Abstract
The microbial communities that live in and on our bodies play complex roles in maintaining our health and in causing disease. The recent application of high-throughput DNA sequencing to examine these communities, both in terms of species present and in their activities, has proven to be a very powerful tool for examining the influences of microbes on human health. Whilst we are only just beginning to understand the role of our microbial ‘second’ genome, what is clear is that certain shifts and alterations in our microbiome are associated with, and may ultimately cause or cure, disease. The interaction between human host and microbes is multifaceted, however, and such interactions must therefore be examined in overall context of disease, diet, medications as well as underlying host genetics.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT (2012) Structure, function and diversity of the healthy human microbiome. Nature 486:207–214
Burns M, Lynch J, Starr T, Knights D, Blekhman R (2015) Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment. Genome Med 7(1):55
Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE et al (2009) A core gut microbiome in obese and lean twins. Nature 457(7228):480–484
Gevers D, Kugathasan S, Denson LA, Vazquez-Baeza Y, Van† Treuren W, Ren B et al (2014) The treatment-naive microbiome in new-onset Crohn s disease. Cell Host Microbe 15(3):382–392
Knights D, Silverberg M, Weersma R, Gevers D, Dijkstra G, Huang H et al (2014) Complex host genetics influence the microbiome in inflammatory bowel disease. Genome Med 6(12):107
Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N et al (2010) Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci 107(26):11971–11975
Huh SY, Rifas-Shiman SL, Zera CA, Edwards JWR, Oken E, Weiss ST, et al (2012) Delivery by caesarean section and risk of obesity in preschool age children: a prospective cohort study. Arch Dis Child 97(7):610–616
Bager P (2011) Birth by caesarean section and wheezing, asthma, allergy, and intestinal disease. Clin Exp Allergy 41(2):147–148
Arrieta M-C, Stiemsma LT, Dimitriu PA, Thorson L, Russell S, Yurist-Doutsch S et al (2015) Early infancy microbial and metabolic alterations affect risk of childhood asthma. Sci Transl Med 7(307):307ra152–307ra152
Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende D et al (2011) Enterotypes of the human gut microbiome. Nature 473:174–180
Ursell LK, Haiser HJ, Van Treuren W, Garg N, Reddivari L, Vanamala J et al (2014) The intestinal metabolome: an intersection between microbiota and host. Gastroenterology 146(6):1470–1476
Round JL, Mazmanian SK (2009) The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol 9(5):313–323
Clemente J, Ursell L, Parfrey L, Knight R (2012) The impact of the gut microbiota on human health: an integrative view. Cell 148:1258–1270
Turnbaugh PJ, Backhed F, Fulton L, Gordon JI (2008) Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3:213–223
Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M et al (2012) Human gut microbiome viewed across age and geography. Nature 486(7402):222–227
Maslowski KM, Mackay CR (2011) Diet, gut microbiota and immune responses. Nat Immunol 12(1):5–9
Kranich J, Maslowski KM, Mackay CR (2011) Commensal flora and the regulation of inflammatory and autoimmune responses. Semin Immunol 23(2):139–145
Perdomo OJ, Cavaillon JM, Huerre M, Ohayon H, Gounon P, Sansonetti PJ (1994) Acute inflammation causes epithelial invasion and mucosal destruction in experimental shigellosis. J Exp Med 180(4):1307–1319
Vaishnava S, Behrendt CL, Ismail AS, Eckmann L, Hooper LV (2008) Paneth Cells directly sense gut commensals and maintain homeostasis at the intestinal host-microbial interface. Proc Natl Acad Sci 105(52):20858–20863
Ivanov II, Atarashi K, Manel N, Brodie EL, Shima T, Karaoz U et al (2009) Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139(3):485–498
Duan J, Chung H, Troy E, Kasper DL (2010) Microbial colonization drives expansion of IL-1 receptor 1-expressing and IL-17-producing [gamma]/[delta] T cells. Cell Host Microbe 7(2):140–150
Cho I, Blaser M (2012) The human microbiome: at the interface of health and disease. Nat Rev Genet 13:10
Reid G, Younes JA, Van der Mei HC, Gloor GB, Knight R, Busscher HJ (2011) Microbiota restoration: natural and supplemented recovery of human microbial communities. Nat Rev Micro 9(1):27–38
Laurence A, O’Shea JJ, Watford WT (2008) Interleukin-22: a sheep in wolf’s clothing. Nat Med 14(3):247–249
Salzman NH, Hung K, Haribhai D, Chu H, Karlsson-Sjoberg J, Amir E et al (2010) Enteric defensins are essential regulators of intestinal microbial ecology. Nat Immunol 11(1):76–82
Maloy KJ, Powrie F (2011) Intestinal homeostasis and its breakdown in inflammatory bowel disease. Nature 474(7351):298–306
Koslowski MJ, Beisner J, Stange EF, Wehkamp J (2010) Innate antimicrobial host defense in small intestinal Crohn’s disease. Int J Med Microbiol 300(1):34–40
Wehkamp J, Koslowski M, Wang G, Stange EF (2008) Barrier dysfunction due to distinct defensin deficiencies in small intestinal and colonic Crohn’s disease. Mucosal Immunol 1(1s):S67–S74
Artis D (2008) Epithelial-cell recognition of commensal bacteria and maintenance of immune homeostasis in the gut. Nat Rev Immunol 8(6):411–420
Hooper LV, Macpherson AJ (2010) Immune adaptations that maintain homeostasis with the intestinal microbiota. Nat Rev Immunol 10(3):159–169
Shan M, Gentile M, Yeiser JR, Walland AC, Bornstein VU, Chen K et al (2013) Mucus enhances gut homeostasis and oral tolerance by delivering immunoregulatory signals. Science 342(6157):447–453
Heazlewood C, Cook M, Eri R, Price G, Tauro S, Taupin D et al (2008) Aberrant mucin assembly in mice causes endoplasmic reticulum stress and spontaneous inflammation resembling ulcerative colitis. PLoS Med 5:e54
Sherlock J, Joyce-Shaikh B, Turner S, Chao C, Sathe M, Grein J et al (2012) IL-23 induces spondyloarthropathy by acting on ROR-gammat+ CD3+CD4-CD8- entheseal resident T cells. Nat Med 18:1069–1076
Fasano A, Nataro JP (2004) Intestinal epithelial tight junctions as targets for enteric bacteria-derived toxins. Adv Drug Deliv Rev 56(6):795–807
Collins SM. IV (2001) Modulation of intestinal inflammation by stress: basic mechanisms and clinical relevance. 2001-03-01 00:00:00. G315-G8 p
Bruewer M, Luegering A, Kucharzik T, Parkos CA, Madara JL, Hopkins AM et al (2003) Proinflammatory cytokines disrupt epithelial barrier function by apoptosis-independent mechanisms. J Immunol 171(11):6164–6172
Nusrat A, Turner JR, Madara JL. IV (2000) Regulation of tight junctions by extracellular stimuli: nutrients, cytokines, and immune cells. 2000-11-01 00:00:00. G851-G7 p
Teahon K, Smethurst P, Levi AJ, Menzies IS, Bjarnason I (1992) Intestinal permeability in patients with Crohn’s disease and their first degree relatives. Gut 33(3):320–323
Lubrano E, Ciacci C, Ames P, Mazzacca G, Oriente P, Scarpa R (1996) The arthritis of coeliac disease: prevalence and pattern in 200 adult patients. Rheumatology 35:1314–1318
Podolsky DK (2002) Inflammatory bowel disease. N Eng J Med 347(6):417–429
Mielants H, Veys EM, Goemaere S, Goethals K, Cuvelier C, De Vos M (1991) Gut inflammation in the spondyloarthropathies: clinical, radiologic, biologic and genetic features in relation to the type of histology. A prospective study. J Rheumatol 18(10):1542–1551
Vaile J, Meddings J, Yacyshyn B, Russell A, Maksymowych W (1999) Bowel permeability and CD45RO expression on circulating CD20+ B cells in patients with ankylosing spondylitis and their relatives. J Rheumatol 26:128–135
Martinez-Gonzalez O, Cantero-Hinojosa J, Paule-Sastre P, Gomez-Magan JC, Salvatierra-Rios D (1994) Intestinal permeability in patients with ankylosing spondyllitis and their healthy relatives. Rheumatology 33(7):644–647
Chabot S, Wagner JS, Farrant S, Neutra MR (2006) TLRs regulate the gatekeeping functions of the intestinal follicle-associated epithelium. J Immunol 176(7):4275–4283
Suzuki K, Ha S, Tsuji M, Fagarasan S (2007) Intestinal IgA synthesis: a primitive form of adaptive immunity that regulates microbial communities in the gut. Semin Immunol 19:127–135
Wesa A, Galy A (2002) Increased production of pro-inflammatory cytokines and enhanced T cell responses after activation of human dendritic cells with IL-1 and CD40 ligand. BMC Immunol 3:14
Cruz CM, Rinna A, Forman HJ, Ventura ALM, Persechini PM, Ojcius DM (2007) ATP activates a reactive oxygen species-dependent oxidative stress response and secretion of proinflammatory cytokines in macrophages. J Biol Chem 282(5):2871–2879
Hirotani T, Lee PY, Kuwata H, Yamamoto M, Matsumoto M, Kawase I et al (2005) The nuclear IkB protein IkBNS selectively inhibits lipopolysaccharide-induced IL-6 production in macrophages of the colonic lamina propria. J Immunol 174(6):3650–3657
Denning T, Wang Y-C, Patel S, Williams I, Pulendran B (2007) Lamina propria macrophages and dendritic cells differentially induce regulatory and interleukin 17-producing T cell responses. Nat Immunol 8:1086–1094
Glocker E, Kotlarz D, Boztug K, Gertz E, Schaffer A, Noyan F et al (2009) Inflammatory bowel disease and mutations affecting the interleukin-10 receptor. N Engl J Med 361:2033–2045
Consortium TUIGCtWTCC (2009) Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region. Nat Genet 41(12):1330–1334
Franke A, Balschun T, Sina C, Ellinghaus D, Hasler R, Mayr G et al (2010) Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL). Nat Genet 42(4):292–294
Oppmann B, Lesley R, Blom B, Timans J, Xu Y, Hunte B et al (2000) Novel p19 protein engages IL-12p40 to form a cytokine, IL-23, with biological activities similar as well as distinct from IL-12. Immunity 13:715–725
Burton P, Clayton D, Cardon L, Craddock N, Deloukas P, Duncanson A et al (2007) Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants. Nat Genet 39:1329–1337
Cargill M, Schrodi S, Chang M, Garcia V, Brandon R, Callis K et al (2007) A large-scale genetic association study confirms IL12B and leads to the identification of IL23R as psoriasis-risk genes. Am J Hum Gen 80:273–290
Duerr R, Taylor K, Brant S, Rioux J, Silverberg M, Daly M et al (2006) A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science 314:1461–1463
Xavier JM, Shahram F, Davatchi F, Rosa A, Crespo J, Abdollahi BS et al (2012) Association study of IL10 and IL23R–IL12RB2 in Iranian patients with Behçet’s disease. Arthritis Rheum 64(8):2761–2772
Ogawa A, Andoh A, Araki Y, Bamba T, Fujiyama Y (2004) Neutralization of interleukin-17 aggravates dextran sulfate sodium-induced colitis in mice. Clin Immunol 110:55–62
Zheng S, Wang J, Horwitz D (2008) Cutting edge: Foxp3+CD4+CD25+ regulatory T cells induced by IL-2 and TGF-beta are resistant to Th17 conversion by IL-6. J Immunol 180:7112–7116
Takatori H, Kanno Y, Watford WT, Tato CM, Weiss G, Ivanov II et al (2009) Lymphoid tissue inducer–like cells are an innate source of IL-17 and IL-22. J Exp Med 206(1):35–41
Kobori A, Yagi Y, Imaeda H, Ban H, Bamba S, Tsujikawa T et al (2010) Interleukin-33 expression is specifically enhanced in inflamed mucosa of ulcerative colitis. J Gastroenterol 45(10):999–1007
Lockhart E, Green AM, Flynn JL (2006) IL-17 production is dominated by γδ T cells rather than CD4 T cells during mycobacterium tuberculosis infection. J Immunol 177(7):4662–4669
Sonnenberg GF, Fouser LA, Artis D (2011) Border patrol: regulation of immunity, inflammation and tissue homeostasis at barrier surfaces by IL-22. Nat Immunol 12(5):383–390
Cua DJ, Tato CM (2010) Innate IL-17-producing cells: the sentinels of the immune system. Nat Rev Immunol 10(7):479–489
Mokuno Y, Matsuguchi T, Takano M, Nishimura H, Washizu J, Ogawa T et al (2000) Expression of toll-like receptor 2 on gammadelta T cells bearing invariant Vgamma6/Vdelta1 induced by Escherichia coli infection in mice. J Immunol 165:931–940
Martin B, Hirota K, Cua DJ, Stockinger B, Veldhoen M (2009) Interleukin-17-producing [gamma][delta] T cells selectively expand in response to pathogen products and environmental signals. Immunity 31(2):321–330
Shibata K, Yamada H, Hara H, Kishihara K, Yoshikai Y (2007) Resident Vdelta1+ gammadelta T cells control early infiltration of neutrophils after Escherichia coli infection via IL-17 production. J Immunol 178:4466–4472
Roark C, French J, Taylor M, Bendele A, Born W, O’Brien R (2007) Exacerbation of collagen-induced arthritis by oligoclonal, IL-17-producing gamma delta T cells. J Immunol 179:5576–5583
Nanno M, Kanari Y, Naito T, Inoue N, Hisamatsu T, Chinen H et al (2008) Exacerbating role of gammadelta T cells in chronic colitis of T-cell receptor alpha mutant mice. Gastroenterology 134:481–490
Kenna T, Davidson S, Duan R, Bradbury L, McFarlane J, Smith M et al (2012) Enrichment of circulating interleukin-17-secreting interleukin-23 receptor-positive gamma/delta T cells in patients with active ankylosing spondylitis. Arthritis Rheum 64:1420–1429
Bendelac A, Savage P, Teyton L (2007) The biology of NKT cells. Ann Rev Immunol 25:297–336
Rachitskaya A, Hansen A, Horai R, Li Z, Villasmil R, Luger D et al (2008) Cutting edge: NKT cells constitutively express IL-23 receptor and RORgammat and rapidly produce IL-17 upon receptor ligation in an IL-6- independent fashion. J Immunol 180:5167–5171
Akbari O, Stock P, Meyer E, Kronenberg M, Sidobre S, Nakayama T et al (2003) Essential role of NKT cells producing IL-4 and IL-13 in the development of allergen-induced airway hyperreactivity. Nat Med 9:582–588
Baxter A, Kinder S, Hammond K, Scollay R, Godfrey D (1997) Association between alphabetaTCR+CD4-CD8- T-cell deficiency and IDDM in NOD/Lt mice. Diabetes 46:572–582
Heller F, Fuss IJ, Nieuwenhuis EE, Blumberg RS, Strober W (2002) Oxazolone colitis, a Th2 colitis model resembling ulcerative colitis, is mediated by IL-13-producing NK-T cells. Immunity 17(5):629–638
Ueno Y, Tanaka S, Sumii M, Miyake S, Tazuma S, Taniguchi M et al (2005) Single dose of OCH improves mucosal T helper type 1/T helper type 2 cytokine balance and prevents experimental colitis in the presence of Vα14 natural killer T cells in mice. Inflamm Bowel Dis 11(1):35–41
Wingender G, Stepniak D, Krebs P, Lin L, McBride S, Wei B et al (2012) Intestinal microbes affect phenotypes and functions of invariant natural killer T cells in mice. Gastroenterology 143:418–428
Coppieters K, Van Beneden K, Jacques P, Dewint P, Vervloet A, Vander Cruyssen B et al (2007) A single early activation of invariant NK T cells confers long-term protection against collagen-induced arthritis in a ligand-specific manner. J Immunol 179:2300–2309
Jacques P, Venken K, Van Beneden K, Hammad H, Seeuws S, Drennan M et al (2010) Invariant natural killer T cells are natural regulators of murine spondylarthritis. Arthritis Rheum 62:988–999
Singh A, Misra R, Aggarwal A (2011) Th-17 associated cytokines in patients with reactive arthritis/undifferentiated spondyloarthropathy. Clin Rheumatol 30(6):771–776
Gold M, Cerri S, Smyk-Pearson S, Cansler M, Vogt T, Delepine J et al (2010) Human mucosal associated invariant T cells detect bacterially infected cells. PLoS Biol 8:e1000407
Le Bourhis L, Martin E, Peguillet I, Guihot A, Froux N, Core M et al (2010) Antimicrobial activity of mucosal associated invariant T cells. Nat Immunol 11:701–708
Dusseaux M, Martin E, Serriari N, Peguillet I, Premel V, Louis D et al (2011) Human MAIT cells are xenobiotic resistant, tissue-targeted, CD161hi IL-17-secreting T cells. Blood 117:1250–1259
Treiner E, Duban L, Bahram S, Radosavljevic M, Wanner V, Tilloy F et al (2003) Selection of evolutionarily conserved mucosalassociated invariant T cells by MR1. Nature 422:164–169
Savage A, Constantinides M, Han J, Picard D, Martin E, Li B et al (2008) The transcription factor PLZF directs the effector program of the NKT cell lineage. Immunity 29:391–403
Billerbeck E, Kang Y, Walker L, Lockstone H, Grafmueller S, Fleming V et al (2010) Analysis of CD161 expression on human CD8+ T cells defines a distinct functional subset with tissue-homing properties. Proc Natl Acad Sci U S A 107:3006–3011
Le Bourhis L, Guerri L, Dusseaux M, Martin E, Soudais C, Lantz O (2011) Mucosal associated invariant T cells: unconventional development and function. Trends Immunol 32:212–218
Leeansyah E, Loh L, Nixon DF, Sandberg JK (2014) Acquisition of innate-like microbial reactivity in mucosal tissues during human fetal MAIT-cell development. Nat Commun 5:3143
Qiu J, Heller Jennifer J, Guo X, Chen Z-ming E, Fish K, Fu Y-X et al (2012) The aryl hydrocarbon receptor regulates gut immunity through modulation of innate lymphoid cells. Immunity 36(1):92–104
Sawa S, Lochner M, Satoh-Takayama N, Dulauroy S, Berard M, Kleinschek M et al (2011) ROR[gamma]t+ innate lymphoid cells regulate intestinal homeostasis by integrating negative signals from the symbiotic microbiota. Nat Immunol 12(4):320–326
Buonocore S, Ahern PP, Uhlig HH, Ivanov II, Littman DR, Maloy KJ et al (2010) Innate lymphoid cells drive interleukin-23-dependent innate intestinal pathology. Nature 464(7293):1371–1375
Cella M, Fuchs A, Vermi W, Facchetti F, Otero K, Lennerz J et al (2009) A human natural killer cell subset provides an innate source of IL-22 for mucosal immunity. Nature 457:722–725
Wu H-J, Ivanov II, Darce J, Hattori K, Shima T, Umesaki Y et al (2010) Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells. Immunity 32(6):815–827
Wang S, Charbonnier L-M, Noval Rivas M, Georgiev P, Li N, Gerber G et al (2015) MyD88 adaptor-dependent microbial sensing by regulatory T cells promotes mucosal tolerance and enforces commensalism. Immunity 43(2):289–303
Frank DN, St. Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR (2007) Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci 104(34):13780–13785
Papa E, Docktor M, Smillie C, Weber S, Preheim SP, Gevers D et al (2012) Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease. PLoS One 7(6):e39242
Elinav E, Strowig T, Kau Andrew L, Henao-Mejia J, Thaiss Christoph A, Booth Carmen J et al (2011) NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell 145(5):745–757
Atarashi K, Tanoue T, Shima T, Imaoka A, Kuwahara T, Momose Y et al (2011) Induction of colonic regulatory T cells by indigenous clostridium species. Science 331:337–341
David L, Materna A, Friedman J, Campos-Baptista M, Blackburn M, Perrotta A et al (2014) Host lifestyle affects human microbiota on daily timescales. Genome Biol 15(7):R89
David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE et al (2014) Diet rapidly and reproducibly alters the human gut microbiome. Nature 505(7484):559–563
Group TNHW, Peterson J, Garges S, Giovanni M, McInnes P, Wang L et al (2009) The NIH human microbiome project. Genome Res 19(12):2317–2323
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C et al (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464(7285):59–65
Consortium HMP (2012) Structure, function and diversity of the healthy human microbiome. Nature 486(7402):207–214
Caporaso JG, Lauber C, Costello E, Berg-Lyons D, Gonzalez A, Stombaugh J et al (2011) Moving pictures of the human microbiome. Genome Biol 12(5):R50
Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R (2009) Bacterial community variation in human body habitats across space and time. Science 326(5960):1694–1697
Woese CR (1987) Bacterial evolution. Microbiol Rev 51(2):221–271
Booijink CCGM, Boekhorst J, Zoetendal EG, Smidt H, Kleerebezem M, de Vos WM (2010) Metatranscriptome analysis of the human fecal microbiota reveals subject-specific expression profiles, with genes encoding proteins involved in carbohydrate metabolism being dominantly expressed. Appl Environ Microbiol 76(16):5533–5540
Spor A, Koren O, Ley R (2011) Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Micro 9(4):279–290
Benson AK, Kelly SA, Legge R, Ma F, Low SJ, Kim J et al (2010) Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc Natl Acad Sci 107(44):18933–18938
Zoetendal EG, Raes J, van den Bogert B, Arumugam M, Booijink CCGM, Troost FJ et al (2012) The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. ISME J 6(7):1415–1426
Leimena M, Ramiro-Garcia J, Davids M, van den Bogert B, Smidt H, Smid E et al (2013) A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets. BMC Genomics 14(1):530
Stebbings S, Munro K, Simon MA, Tannock G, Highton J, Harmsen H et al (2002) Comparison of the faecal microflora of patients with ankylosing spondylitis and controls using molecular methods of analysis. Rheumatology 41(12):1395–1401
Stone MA, Payne U, Schentag C, Rahman P, Pacheco-Tena C, Inman RD (2004) Comparative immune responses to candidate arthritogenic bacteria do not confirm a dominant role for Klebsiella pneumonia in the pathogenesis of familial ankylosing spondylitis. Rheumatology 43(2):148–155
Costello M-E, Ciccia F, Willner D, Warrington N, Robinson PC, Gardiner B et al (2015) Brief report: intestinal dysbiosis in ankylosing spondylitis. Arthritis Rheum 67(3):686–691
Lin P, Bach M, Asquith M, Lee AY, Akileswaran L, Stauffer P et al (2014) HLA-B27 and human β2-microglobulin affect the gut microbiota of transgenic rats. PLoS One 9(8):e105684
Rath H, Herfarth H, Ikeda J, Grenther W, Hamm T, Balish E et al (1996) Normal luminal bacteria, especially bacteroides species, mediate chronic colitis, gastritis, and arthritis in HLA-B27/human beta2 microglobulin transgenic rats. J Clin Invest 98:945–953
Rehaume LM, Mondot S, Aguirre de Cárcer D, Velasco J, Benham H, Hasnain SZ et al (2014) ZAP-70 genotype disrupts the relationship between microbiota and host, leading to spondyloarthritis and ileitis in SKG mice. Arthritis Rheum 66(10):2780–2792
Eerola E, Mottonen T, Hannonen P, Luukkainen R, Kantola I, Vuori K et al (1994) Intestinal flora in early rheumatoid arthritis. Rheumatology 33:1030–1038
Vaahtovuo J, Munukka E, Korkeamaki M, Luukainen R, Toivanen P (2008) Fecal microbiota in early rheumatoid arthritis. J Rheumatol 35(8):1500–1505
Eckburg P, Bik E, Bernstein C, Purdom E, Dethlefsen L, Sargent M et al (2005) Diversity of the human intestinal microbial flora. Science 308:1635–1638
Martinez-Martinez RE, Abud-Mendoza C, Patiño-Marin N, Rizo-Rodríguez JC, Little JW, Loyola-Rodríguez JP (2009) Detection of periodontal bacterial DNA in serum and synovial fluid in refractory rheumatoid arthritis patients. J Clin Periodontol 36(12):1004–1010
Wegner N, Wait R, Sroka A, Eick S, Nguyen K-A, Lundberg K et al (2010) Peptidylarginine deiminase from Porphyromonas gingivalis citrullinates human fibrinogen and α-enolase: implications for autoimmunity in rheumatoid arthritis. Arthritis Rheum 62(9):2662–2672
Gaiffer MH, Holdsworth CD, Duerden BI (1991) The assessment of faecal flora in patients with inflammatory bowel disease by a simplified bacteriological technique. J Med Microbiol 35(4):238–243
Seksik P, Rigottier-Gois L, Gramet G, Sutren M, Pochart P, Marteau P et al (2003) Alterations of the dominant faecal bacterial groups in patients with Crohn’s disease of the colon. Gut 52(2):237–242
Ott SJ, Musfeldt M, Ullmann U, Hampe J, Schreiber S (2004) Quantification of intestinal bacterial populations by real-time PCR with a universal primer set and minor groove binder probes: a global approach to the enteric flora. J Clin Microbiol 42(6):2566–2572
Walker A, Sanderson J, Churcher C, Parkes G, Hudspith B, Rayment N et al (2011) High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease. BMC Microbiol 11:7
Quinton JF (1998) Anti-Saccharomyces cerevisiae mannan antibodies combined with antineutrophil cytoplasmic autoantibodies in inflammatory bowel disease: prevalence and diagnostic role. Gut 42:788–791
Targan SR (2005) Antibodies to CBir1 flagellin define a unique response that is associated independently with complicated Crohn’s disease. Gastroenterology 128:2020–2028
Mundwiler M, Mei L, Landers C, Reveille J, Targan S, Weisman M (2009) Inflammatory bowel disease serologies in ankylosing spondylitis patients: a pilot study. Arthritis Res Ther 11(6):R177
Wallis D (2013) Elevated serum anti-flagellin antibodies implicate subclinical bowel inflammation in ankylosing spondylitis: an observational study. Arthritis Res Ther 15:R166
van Praet L (2013) Microscopic gut inflammation in axial spondyloarthritis: a multiparametric predictive model. Ann Rheum Dis 72:414–417
Krueger JG (2002) The immunologic basis for the treatment of psoriasis with new biologic agents. J Am Acad Dermatol 46(1):1–26
Fahlen A, Engstrand L, Baker B, Powles A, Fry L (2012) Comparison of bacterial microbiota in skin biopsies from normal and psoriatic skin. Arch Dermatol Res 304:15–22
Scher JU, Ubeda C, Artacho A, Attur M, Isaac S, Reddy SM et al (2015) Decreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease. Arthritis Rheum 67(1):128–139
Dethlefsen L, Relman DA (2011) Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci 108(Supplement 1):4554–4561
Jakobsson HE, Jernberg C, Andersson AF, Sjölund-Karlsson M, Jansson JK, Engstrand L (2010) Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS One 5(3):e9836
Buffie CG, Jarchum I, Equinda M, Lipuma L, Gobourne A, Viale A et al (2012) Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to clostridium difficile-induced colitis. Infect Immun 80(1):62–73
Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL et al (2013) Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 341(6150):1241214
Devkota S, Wang Y, Musch MW, Leone V, Fehlner-Peach H, Nadimpalli A et al (2012) Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il102/2 mice. Nature 487(7405):104–108
Scher JU, Sczesnak A, Longman RS, Segata N, Ubeda C, Bielski C et al. (2013) Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. Mathis D, editor. 2013-11-05 15:22:27
Scher JU, Abramson SB (2011) The microbiome and rheumatoid arthritis. Nat Rev Rheumatol 7(10):569–578
Norman JM, Handley SA, Virgin HW (2014) Kingdom-agnostic metagenomics and the importance of complete characterization of enteric microbial communities. Gastroenterology 146(6):1459–1469
Virgin HW (2014) The virome in mammalian physiology and disease. Cell 157(1):142–150
Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL et al (2013) The long-term stability of the human gut microbiota. Science (New York, NY) 341(6141):1237439
Ley RE, Turnbaugh PJ, Klein S, Gordon JI (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444:1022–1023
Gill SR, Pop M, DeBoy RT, Eckburg PB, Turnbaugh PJ, Samuel BS et al (2006) Metagenomic analysis of the human distal gut microbiome. Science 312(5778):1355–1359
van Nood E, Speelman P, Nieuwdorp M, Keller J (2014) Fecal microbiota transplantation: facts and controversies. Curr Opin Gastroenterol 30(1):34–39. doi:10.1097/MOG.0000000000000024
Smith M, Kassam Z, Edelstein C, Burgess J, Alm E (2014) OpenBiome remains open to serve the medical community. Nat Biotech 32(9):867
Kassam Z, Lee CH, Yuan Y, Hunt RH (2013) Fecal microbiota transplantation for clostridium difficile infection: systematic review and meta-analysis. Am J Gastroenterol 108(4):500–508
van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM et al (2013) Duodenal infusion of donor feces for recurrent clostridium difficile. N Eng J Med 368(5):407–415
Youngster I, Sauk J, Pindar C, Wilson RG, Kaplan JL, Smith MB et al (2014) Fecal microbiota transplant for relapsing clostridium difficile infection using a frozen inoculum from unrelated donors: a randomized, open-label, controlled pilot study. Clin Infect Dis 58(11):1515–1522
Alang N, Kelly CR (2015) Weight gain after fecal microbiota transplantation. Open Forum Infect Dis 2(1):ofv004
Petrof E, Gloor G, Vanner S, Weese S, Carter D, Daigneault M et al (2013) Stool substitute transplant therapy for the eradication of clostridium difficile infection: ‘RePOOPulating’ the gut. Microbiome 1(1):1–12
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Costello, ME., Brown, M.A. (2017). The Intestinal Microbiome, the Immune System and Spondyloarthropathy. In: Mina-Osorio, P. (eds) Next-Generation Therapies and Technologies for Immune-Mediated Inflammatory Diseases. Progress in Inflammation Research. Springer, Cham. https://doi.org/10.1007/978-3-319-42252-7_8
Download citation
DOI: https://doi.org/10.1007/978-3-319-42252-7_8
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-42251-0
Online ISBN: 978-3-319-42252-7
eBook Packages: MedicineMedicine (R0)