Abstract
Major research efforts during the past decades have revealed the close interaction between the host immune system and the symbionts colonizing the surfaces of the human body. Due to the high number of microbes found in this environment correlating with its role as an essential immune organ, the gastrointestinal tract has been a major focus of research. This chapter reviews current knowledge regarding the role of microbial colonization with beneficial microbes and the influence of released mediators on innate as well as adaptive immune cells. Several life style factors seems to substantially influence the composition of the microbiome especially during the first period of life. Nevertheless, also later in life factors such as dietary habits, medication intake or life style might alter the gut microbiota. Thus, strategies to beneficially modulate the overall microbial composition are essential to treat dysbiosis, which has been described to contribute to the onset or progression of various immune mediated intestinal diseases.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Aagaard K, Ma J, Antony KM, Ganu R, Petrosino J, Versalovic J (2014) The placenta harbors a unique microbiome. Sci Transl Med 6(237):237–265. https://doi.org/10.1126/scitranslmed.3008599
Aroniadis OC, Brandt LJ, Greenberg A, Borody T, Kelly CR, Mellow M, Surawicz C, Cagle L, Neshatian L, Stollman N, Giovanelli A, Ray A, Smith R (2016) Long-term follow-up study of fecal microbiota transplantation for severe and/or complicated clostridium difficile infection: a multicenter experience. J Clin Gastroenterol 50(5):398–402. https://doi.org/10.1097/MCG.0000000000000374
Atarashi K, Tanoue T, Shima T, Imaoka A, Kuwahara T, Momose Y, Cheng G, Yamasaki S, Saito T, Ohba Y, Taniguchi T, Takeda K, Hori S, Ivanov II, Umesaki Y, Itoh K, Honda K (2011) Induction of colonic regulatory T cells by indigenous Clostridium species. Science 331(6015):337–341. https://doi.org/10.1126/science.1198469
Atarashi K, Tanoue T, Oshima K, Suda W, Nagano Y, Nishikawa H, Fukuda S, Saito T, Narushima S, Hase K, Kim S, Fritz JV, Wilmes P, Ueha S, Matsushima K, Ohno H, Olle B, Sakaguchi S, Taniguchi T, Morita H, Hattori M, Honda K (2013) Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature 500(7461):232–236. https://doi.org/10.1038/nature12331
Backhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI (2005) Host-bacterial mutualism in the human intestine. Science 307(5717):1915–1920. https://doi.org/10.1126/science.1104816
Barcik W, Untersmayr E, Pali-Schöll I, O’Mahony L, Frei R (2016) Influence of microbiome and diet on immune responses in food allergy models. Drug Discov Today Dis Model 17:71–82
Berin MC, Shreffler WG (2016) Mechanisms underlying induction of tolerance to foods. Immunol Allergy Clin N Am 36(1):87–102. https://doi.org/10.1016/j.iac.2015.08.002
Bezirtzoglou E, Tsiotsias A, Welling GW (2011) Microbiota profile in feces of breast- and formula-fed newborns by using fluorescence in situ hybridization (FISH). Anaerobe 17(6):478–482. https://doi.org/10.1016/j.anaerobe.2011.03.009
Bosch AA, Levin E, van Houten MA, Hasrat R, Kalkman G, Biesbroek G, de Steenhuijsen Piters WA, de Groot PK, Pernet P, Keijser BJ, Sanders EA, Bogaert D (2016) Development of upper respiratory tract microbiota in infancy is affected by mode of delivery. EBioMedicine 9:336–345. https://doi.org/10.1016/j.ebiom.2016.05.031
Brahe LK, Astrup A, Larsen LH (2016) Can we prevent obesity-related metabolic diseases by dietary modulation of the gut microbiota? Adv Nutr 7(1):90–101. https://doi.org/10.3945/an.115.010587
Burger-van Paassen N, Vincent A, Puiman PJ, van der Sluis M, Bouma J, Boehm G, van Goudoever JB, van Seuningen I, Renes IB (2009) The regulation of intestinal mucin MUC2 expression by short-chain fatty acids: implications for epithelial protection. Biochem J 420(2):211–219. https://doi.org/10.1042/BJ20082222
Burrage S (1927) Bacteria in the supposedly sterile meconium. J Bacteriol 13(1):47–48
Cao S, Feehley TJ, Nagler CR (2014) The role of commensal bacteria in the regulation of sensitization to food allergens. FEBS Lett 588(22):4258–4266. https://doi.org/10.1016/j.febslet.2014.04.026
Chassaing B, Koren O, Goodrich JK, Poole AC, Srinivasan S, Ley RE, Gewirtz AT (2015) Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature 519(7541):92–96. https://doi.org/10.1038/nature14232
Chen CC, Chen KJ, Kong MS, Chang HJ, Huang JL (2016) Alterations in the gut microbiotas of children with food sensitization in early life. Pediatr Allergy Immunol 27(3):254–262. https://doi.org/10.1111/pai.12522
Chinthrajah RS, Hernandez JD, Boyd SD, Galli SJ, Nadeau KC (2016) Molecular and cellular mechanisms of food allergy and food tolerance. J Allergy Clin Immunol 137(4):984–997. https://doi.org/10.1016/j.jaci.2016.02.004
Claesson MJ, Jeffery IB, Conde S, Power SE, O’Connor EM, Cusack S, Harris HM, Coakley M, Lakshminarayanan B, O’Sullivan O, Fitzgerald GF, Deane J, O’Connor M, Harnedy N, O’Connor K, O’Mahony D, van Sinderen D, Wallace M, Brennan L, Stanton C, Marchesi JR, Fitzgerald AP, Shanahan F, Hill C, Ross RP, O’Toole PW (2012) Gut microbiota composition correlates with diet and health in the elderly. Nature 488(7410):178–184. https://doi.org/10.1038/nature11319
Cotter PD, Stanton C, Ross RP, Hill C (2012) The impact of antibiotics on the gut microbiota as revealed by high throughput DNA sequencing. Discov Med 13(70):193–199
David LA, Materna AC, Friedman J, Campos-Baptista MI, Blackburn MC, Perrotta A, Erdman SE, Alm EJ (2014a) Host lifestyle affects human microbiota on daily timescales. Genome Biol 15(7):R89. https://doi.org/10.1186/gb-2014-15-7-r89
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 PJ (2014b) Diet rapidly and reproducibly alters the human gut microbiome. Nature 505(7484):559–563. https://doi.org/10.1038/nature12820
De Angelis M, Montemurno E, Vannini L, Cosola C, Cavallo N, Gozzi G, Maranzano V, Di Cagno R, Gobbetti M, Gesualdo L (2015) Effect of whole-grain barley on the human fecal microbiota and metabolome. Appl Environ Microbiol 81(22):7945–7956. https://doi.org/10.1128/AEM.02507-15
De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G, Lionetti P (2010) Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci USA 107(33):14691–14696. https://doi.org/10.1073/pnas.1005963107
De Palma G, Nadal I, Collado MC, Sanz Y (2009) Effects of a gluten-free diet on gut microbiota and immune function in healthy adult human subjects. Br J Nutr 102(8):1154–1160. https://doi.org/10.1017/S0007114509371767
Diesner SC, Bergmayr C, Pfitzner B, Assmann V, Krishnamurthy D, Starkl P, Endesfelder D, Rothballer M, Welzl G, Rattei T, Eiwegger T, Szepfalusi Z, Fehrenbach H, Jensen-Jarolim E, Hartmann A, Pali-Scholl I, Untersmayr E (2016) A distinct microbiota composition is associated with protection from food allergy in an oral mouse immunization model. Clin Immunol 173:10–18. https://doi.org/10.1016/j.clim.2016.10.009
Dobber R, Hertogh-Huijbregts A, Rozing J, Bottomly K, Nagelkerken L (1992) The involvement of the intestinal microflora in the expansion of CD4+ T cells with a naive phenotype in the periphery. Dev Immunol 2(2):141–150
Dominguez-Bello MG, De Jesus-Laboy KM, Shen N, Cox LM, Amir A, Gonzalez A, Bokulich NA, Song SJ, Hoashi M, Rivera-Vinas JI, Mendez K, Knight R, Clemente JC (2016) Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nat Med 22(3):250–253. https://doi.org/10.1038/nm.4039
Dowds CM, Blumberg RS, Zeissig S (2015) Control of intestinal homeostasis through crosstalk between natural killer T cells and the intestinal microbiota. Clin Immunol 159(2):128–133. https://doi.org/10.1016/j.clim.2015.05.008
Edwards CA, Parrett AM (2002) Intestinal flora during the first months of life: new perspectives. Br J Nutr 88(Suppl 1):S11–S18. https://doi.org/10.1079/BJN2002625
Faith JJ, Ahern PP, Ridaura VK, Cheng J, Gordon JI (2014) Identifying gut microbe-host phenotype relationships using combinatorial communities in gnotobiotic mice. Sci Transl Med 6(220):220ra211. https://doi.org/10.1126/scitranslmed.3008051
Forsberg A, West CE, Prescott SL, Jenmalm MC (2016) Pre- and probiotics for allergy prevention: time to revisit recommendations? Clin Exp Allergy 46(12):1506–1521. https://doi.org/10.1111/cea.12838
Fouhy F, Ross RP, Fitzgerald GF, Stanton C, Cotter PD (2012) Composition of the early intestinal microbiota: knowledge, knowledge gaps and the use of high-throughput sequencing to address these gaps. Gut Microbes 3(3):203–220. https://doi.org/10.4161/gmic.20169
Franzosa EA, Huang K, Meadow JF, Gevers D, Lemon KP, Bohannan BJ, Huttenhower C (2015) Identifying personal microbiomes using metagenomic codes. Proc Natl Acad Sci USA 112(22):E2930–E2938. https://doi.org/10.1073/pnas.1423854112
Fredricks DN, Fiedler TL, Marrazzo JM (2005) Molecular identification of bacteria associated with bacterial vaginosis. N Engl J Med 353(18):1899–1911. https://doi.org/10.1056/NEJMoa043802
Fujiya M, Musch MW, Nakagawa Y, Hu S, Alverdy J, Kohgo Y, Schneewind O, Jabri B, Chang EB (2007) The Bacillus subtilis quorum-sensing molecule CSF contributes to intestinal homeostasis via OCTN2, a host cell membrane transporter. Cell Host Microbe 1(4):299–308. https://doi.org/10.1016/j.chom.2007.05.004
Garn H, Neves JF, Blumberg RS, Renz H (2013) Effect of barrier microbes on organ-based inflammation. J Allergy Clin Immunol 131(6):1465–1478. https://doi.org/10.1016/j.jaci.2013.04.031
Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE (2006) Metagenomic analysis of the human distal gut microbiome. Science 312(5778):1355–1359. https://doi.org/10.1126/science.1124234
Gosalbes MJ, Llop S, Valles Y, Moya A, Ballester F, Francino MP (2013) Meconium microbiota types dominated by lactic acid or enteric bacteria are differentially associated with maternal eczema and respiratory problems in infants. Clin Exp Allergy 43(2):198–211. https://doi.org/10.1111/cea.12063
Goto Y, Obata T, Kunisawa J, Sato S, Ivanov II, Lamichhane A, Takeyama N, Kamioka M, Sakamoto M, Matsuki T, Setoyama H, Imaoka A, Uematsu S, Akira S, Domino SE, Kulig P, Becher B, Renauld JC, Sasakawa C, Umesaki Y, Benno Y, Kiyono H (2014) Innate lymphoid cells regulate intestinal epithelial cell glycosylation. Science 345(6202):1254009. https://doi.org/10.1126/science.1254009
Gur TL, Bailey MT (2016) Effects of stress on commensal microbes and immune system activity. Adv Exp Med Biol 874:289–300. https://doi.org/10.1007/978-3-319-20215-0_14
Haghikia A, Jorg S, Duscha A, Berg J, Manzel A, Waschbisch A, Hammer A, Lee DH, May C, Wilck N, Balogh A, Ostermann AI, Schebb NH, Akkad DA, Grohme DA, Kleinewietfeld M, Kempa S, Thone J, Demir S, Muller DN, Gold R, Linker RA (2015) Dietary fatty acids directly impact central nervous system autoimmunity via the small intestine. Immunity 43(4):817–829. https://doi.org/10.1016/j.immuni.2015.09.007
Hall IC, O’Toole E (1934) Bacterial flora of first specimens of meconium passaed by fifty new-born infants. Am J Dis Child 47(6):1279–1285
Hirsch AG, Pollak J, Glass TA, Poulsen MN, Bailey-Davis L, Mowery J, Schwartz BS (2017) Early-life antibiotic use and subsequent diagnosis of food allergy and allergic diseases. Clin Exp Allergy 47(2):236–244. https://doi.org/10.1111/cea.12807
Honda K, Littman DR (2016) The microbiota in adaptive immune homeostasis and disease. Nature 535(7610):75–84. https://doi.org/10.1038/nature18848
Hua X, Goedert JJ, Pu A, Yu G, Shi J (2016) Allergy associations with the adult fecal microbiota: analysis of the American Gut Project. EBioMedicine 3:172–179. https://doi.org/10.1016/j.ebiom.2015.11.038
Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome. Nature 486(7402):207–214. https://doi.org/10.1038/nature11234
Imhann F, Bonder MJ, Vich Vila A, Fu J, Mujagic Z, Vork L, Tigchelaar EF, Jankipersadsing SA, Cenit MC, Harmsen HJ, Dijkstra G, Franke L, Xavier RJ, Jonkers D, Wijmenga C, Weersma RK, Zhernakova A (2016) Proton pump inhibitors affect the gut microbiome. Gut 65(5):740–748. https://doi.org/10.1136/gutjnl-2015-310376
Jimenez E, Fernandez L, Marin ML, Martin R, Odriozola JM, Nueno-Palop C, Narbad A, Olivares M, Xaus J, Rodriguez JM (2005) Isolation of commensal bacteria from umbilical cord blood of healthy neonates born by cesarean section. Curr Microbiol 51(4):270–274. https://doi.org/10.1007/s00284-005-0020-3
Johansson ME, Phillipson M, Petersson J, Velcich A, Holm L, Hansson GC (2008) The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria. Proc Natl Acad Sci USA 105(39):15064–15069. https://doi.org/10.1073/pnas.0803124105
Johansson ME, Ambort D, Pelaseyed T, Schutte A, Gustafsson JK, Ermund A, Subramani DB, Holmen-Larsson JM, Thomsson KA, Bergstrom JH, van der Post S, Rodriguez-Pineiro AM, Sjovall H, Backstrom M, Hansson GC (2011) Composition and functional role of the mucus layers in the intestine. Cell Mol Life Sci 68(22):3635–3641. https://doi.org/10.1007/s00018-011-0822-3
Jones HE, Harris KA, Azizia M, Bank L, Carpenter B, Hartley JC, Klein N, Peebles D (2009) Differing prevalence and diversity of bacterial species in fetal membranes from very preterm and term labor. PLoS One 4(12):e8205. https://doi.org/10.1371/journal.pone.0008205
Karimi K, Inman MD, Bienenstock J, Forsythe P (2009) Lactobacillus reuteri-induced regulatory T cells protect against an allergic airway response in mice. Am J Respir Crit Care Med 179(3):186–193. https://doi.org/10.1164/rccm.200806-951OC
Kawaguchi M, Nanno M, Umesaki Y, Matsumoto S, Okada Y, Cai Z, Shimamura T, Matsuoka Y, Ohwaki M, Ishikawa H (1993) Cytolytic activity of intestinal intraepithelial lymphocytes in germ-free mice is strain dependent and determined by T cells expressing gamma delta T-cell antigen receptors. Proc Natl Acad Sci USA 90(18):8591–8594
Kelly D, King T, Aminov R (2007) Importance of microbial colonization of the gut in early life to the development of immunity. Mutat Res 622(1–2):58–69. https://doi.org/10.1016/j.mrfmmm.2007.03.011
Kinnebrew MA, Buffie CG, Diehl GE, Zenewicz LA, Leiner I, Hohl TM, Flavell RA, Littman DR, Pamer EG (2012) Interleukin 23 production by intestinal CD103(+)CD11b(+) dendritic cells in response to bacterial flagellin enhances mucosal innate immune defense. Immunity 36(2):276–287. https://doi.org/10.1016/j.immuni.2011.12.011
Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, Angenent LT, Ley RE (2011) Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci USA 108(Suppl 1):4578–4585. https://doi.org/10.1073/pnas.1000081107
Koleva PT, Kim JS, Scott JA, Kozyrskyj AL (2015) Microbial programming of health and disease starts during fetal life. Birth Defects Res C Embryo Today 105(4):265–277. https://doi.org/10.1002/bdrc.21117
Kozakova H, Schwarzer M, Tuckova L, Srutkova D, Czarnowska E, Rosiak I, Hudcovic T, Schabussova I, Hermanova P, Zakostelska Z, Aleksandrzak-Piekarczyk T, Koryszewska-Baginska A, Tlaskalova-Hogenova H, Cukrowska B (2016) Colonization of germ-free mice with a mixture of three lactobacillus strains enhances the integrity of gut mucosa and ameliorates allergic sensitization. Cell Mol Immunol 13(2):251–262. https://doi.org/10.1038/cmi.2015.09
Kump P, Hogenauer C (2016) Any future for fecal microbiota transplantation as treatment strategy for inflammatory bowel diseases? Dig Dis 34(Suppl 1):74–81. https://doi.org/10.1159/000447379
Le Huerou-Luron I, Blat S, Boudry G (2010) Breast- v. formula-feeding: impacts on the digestive tract and immediate and long-term health effects. Nutr Res Rev 23(1):23–36. https://doi.org/10.1017/S0954422410000065
Levy M, Thaiss CA, Zeevi D, Dohnalova L, Zilberman-Schapira G, Mahdi JA, David E, Savidor A, Korem T, Herzig Y, Pevsner-Fischer M, Shapiro H, Christ A, Harmelin A, Halpern Z, Latz E, Flavell RA, Amit I, Segal E, Elinav E (2015) Microbiota-modulated metabolites shape the intestinal microenvironment by regulating NLRP6 inflammasome signaling. Cell 163(6):1428–1443. https://doi.org/10.1016/j.cell.2015.10.048
Lima MT, Andrade AC, Oliveira GP, Calixto RS, Oliveira DB, Souza EL, Trindade GS, Nicoli JR, Kroon EG, Martins FS, Abrahao JS (2016) Microbiota is an essential element for mice to initiate a protective immunity against Vaccinia virus. FEMS Microbiol Ecol 92(2). https://doi.org/10.1093/femsec/fiv147
Lin L, Zhang J (2017) Role of intestinal microbiota and metabolites on gut homeostasis and human diseases. BMC Immunol 18(1):2. https://doi.org/10.1186/s12865-016-0187-3
Linares DM, Ross P, Stanton C (2016) Beneficial microbes: the pharmacy in the gut. Bioengineered 7(1):11–20. https://doi.org/10.1080/21655979.2015.1126015
Lyons A, O’Mahony D, O’Brien F, MacSharry J, Sheil B, Ceddia M, Russell WM, Forsythe P, Bienenstock J, Kiely B, Shanahan F, O’Mahony L (2010) Bacterial strain-specific induction of Foxp3+ T regulatory cells is protective in murine allergy models. Clin Exp Allergy 40(5):811–819. https://doi.org/10.1111/j.1365-2222.2009.03437.x
Macpherson AJ, Uhr T (2004) Induction of protective IgA by intestinal dendritic cells carrying commensal bacteria. Science 303(5664):1662–1665. https://doi.org/10.1126/science.1091334
Macpherson AJ, Gatto D, Sainsbury E, Harriman GR, Hengartner H, Zinkernagel RM (2000) A primitive T cell-independent mechanism of intestinal mucosal IgA responses to commensal bacteria. Science 288(5474):2222–2226
Mandal RS, Saha S, Das S (2015) Metagenomic surveys of gut microbiota. Genomics Proteomics Bioinformatics 13(3):148–158. https://doi.org/10.1016/j.gpb.2015.02.005
Marchesi JR (2010) Prokaryotic and eukaryotic diversity of the human gut. Adv Appl Microbiol 72:43–62. https://doi.org/10.1016/S0065-2164(10)72002-5
Maynard CL, Elson CO, Hatton RD, Weaver CT (2012) Reciprocal interactions of the intestinal microbiota and immune system. Nature 489(7415):231–241. https://doi.org/10.1038/nature11551
Moon C, Baldridge MT, Wallace MA, Burnham CA, Virgin HW, Stappenbeck TS (2015) Vertically transmitted faecal IgA levels determine extra-chromosomal phenotypic variation. Nature 521(7550):90–93. https://doi.org/10.1038/nature14139
Mortha A, Chudnovskiy A, Hashimoto D, Bogunovic M, Spencer SP, Belkaid Y, Merad M (2014) Microbiota-dependent crosstalk between macrophages and ILC3 promotes intestinal homeostasis. Science 343(6178):1249288. https://doi.org/10.1126/science.1249288
Nagai A, Takebe K, Nio-Kobayashi J, Takahashi-Iwanaga H, Iwanaga T (2010) Cellular expression of the monocarboxylate transporter (MCT) family in the placenta of mice. Placenta 31(2):126–133. https://doi.org/10.1016/j.placenta.2009.11.013
Narushima S, Sugiura Y, Oshima K, Atarashi K, Hattori M, Suematsu M, Honda K (2014) Characterization of the 17 strains of regulatory T cell-inducing human-derived Clostridia. Gut Microbes 5(3):333–339. https://doi.org/10.4161/gmic.28572
Nistal E, Caminero A, Herran AR, Perez-Andres J, Vivas S, Ruiz de Morales JM, Saenz de Miera LE, Casqueiro J (2016) Study of duodenal bacterial communities by 16S rRNA gene analysis in adults with active celiac disease vs non-celiac disease controls. J Appl Microbiol 120(6):1691–1700. https://doi.org/10.1111/jam.13111
Okamoto K, Fujiya M, Nata T, Ueno N, Inaba Y, Ishikawa C, Ito T, Moriichi K, Tanabe H, Mizukami Y, Chang EB, Kohgo Y (2012) Competence and sporulation factor derived from Bacillus subtilis improves epithelial cell injury in intestinal inflammation via immunomodulation and cytoprotection. Int J Color Dis 27(8):1039–1046. https://doi.org/10.1007/s00384-012-1416-8
Oliveira MR, Tafuri WL, Afonso LC, Oliveira MA, Nicoli JR, Vieira EC, Scott P, Melo MN, Vieira LQ (2005) Germ-free mice produce high levels of interferon-gamma in response to infection with Leishmania major but fail to heal lesions. Parasitology 131(Pt 4):477–488. https://doi.org/10.1017/S0031182005008073
Penders J, Thijs C, Vink C, Stelma FF, Snijders B, Kummeling I, van den Brandt PA, Stobberingh EE (2006) Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics 118(2):511–521. https://doi.org/10.1542/peds.2005-2824
Perez Martinez G, Bauerl C, Collado MC (2014) Understanding gut microbiota in elderly’s health will enable intervention through probiotics. Benef Microbes 5(3):235–246. https://doi.org/10.3920/BM2013.0079
Pineiro M, Stanton C (2007) Probiotic bacteria: legislative framework—requirements to evidence basis. J Nutr 137(3 Suppl 2):850S–853S
Quercia S, Candela M, Giuliani C, Turroni S, Luiselli D, Rampelli S, Brigidi P, Franceschi C, Bacalini MG, Garagnani P, Pirazzini C (2014) From lifetime to evolution: timescales of human gut microbiota adaptation. Front Microbiol 5(587). https://doi.org/10.3389/fmicb.2014.00587
Rodriguez B, Prioult G, Bibiloni R, Nicolis I, Mercenier A, Butel MJ, Waligora-Dupriet AJ (2011) Germ-free status and altered caecal subdominant microbiota are associated with a high susceptibility to cow’s milk allergy in mice. FEMS Microbiol Ecol 76(1):133–144. https://doi.org/10.1111/j.1574-6941.2010.01035.x
Roduit C, Frei R, Depner M, Schaub B, Loss G, Genuneit J, Pfefferle P, Hyvarinen A, Karvonen AM, Riedler J, Dalphin JC, Pekkanen J, von Mutius E, Braun-Fahrlander C, Lauener R (2014) Increased food diversity in the first year of life is inversely associated with allergic diseases. J Allergy Clin Immunol 133(4):1056–1064. https://doi.org/10.1016/j.jaci.2013.12.1044
Scarpellini E, Ianiro G, Attili F, Bassanelli C, De Santis A, Gasbarrini A (2015) The human gut microbiota and virome: potential therapeutic implications. Dig Liver Dis 47(12):1007–1012. https://doi.org/10.1016/j.dld.2015.07.008
Segain JP, Raingeard de la Bletiere D, Bourreille A, Leray V, Gervois N, Rosales C, Ferrier L, Bonnet C, Blottiere HM, Galmiche JP (2000) Butyrate inhibits inflammatory responses through NFkappaB inhibition: implications for Crohn’s disease. Gut 47(3):397–403
Smolinska S, Groeger D, O’Mahony L (2017) Biology of the Microbiome 1. Interactions with the Host Immune Response. Gastroenterol Clin N Am 46(1):19–35. https://doi.org/10.1016/j.gtc.2016.09.004
Snyder ML (1936) The bacterial flora of meconium specimens collected from sixty-four infants within four hours after delivery. J Pediatr 9:624–632
Souza DG, Vieira AT, Soares AC, Pinho V, Nicoli JR, Vieira LQ, Teixeira MM (2004) The essential role of the intestinal microbiota in facilitating acute inflammatory responses. J Immunol 173(6):4137–4146
Stefka AT, Feehley T, Tripathi P, Qiu J, McCoy K, Mazmanian SK, Tjota MY, Seo GY, Cao S, Theriault BR, Antonopoulos DA, Zhou L, Chang EB, YX F, Nagler CR (2014) Commensal bacteria protect against food allergen sensitization. Proc Natl Acad Sci USA 111(36):13145–13150. https://doi.org/10.1073/pnas.1412008111
Tang C, Kamiya T, Liu Y, Kadoki M, Kakuta S, Oshima K, Hattori M, Takeshita K, Kanai T, Saijo S, Ohno N, Iwakura Y (2015) Inhibition of dectin-1 signaling ameliorates colitis by inducing lactobacillus-mediated regulatory T cell expansion in the intestine. Cell Host Microbe 18(2):183–197. https://doi.org/10.1016/j.chom.2015.07.003
Tlaskalova-Hogenova H, Sterzl J, Stepankova R, Dlabac V, Veticka V, Rossmann P, Mandel L, Rejnek J (1983) Development of immunological capacity under germfree and conventional conditions. Ann N Y Acad Sci 409:96–113
Trikha A, Baillargeon JG, Kuo YF, Tan A, Pierson K, Sharma G, Wilkinson G, Bonds RS (2013) Development of food allergies in patients with gastroesophageal reflux disease treated with gastric acid suppressive medications. Pediatr Allergy Immunol 24(6):582–588. https://doi.org/10.1111/pai.12103
Tsilingiri K, Rescigno M (2013) Postbiotics: what else? Benef Microbes 4(1):101–107. https://doi.org/10.3920/BM2012.0046
Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI (2007) The human microbiome project. Nature 449(7164):804–810. https://doi.org/10.1038/nature06244
Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI (2009) A core gut microbiome in obese and lean twins. Nature 457(7228):480–484. https://doi.org/10.1038/nature07540
Umesaki Y, Setoyama H, Matsumoto S, Okada Y (1993) Expansion of alpha beta T-cell receptor-bearing intestinal intraepithelial lymphocytes after microbial colonization in germ-free mice and its independence from thymus. Immunology 79(1):32–37
Untersmayr E, Bakos N, Scholl I, Kundi M, Roth-Walter F, Szalai K, Riemer AB, Ankersmit HJ, Scheiner O, Boltz-Nitulescu G, Jensen-Jarolim E (2005) Anti-ulcer drugs promote IgE formation toward dietary antigens in adult patients. FASEB J 19(6):656–658. https://doi.org/10.1096/fj.04-3170fje
Vaishampayan PA, Kuehl JV, Froula JL, Morgan JL, Ochman H, Francino MP (2010) Comparative metagenomics and population dynamics of the gut microbiota in mother and infant. Genome Biol Evol 2:53–66. https://doi.org/10.1093/gbe/evp057
Vaishnava S, Yamamoto M, Severson KM, Ruhn KA, Yu X, Koren O, Ley R, Wakeland EK, Hooper LV (2011) The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine. Science 334(6053):255–258. https://doi.org/10.1126/science.1209791
van den Berk LC, Jansen BJ, Siebers-Vermeulen KG, Netea MG, Latuhihin T, Bergevoet S, Raymakers RA, Kogler G, Figdor CC, Adema GJ, Torensma R (2009) Toll-like receptor triggering in cord blood mesenchymal stem cells. J Cell Mol Med 13(9B):3415–3426. https://doi.org/10.1111/j.1582-4934.2009.00653.x
van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, Visser CE, Kuijper EJ, Bartelsman JF, Tijssen JG, Speelman P, Dijkgraaf MG, Keller JJ (2013) Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med 368(5):407–415. https://doi.org/10.1056/NEJMoa1205037
Vangay P, Ward T, Gerber JS, Knights D (2015) Antibiotics, pediatric dysbiosis, and disease. Cell Host Microbe 17(5):553–564. https://doi.org/10.1016/j.chom.2015.04.006
Verhasselt V (2010) Oral tolerance in neonates: from basics to potential prevention of allergic disease. Mucosal Immunol 3(4):326–333. https://doi.org/10.1038/mi.2010.25
Vetvicka V, Tlaskalova-Hogenova H, Stepankova R (1983) Effects of microflora antigens on lymphocyte migration patterns in germfree and conventional rats. Folia Biol (Praha) 29(6):412–418
Walsh CJ, Guinane CM, O’Toole PW, Cotter PD (2014) Beneficial modulation of the gut microbiota. FEBS Lett 588(22):4120–4130. https://doi.org/10.1016/j.febslet.2014.03.035
Watanabe Y, Arase S, Nagaoka N, Kawai M, Matsumoto S (2016) Chronic psychological stress disrupted the composition of the murine colonic microbiota and accelerated a murine model of inflammatory bowel disease. PLoS One 11(3):e0150559. https://doi.org/10.1371/journal.pone.0150559
West CE, Renz H, Jenmalm MC, Kozyrskyj AL, Allen KJ, Vuillermin P, Prescott SL (2015) The gut microbiota and inflammatory noncommunicable diseases: associations and potentials for gut microbiota therapies. J Allergy Clin Immunol 135(1):3–13. https://doi.org/10.1016/j.jaci.2014.11.012
Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD (2011) Linking long-term dietary patterns with gut microbial enterotypes. Science 334(6052):105–108. https://doi.org/10.1126/science.1208344
Zheng Y, Valdez PA, Danilenko DM, Hu Y, Sa SM, Gong Q, Abbas AR, Modrusan Z, Ghilardi N, de Sauvage FJ, Ouyang W (2008) Interleukin-22 mediates early host defense against attaching and effacing bacterial pathogens. Nat Med 14(3):282–289. https://doi.org/10.1038/nm1720
Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, Wang J, Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, Cenit MC, Deelen P, Swertz MA, Weersma RK, Feskens EJ, Netea MG, Gevers D, Jonkers D, Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C, Fu J (2016) Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science 352(6285):565–569. https://doi.org/10.1126/science.aad3369
Acknowledgements
The research of the author is supported by grants KLI284-B00 and WKP39 of the Austrian Science Fund FWF, by grant P1621673 of the Austrian Ministry of Science, Research and Economy and a research project supported by Nordmark GmbH.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer International Publishing AG
About this chapter
Cite this chapter
Untersmayr, E. (2017). The Gut Microbiome and Its Marriage to the Immune System: Can We Change It All?. In: Schmidt-Weber, C. (eds) Allergy Prevention and Exacerbation. Birkhäuser Advances in Infectious Diseases. Springer, Cham. https://doi.org/10.1007/978-3-319-69968-4_10
Download citation
DOI: https://doi.org/10.1007/978-3-319-69968-4_10
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-69967-7
Online ISBN: 978-3-319-69968-4
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)