasaki S., Saito T., Ohba Y., et al. Induction of colonic regulatory T cells by indigenous Clostridium species. Science 2011, 331:337-341.
38. Takatori H., Kanno Y., Watford W.T., Tato C.M., Weiss G., Ivanov I.I., Littman D.R., O'Shea J.J. Lymphoid tissue inducer-like cells are an innate source of IL-17 and IL-22. J Exp Med 2009, 206:35-41.
39. Khor B., Gardet A., Xavier R.J. Genetics and pathogenesis of inflammatory bowel disease. Nature 2011, 474:307-317.
40. Lee Y.K., Mazmanian S.K. Microbial learning lessons: SFB educate the immune system. Immunity 2014, 40:457-459.
41. Blumberg R., Powrie F. Microbiota, disease, and back to health: a metastable journey. Sci Transl Med 2012, 4(137):rv7.
42. Sears C.L., Pardoll D.M. Perspective: alpha-bugs, their microbial partners, and the link to colon cancer. J Infect Dis 2011, 203:306-311.
43. Uronis J.M., Mühlbauer M., Herfarth H.H., Rubinas T.C., Jones G.S., Jobin C. Modulation of the intestinal microbiota alters colitis-associated colorectal cancer susceptibility. PLoS ONE 2009, 4:e6026.
44. Ermann J., Staton T., Glickman J.N., de Waal Malefyt R., Glimcher L.H. Nod/Ripk2 signaling in dendritic cells activates IL-17A-secreting innate lymphoid cells and drives colitis in T-bet-/-.Rag2-/- (TRUC) mice. Proc Natl Acad Sci U S A 2014, pii:201408540.
45. Cani P.D., Everard A., Duparc T. Gut microbiota, enteroendocrine functions and metabolism. Curr Opin Pharmacol 2013, 13:935-940.
46. Kaji I., Karaki S., Kuwahara A. Short-chain fatty acid receptor and its contribution to glucagon-like peptide-1 release. Digestion 2014, 89:31-36.
47. De Vadder F., Kovatcheva-Datchary P., Goncalves D., Vinera J., Zitoun C., Duchampt A., Bäckhed F., Mithieux G. Microbiota-generated metabolites promote metabolic benefits via gut-brain neural circuits. Cell 2014, 156:84-96.
48. van Baarlen P., Troost F., van der Meer C., Hooiveld G., Boekschoten M., Brummer R.J., Kleerebezem M. Human mucosal in vivo transcriptome responses to three lactobacilli indicate how probiotics may modulate human cellular pathways. Proc Natl Acad Sci U S A 2011, 108(Suppl. 1):4562-4569.
49. van Baarlen P., Troost F.J., van Hemert S., van der Meer C., de Vos W.M., de Groot P.J., Hooiveld G.J., Brummer R.J., Kleerebezem M. Differential NF-kappaB pathways induction by Lactobacillus plantarum in the duodenum of healthy humans correlating with immune tolerance. Proc Natl Acad Sci U S A 2009, 106:2371-2376.
50. Tremaroli V., Bäckhed F. Functional interactions between the gut microbiota and host metabolism. Nature 2012, 489:242-249.
51. Osto M., Abegg K., Bueter M., le Roux C.W., Cani P.D., Lutz T.A. Roux-en-Y gastric bypass surgery in rats alters gut microbiota profile along the intestine. Physiol Behav 2013, 119:92-96.
52. Furet J.P., Kong L.C., Tap J., Poitou C., Basdevant A., Bouillot J.L., Mariat D., Corthier G., Doré J., Henegar C., 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.
53. 2 consumption triggers HIF-1α causing inflammation and insulin resistance in obesity. Cell 2014, 157:1339-1352.
54. Bojsen-Møller K.N., Dirksen C., Jørgensen N.B., Jacobsen S.H., Hansen D.L., Worm D., Naver L., Kristiansen V.B., Holst J.J., Madsbad S. Increased hepatic insulin clearance after Roux-en-Y gastric bypass. J Clin Endocrinol Metab 2013, 98:E1066-E1071.
55. Ryan K.K., Tremaroli V., Clemmensen C., Kovatcheva-Datchary P., Myronovych A., Karns R., Wilson-Pérez H.E., Sandoval D.A., Kohli R., Bäckhed F., Seeley R.J. FXR is a molecular target for the effects of vertical sleeve gastrectomy. Nature 2014, 509:183-188.
56. Kuipers F., Groen A.K. FXR: the key to benefits in bariatric surgery?. Nat Med 2014, 20:337-338.
57. Duerkop B.A., Vaishnava S., Hooper L.V. Immune responses to the microbiota at the intestinal mucosal surface. Immunity 2009, 31:368-376.