Abstract
The microbiota in our gut performs many different essential functions that help us to stay healthy. These functions include vitamin production, regulation of lipid metabolism and short chain fatty acid production as fuel for epithelial cells and regulation of gene expression. There is a very numerous and diverse microbial community present in the gut, especially in the colon, with reported numbers of species that vary between 400 and 1500, for some those we even do not yet have culture representatives.
A healthy gut microbiota is important for maintaining a healthy host. An aberrant microbiota can cause diseases of different nature and at different ages ranging from allergies at early age to IBD in young adults. This shows that our gut microbiota needs to be treated well to stay healthy. In this chapter we describe what we consider a healthy microbiota and discuss what the role of the microbiota is in various diseases. Research into these described dysbiosis conditions could lead to new strategies for treatment and/or management of our microbiota to improve health.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Adlerberth I, Wold AE (2009) Establishment of the gut microbiota in Western infants. Acta Paediatr 98(2):229–238
Arumugam M, Raes J, Pelletier E, LE Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto J (2011) Enterotypes of the human gut microbiome. Nature 473(7346):174–180
Azad MB, Konya T, Maughan H, Guttman DS, Field CJ, Sears MR, Becker AB, Scott JA, Kozyrskyj AL (2013) Infant gut microbiota and the hygiene hypothesis of allergic disease: impact of household pets and siblings on microbiota composition and diversity. Allergy Asthma Clin Immunol 9(1):15
Backhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, Semenkovich CF, Gordon JI (2004) The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A 101(44):15718–15723
Backhed F, Manchester JK, Semenkovich CF, Gordon JI (2007) Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc Natl Acad Sci U S A 104(3):979–984
Benjdia A, Martens EC, Gordon JI, Berteau O (2011) Sulfatases and a radical S-adenosyl-L-methionine (AdoMet) enzyme are key for mucosal foraging and fitness of the prominent human gut symbiont, Bacteroides thetaiotaomicron. J Biol Chem 286(29):25973–25982
Bergstrom A, Skov TH, Bahl MI, Roager HM, Christensen LB, Ejlerskov KT, Molgaard C, Michaelsen KF, Licht TR (2014) Establishment of intestinal microbiota during early life: a longitudinal, explorative study of a large cohort of Danish infants. Appl Environ Microbiol 80(9):2889–2900
Brown CT, Davis-Richardson AG, Giongo A, Gano KA, Crabb DB, Mukherjee N, Casella G, Drew JC, Ilonen J, Knip M (2011) Gut microbiome metagenomics analysis suggests a functional model for the development of autoimmunity for type 1 diabetes. PLoS ONE 6(10):e25792
Brugman S, Klatter FA, Visser JT, Wildeboer-Veloo AC, Harmsen HJ, Rozing J, Bos NA (2006) Antibiotic treatment partially protects against type 1 diabetes in the Bio-Breeding diabetes-prone rat. Is the gut flora involved in the development of type 1 diabetes? Diabetologia 49(9):2105–2108
Cani PD, Amar J, Iglesias MA, Poggi M, Knauf C, Bastelica D, Neyrinck AM, Fava F, Tuohy KM, Chabo C, Waget A, Delmee E, Cousin B, Sulpice T, Chamontin B, Ferrieres J, Tanti JF, Gibson GR, Casteilla L, Delzenne NM, Alessi MC, Burcelin R (2007) Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes 56(7):1761–1772
Chen S, Liu X, Liu J, Yang X, Lu F (2014) Ulcerative colitis as a polymicrobial infection characterized by sustained broken mucus barrier. World J Gastroenterol: WJG 20(28):9468
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 (2011) Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc Natl Acad Sci U S A 108(Suppl 1):4586–4591
Cronise RJ, Sinclair DA, Bremer AA (2014) The “metabolic winter” hypothesis: a cause of the current epidemics of obesity and cardiometabolic disease. Metab Syndr Relat Disord 12(7):355–361
David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA (2013) Diet rapidly and reproducibly alters the human gut microbiome. Nature 505(7484):559–563
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 U S A 107(33):14691–14696
DE Goffau MC, Luopajarvi K, Knip M, Ilonen J, Ruohtula T, Harkonen T, Orivuori L, Hakala S, Welling GW, Harmsen HJ, Vaarala O (2013) Fecal microbiota composition differs between children with beta-cell autoimmunity and those without. Diabetes 62(4):1238–1244
DE Goffau MC, Fuentes S, VAN DEN Bogert B, Honkanen H, DE Vos WM, Welling GW, Hyöty H, Harmsen HJ (2014) Aberrant gut microbiota composition at the onset of type 1 diabetes in young children. Diabetologia 57(8):1569–1577
De Vrieze J (2014) Gut instinct. Science (New York, NY) 343(6168):241–243
Derrien M, Vaughan EE, Plugge CM, DE Vos WM (2004) Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. Int J Syst Evol Microbiol 54(Pt 5):1469–1476
Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, Knight R (2010) Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A 107(26):11971–11975
Dunne J, Triplett E, Gevers D, Xavier R, Insel R, Danska J, Atkinson M (2014) The intestinal microbiome in type 1 diabetes. Clin Exp Immunol 177:30–7
Ellis RJ, Bruce KD, Jenkins C, Stothard JR, Ajarova L, Mugisha L, Viney ME (2013) Comparison of the distal gut microbiota from people and animals in Africa. PLoS ONE 8(1):e54783
Everard A, Geurts L, Caesar R, Van Hul M, Matamoros S, Duparc T, Denis RG, Cochez P, Pierard F, Castel J (2014) Intestinal epithelial MyD88 is a sensor switching host metabolism towards obesity according to nutritional status. Nat Commun 5:5648
Fasano A (2012) Intestinal permeability and its regulation by zonulin: diagnostic and therapeutic implications. Clin Gastroenterol Hepatol 10(10):1096–1100
Favier CF, Vaughan EE, DE Vos WM, Akkermans AD (2002) Molecular monitoring of succession of bacterial communities in human neonates. Appl Environ Microbiol 68(1):219–226
Fiocchi C (1998) Inflammatory bowel disease: etiology and pathogenesis. Gastroenterology 115(1):182–205
Fleissner CK, Huebel N, Abd El-Bary MM, Loh G, Klaus S, Blaut M (2010) Absence of intestinal microbiota does not protect mice from diet-induced obesity. Br J Nutr 104(06):919–929
Flint HJ, Bayer EA, Rincon MT, Lamed R, White BA (2008) Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nat Rev Microbiol 6(2):121–131
Flint HJ, Scott KP, Louis P, Duncan SH (2012a) The role of the gut microbiota in nutrition and health. Nat Rev Gastroenterol Hepatol 9(10):577–589
Flint HJ, Scott KP, Duncan SH, Louis P, Forano E (2012b) Microbial degradation of complex carbohydrates in the gut. Gut Microbes 3(4):289–306
Flint HJ, Duncan SH, Scott KP, Louis P (2014) Links between diet, gut microbiota composition and gut metabolism. Proc Nutr Soc 74:1–10
Fries W, Comunale S (2011) Ulcerative colitis: pathogenesis. Curr Drug Targets 12(10):1373–1382
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 (New York, NY) 312(5778):1355–1359
Giongo A, Gano KA, Crabb DB, Mukherjee N, Novelo LL, Casella G, Drew JC, Ilonen J, Knip M, Hyöty H (2010) Toward defining the autoimmune microbiome for type 1 diabetes. ISME J 5(1):82–91
Grönlund M, Gueimonde M, Laitinen K, Kociubinski G, Grönroos T, Salminen S, Isolauri E (2007) Maternal breast‐milk and intestinal bifidobacteria guide the compositional development of the Bifidobacterium microbiota in infants at risk of allergic disease. Clin Exp Allergy 37(12):1764–1772
Hague A, Butt AJ, Paraskeva C (1996) The role of butyrate in human colonic epithelial cells: an energy source or inducer of differentiation and apoptosis? Proc Nutr Soc 55(03):937–943
Hamer HM, Jonkers DM, Bast A, Vanhoutvin SA, Fischer MA, Kodde A, Troost FJ, Venema K, Brummer RM (2009) Butyrate modulates oxidative stress in the colonic mucosa of healthy humans. Clin Nutr 28(1):88–93
Harmsen HJ, Wildeboer-Veloo AC, Raangs GC, Wagendorp AA, Klijn N, Bindels JG, Welling GW (2000) Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods. J Pediatr Gastroenterol Nutr 30(1):61–67
Harmsen HJ, Raangs GC, He T, Degener JE, Welling GW (2002) Extensive set of 16S rRNA-based probes for detection of bacteria in human feces. Appl Environ Microbiol 68(6):2982–2990
Harmsen HJ, Pouwels SD, Funke A, Bos NA, Dijkstra G (2012) Crohn’s disease patients have more IgG-binding fecal bacteria than controls. Clin Vaccine Immunol: CVI 19(4):515–521
Heaton KW, Radvan J, Cripps H, Mountford RA, Braddon FE, Hughes AO (1992) Defecation frequency and timing, and stool form in the general population: a prospective study. Gut 33(6):818–824
Holmes E, Li JV, Marchesi JR, Nicholson JK (2012) Gut microbiota composition and activity in relation to host metabolic phenotype and disease risk. Cell Metab 16(5):559–564
Hooper LV, Gordon JI (2001) Commensal host-bacterial relationships in the gut. Science 292(5519):1115–1118
Isolauri E (2012) Development of healthy gut microbiota early in life. J Paediatr Child Health 48(s3):1–6
Kernbauer E, Ding Y, Cadwell K (2014) An enteric virus can replace the beneficial function of commensal bacteria. Nature 516(7529):94–98
Khan MT, Nieuwdorp M, Bäckhed F (2014) Microbial modulation of insulin sensitivity. Cell Metab 20:753–760
Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI (2005) Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A 102(31):11070–11075
Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R, Gordon JI (2008) Evolution of mammals and their gut microbes. Science (New York, NY) 320(5883):1647–1651
Liverani E, Scaioli E, Cardamone C, Dal Monte P, Belluzzi A (2014) Mycobacterium avium subspecies paratuberculosis in the etiology of Crohn’s disease, cause or epiphenomenon? World J Gastroenterol: WJG 20(36):13060
Lopez-Siles M, Khan TM, Duncan SH, Harmsen HJ, Garcia-Gil LJ, Flint HJ (2012) Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth. Appl Environ Microbiol 78(2):420–428
Lozupone CA, Stombaugh J, Gonzalez A, Ackermann G, Wendel D, Vazquez-Baeza Y, Jansson JK, Gordon JI, Knight R (2013) Meta-analyses of studies of the human microbiota. Genome Res 23(10):1704–1714
Martens EC, Koropatkin NM, Smith TJ, Gordon JI (2009) Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm. J Biol Chem 284(37):24673–24677
Martín R, Heilig HG, Zoetendal EG, Jiménez E, Fernández L, Smidt H, Rodríguez JM (2007) Cultivation-independent assessment of the bacterial diversity of breast milk among healthy women. Res Microbiol 158(1):31–37
Martin R, Jimenez E, Heilig H, Fernandez L, Marin ML, Zoetendal EG, Rodriguez JM (2009) Isolation of bifidobacteria from breast milk and assessment of the bifidobacterial population by PCR-denaturing gradient gel electrophoresis and quantitative real-time PCR. Appl Environ Microbiol 75(4):965–969
Mejía-León ME, Petrosino JF, Ajami NJ, Domínguez-Bello MG, Calderón DLBAM (2014) Fecal microbiota imbalance in Mexican children with type 1 diabetes. Sci Rep 4:3814
Miquel S, Martin R, Rossi O, Bermudez-Humaran LG, Chatel JM, Sokol H, Thomas M, Wells JM, Langella P (2013) Faecalibacterium prausnitzii and human intestinal health. Curr Opin Microbiol 16(3):255–261
Moore L, Moore E, Murray R, Stackebrandt E, Starr M (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464
Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV, Reyes JA, Shah SA, Leleiko N, Snapper SB (2012) Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol 13(9):R79
Morotomi M, Nagai F, Watanabe Y (2012) Description of Christensenella minuta gen. nov., sp. nov., isolated from human faeces, which forms a distinct branch in the order Clostridiales, and proposal of Christensenellaceae fam. nov. Int J Syst Evol Microbiol 62(Pt 1):144–149
Murri M, Leiva I, Gomez-Zumaquero JM, Tinahones FJ, Cardona F, Soriguer F, Queipo-Ortuno MI (2013) Gut microbiota in children with type 1 diabetes differs from that in healthy children: a case-control study. BMC Med 11:46, 7015-11-46
Ouwerkerk JP, DE Vos WM, Belzer C (2013) Glycobiome: bacteria and mucus at the epithelial interface. Best Pract Res Clin Gastroenterol 27(1):25–38
Parfrey LW, Walters WA, Knight R (2011) Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions. Front Microbiol 2:153
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
Penders J, Thijs C, van den Brandt PA, Kummeling I, Snijders B, Stelma F, Adams H, van Ree R, Stobberingh EE (2007) Gut microbiota composition and development of atopic manifestations in infancy: the KOALA Birth Cohort Study. Gut 56(5):661–667
Peng L, Li ZR, Green RS, Holzman IR, Lin J (2009) Butyrate enhances the intestinal barrier by facilitating tight junction assembly via activation of AMP-activated protein kinase in Caco-2 cell monolayers. J Nutr 139(9):1619–1625
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59–65
Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, Zhang W, Guan Y, Shen D (2012) A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490(7418):55–60
Qin N, Yang F, Li A, Prifti E, Chen Y, Shao L, Guo J, Le Chatelier E, Yao J, Wu L (2014) Alterations of the human gut microbiome in liver cirrhosis. Nature 513(7516):59–64
Rajilić‐Stojanović M, Vos WM (2014) The First 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiol Rev 38(5):996–1047
Roelofsen H, Priebe M, Vonk R (2010) The interaction of short-chain fatty acids with adipose tissue: relevance for prevention of type 2 diabetes. Benefic Microbes 1(4):433–437
Sadaghian Sadabad M, Regeling A, De Goffau MC, Blokzijl T, Weersma RK, Penders J, Faber KN, Harmsen HJ, Dijkstra G (2014) The ATG16L1-T300A allele impairs clearance of pathosymbionts in the inflamed ileal mucosa of Crohn’s disease patients. Gut 64(10):1546–1552
Samuel BS, Hansen EE, Manchester JK, Coutinho PM, Henrissat B, Fulton R, Latreille P, Kim K, Wilson RK, Gordon JI (2007) Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc Natl Acad Sci U S A 104(25):10643–10648
Schwiertz A, Taras D, Schäfer K, Beijer S, Bos NA, Donus C, Hardt PD (2010) Microbiota and SCFA in lean and overweight healthy subjects. Obesity 18(1):190–195
Sekirov I, Russell SL, Antunes LC, Finlay BB (2010) Gut microbiota in health and disease. Physiol Rev 90(3):859–904
Sela DA, Chapman J, Adeuya A, Kim JH, Chen F, Whitehead TR, Lapidus A, Rokhsar DS, Lebrilla CB, German JB, Price NP, Richardson PM, Mills DA (2008) The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome. Proc Natl Acad Sci U S A 105(48):18964–18969
Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermudez-Humaran LG, Gratadoux JJ, Blugeon S, Bridonneau C, Furet JP, Corthier G, Grangette C, Vasquez N, Pochart P, Trugnan G, Thomas G, Blottiere HM, Dore J, Marteau P, Seksik P, Langella P (2008) Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A 105(43):16731–16736
Sokol H, Seksik P, Furet JP, Firmesse O, Nion-Larmurier I, Beaugerie L, Cosnes J, Corthier G, Marteau P, Dore J (2009) Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm Bowel Dis 15:1183–1189
Spees AM, Wangdi T, Lopez CA, Kingsbury DD, Xavier MN, Winter SE, Tsolis RM, Baumler AJ (2013) Streptomycin-induced inflammation enhances Escherichia coli gut colonization through nitrate respiration. mBio 4(4):e00430-13. doi:10.1128/mBio.00430-13
Strober W (2011) Adherent-invasive E. coli in Crohn disease: bacterial “agent provocateur”. J Clin Invest 121(3):841–844
Tap J, Mondot S, Levenez F, Pelletier E, Caron C, Furet J, Ugarte E, Muñoz‐Tamayo R, Paslier DL, Nalin R (2009) Towards the human intestinal microbiota phylogenetic core. Environ Microbiol 11(10):2574–2584
Tims S, Derom C, Jonkers DM, Vlietinck R, Saris WH, Kleerebezem M, DE Vos WM, Zoetendal EG (2012) Microbiota conservation and BMI signatures in adult monozygotic twins. ISME J 7(4):707–717
Turnbaugh PJ, Gordon JI (2009) The core gut microbiome, energy balance and obesity. J Physiol 587:4153–4158
Turnbaugh PJ, Quince C, Faith JJ, Mchardy AC, Yatsunenko T, Niazi F, Affourtit J, Egholm M, Henrissat B, Knight R, Gordon JI (2010) Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci U S A 107(16):7503–7508
Vaarala O, Atkinson MA, Neu J (2008) The “perfect storm” for type 1 diabetes: the complex interplay between intestinal microbiota, gut permeability, and mucosal immunity. Diabetes 57(10):2555–2562
Van Nimwegen FA, Penders J, Stobberingh EE, Postma DS, Koppelman GH, Kerkhof M, Reijmerink NE, Dompeling E, Van Den Brandt PIETA, Ferreira I (2011) Mode and place of delivery, gastrointestinal microbiota, and their influence on asthma and atopy. J Allergy Clin Immunol 128(5):948–955, e3
Vignini A, Giulietti A, Nanetti L, Raffaelli F, Giusti L, Mazzanti L, Provinciali L (2013) Alzheimer’s disease and diabetes: new insights and unifying therapies. Curr Diabet Rev 9(3):218–227
Vrieze A, Van Nood E, Holleman F, Salojärvi J, Kootte RS, Bartelsman JF, Dallinga–Thie GM, Ackermans MT, Serlie MJ, Oozeer R (2012) Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome. Gastroenterology 143(4):913–916, e7
Walker AW, Ince J, Duncan SH, Webster LM, Holtrop G, Ze X, Brown D, Stares MD, Scott P, Bergerat A (2010) Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J 5(2):220–230
Walter J, Ley R (2011) The human gut microbiome: ecology and recent evolutionary changes. Annu Rev Microbiol 65:411–429
Weinstock JV, Elliott DE (2009) Helminths and the IBD hygiene hypothesis. Inflamm Bowel Dis 15(1):128–133
Whitman WB, Parte AC (2009) Systematic bacteriology. Springer, New York
Willing B, Halfvarson J, Dicksved J, Rosenquist M, Järnerot G, Engstrand L, Tysk C, Jansson JK (2009) Twin studies reveal specific imbalances in the mucosa‐associated microbiota of patients with ileal Crohn’s disease. Inflamm Bowel Dis 15(5):653–660
Winter SE, Winter MG, Xavier MN, Thiennimitr P, Poon V, Keestra AM, Laughlin RC, Gomez G, Wu J, Lawhon SD, Popova IE, Parikh SJ, Adams LG, Tsolis RM, Stewart VJ, Baumler AJ (2013) Host-derived nitrate boosts growth of E. coli in the inflamed gut. Science (New York, NY) 339(6120):708–711
Wrzosek L, Miquel S, Noordine ML, Bouet S, Joncquel Chevalier-Curt M, Robert V, Philippe C, Bridonneau C, Cherbuy C, Robbe-Masselot C, Langella P, Thomas M (2013) Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii influence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent. BMC Biol 11:61, 7007-11-61
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 (New York, NY) 334(6052):105–108
Xavier R, Podolsky D (2007) Unravelling the pathogenesis of inflammatory bowel disease. Nature 448(7152):427–434
Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP (2012) Human gut microbiome viewed across age and geography. Nature 486(7402):222–227
Yutin N, Galperin MY (2013) A genomic update on clostridial phylogeny: gram‐negative spore formers and other misplaced clostridia. Environ Microbiol 15(10):2631–2641
Ze X, Duncan SH, Louis P, Flint HJ (2012) Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. ISME J 6(8):1535–1543
Zivkovic AM, German JB, Lebrilla CB, Mills DA (2011) Human milk glycobiome and its impact on the infant gastrointestinal microbiota. Proc Natl Acad Sci U S A 108(Suppl 1):4653–4658
Zoetendal E, Akkermans A, Vliet W, Arjan J, De Visser GM, De Vos W (2001) The host genotype affects the bacterial community in the human gastronintestinal tract. Microb Ecol Health Dis 13(3):129–134
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer International Publishing Switzerland
About this chapter
Cite this chapter
Harmsen, H.J.M., de Goffau, M.C. (2016). The Human Gut Microbiota. In: Schwiertz, A. (eds) Microbiota of the Human Body. Advances in Experimental Medicine and Biology, vol 902. Springer, Cham. https://doi.org/10.1007/978-3-319-31248-4_7
Download citation
DOI: https://doi.org/10.1007/978-3-319-31248-4_7
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-31246-0
Online ISBN: 978-3-319-31248-4
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)