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Review Article

The human microbiota associated with overall health

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Pages 129-140 | Received 27 Jul 2012, Accepted 09 Jun 2013, Published online: 05 Aug 2013

References

  • Atarashi K, Tanoue T, Shima T, et al. (2011). Induction of colonic regulatory T cells by indigenous Clostridium species. Science, 331, 337–41
  • Barton ES, White DW, Cathelyn JS, et al. (2007). Herpesvirus latency confers symbiotic protection from bacterial infection. Nature, 447, 326–9
  • Benson AK, Kelly SA, Legge R, 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 USA, 107, 18933–8
  • Bercik P, Denou E, Collins J, et al. (2011). The intestinal microbiota affect central levels of brain-derived neurotropic factor and behavior in mice. Gastroenterology, 141, 599–609
  • 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, 478–82
  • Biasucci G, Rubini M, Riboni S, et al. (2010). Mode of delivery affects the bacterial community in the newborn gut. Early Hum Dev, 86, 13–15
  • Bouilly-Gauthier D, Jeannes C, et al. (2010). Clinical evidence of benefits of a dietary supplement containing probiotic and carotenoids on ultraviolet-induced skin damage. Br J Dermatol, 163, 536–43
  • Buhnik-Rosenblau K, Danin-Poleg Y, Kashi Y. (2011). Predominant effect of host genetics on levels of Lactobacillus johnsonii bacteria in the mouse gut. Appl Environ Microbiol, 77, 6531–8
  • Caporaso JG, Lauber CL, Costello EK, et al. (2011). Moving pictures of the human microbiome. Genome Biol, 12, R50
  • Claesson MJ, Jeffery IB, Conde S, Power SE. (2012). Gut microbiota composition correlates with diet and health in the elderly. Nature, 488, 178--84. DOI: 10.1038/nature11319
  • Clemente JC, Ursell LK, Parfrey LW, Knight R. (2012). The impact of the gut microbiota on human health, an integrative view. Cell, 148, 1258–70
  • De Filippo C, Cavalieri D, Di Paola M, et al. (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, 14691–6
  • Dethlefsen L, Huse S, Sogin ML, Relman DA. (2008). The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol, 6, e280
  • Dethlefsen L, Relman DA. (2011). Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci USA, 108, 4554–61
  • Dominguez-Bello MG, Costello EK, Contreras M, et al. (2010). Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci USA, 107, 11971–5
  • Faure M, Mettraux C, Moennoz D, et al. (2006). Specific amino acids increase mucin synthesis and microbiota in dextran sulfate sodium-treated rats. J Nutr, 136, 1558–64
  • Fukuda S, Toh H, Hase K, et al. (2011). Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature, 469, 543-U791
  • Gaboriau-Routhiau V, Rakotobe S, Lecuyer E, et al. (2009). The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity, 31, 677–89
  • Gao X, Ma Q, Zhao L, et al. (2011). Isolation of Bacillus subtilis, screening for aflatoxins B1, M1, and G1 detoxification. Eur Food Res Technol, 232, 957–62
  • Gerasimov SV, Vasjuta VV, Myhovych OO, Bondarchuk LI. (2010). Probiotic supplement reduces atopic dermatitis in preschool children, a randomized, double-blind, placebo-controlled, clinical trial. Am J Clin Dermatol, 11, 351–61
  • Goto K, Kanaya S, Nishikawa T, et al. (1998). The influence of tea catechins on faecal flora of elderly residents in long-term facilities. Annals of Long Term Care, 6, 43e48
  • Gourbeyre P, Denery S, Bodinier M. (2011). Probiotics, prebiotics, and synbiotics, impact on the gut immune system and allergic reactions. J Leukocyte Biol, 89, 685–95
  • Hansen CH, Nielsen DS, Kverka M, et al. (2012). Patterns of early gut colonization shape future immune responses of the host. PLoS One, 7, e34043
  • Heijtz RD, Wang S, Anuar F, et al. (2011). Normal gut microbiota modulates brain development and behavior. Proc Natl Acad Sci USA, 108, 3047–52
  • Hidalgo M, Oruna-Concha MJ, Kolida S, et al. (2012). Metabolism of anthocyanins by human gut microflora and their influence on gut bacterial growth. J Agric Food Chem, 60, 3882–90
  • Hillman JD. (2002). Genetically modified Streptococcus mutans for the prevention of dental caries. Antonie Van Leeuwenhoek, 82, 361–6
  • Hooper LV, Littman DR, Macpherson AJ. (2012). Interactions between the microbiota and the immune system. Science, 336, 1268–73
  • Inman CF, Haverson K, Konstantinov SR, et al. (2010). Rearing environment affects development of the immune system in neonates. Clin Exp Immunol, 160, 431–9
  • Jernberg C, Löfmark S, Edlund C, Jansson JK. (2007). Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J, 1, 56–66
  • Johnstone AM, Horgan GW, Murison SD, et al. (2008). Effects of a high-protein ketogenic diet on hunger, appetite, and weight loss in obese men feeding ad libitum. Am J Clin Nutr, 87, 44–55
  • 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, 58–69
  • Khoruts A, Dicksved J, Jansson JK, Sadowsky MJ. (2010). Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associated diarrhea. J Clin Gastroenterol, 44, 354–60
  • Kolmeder CA, de Been M, Nikkilä J, et al. (2012). Comparative metaproteomics and diversity analysis of human intestinal microbiota testifies for its temporal stability and expression of core functions. PLoS One, 7, e29913. Epub 2012 Jan 18
  • Kurkivuori J, Salaspuro V, Kaihovaara P, et al. (2007). Acetaldehyde production from ethanol by oral streptococci. Oral Oncol, 43, 181–6
  • Lagenaur LA, Lee PP, Hamer DH, Sanders-Beer BE. (2011). Demonstration of vaginal colonization with GusA-expressing Lactobacillus jensenii following oral delivery in rhesus macaques. Res Microbiol, 162, 1006–10
  • Langevin F, Crossan GP, Rosado IV, et al. (2011). Fancd2 counteracts the toxic effects of naturally produced aldehydes in mice. Nature, 475, 53–8
  • Larrosa M, Yañéz-Gascón MJ, Selma MV, et al. (2009). Effect of a low dose of dietary resveratrol on colon microbiota, inflammation and tissue damage in a DSS-induced colitis rat model. J Agric Food Chem, 57, 2211–20
  • Lawley TD, Clare S, Walker AW, et al. (2012). Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice, PLos Pathog, 8, e1002995. DOI: 10.1371/journal.ppat.1002995
  • Le Gall G, Noor SO, Ridgway K, et al. (2011). Metabolomics of fecal extracts detects altered metabolic activity of gut microbiota in ulcerative colitis and irritable bowel syndrome. J Proteome Res, 10, 4208–18
  • Le Huërou-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, 23–36
  • Lee HC, Jenner AM, Low CS, Lee YK. (2006). Effect of tea phenolics and their aromatic fecal bacterial metabolites on intestinal microbiota. Res Microbiol, 157, 876–84
  • Lee JH, Karamychev VN, Kozyavkin SA, et al. (2008). Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth. BMC Genomics, 9, 247
  • Lee JH, O'Sullivan DJ. (2010). Genomic insights into bifidobacteria. Microbiol Mol Biol Rev, 74, 378–416
  • Leser TD, Molbak L. (2009). Better living through microbial action, the benefits of the mammalian gastrointestinal microbiota on the host. Environ Microbiol, 11, 2194–206
  • Lif Holgerson P, Harnevik L, Hernell O, et al. (2011). Mode of birth delivery affects oral microbiota in infants. J Dent Res, 90, 1183–8
  • Maccaferri S, Klinder A, Brigidi P, et al. (2012). Potential probiotic Kluyveromyces marxianus B0399 modulates the immune response in Caco-2 cells and peripheral blood mononuclear cells and impacts the human gut microbiota in an in vitro colonic model system. Appl Environ Microbiol, 78, 956–64
  • Mäkivuokko H, Lahtinen SJ, Wacklin P, et al. (2012). Association between the ABO blood group and the human intestinal microbiota composition. BMC Microbiol, 12, 94. DOI: 10.1186/1471-2180-12-94
  • Malinen E, Rinttilä T, Kajander K, et al. (2005). Analysis of the fecal microbiota of irritable bowel syndrome patients and healthy controls with real-time PCR. Am J Gastroenterol, 100, 373–82
  • Mangin I, Suau A, Gotteland M, et al. (2010). Amoxicillin treatment modifies the composition of Bifidobacterium species in infant intestinal microbiota. Anaerobe, 16, 433–8
  • Manichanh C, Reeder J, Gibert P, et al. (2010). Reshaping the gut microbiome with bacterial transplantation and antibiotic intake. Genome Res, 20, 1411–19
  • Mao SY, Zhu WY. (2011). Effects of six flavonoid compounds addition on short-chain fatty acids production and human fecal microbial community change during in vitro fermentation. African J Microbiol Res, 5, 4484–91
  • Martínez I, Kim J, Duffy PR, et al. (2010). Resistant starches types 2 and 4 have differential effects on the composition of the fecal microbiota in human subjects. PLoS One, 5, e15046
  • Mestdagh R, Dumas ME, Rezzi S, et al. (2012). Gut microbiota modulate the metabolism of brown adipose tissue in mice. J Proteome Res, 11, 620–30
  • Mills DJ, Tuohy KM, Booth J, et al. (2008). Dietary glycated protein modulates the colonic microbiota towards a more detrimental composition in ulcerative colitis patients and non-ulcerative colitis subjects. J Appl Microbiol, 105, 706–14
  • Minot S, Sinha R, Chen J, et al. (2011). The human gut virome, inter-individual variation and dynamic response to diet. Genome Res, 21, 1616–25
  • Mulder IE, Schmidt B, Stokes CR, et al. (2009). Environmentally-acquired bacteria influence microbial diversity and natural innate immune responses at gut surfaces. BMC Biol, 7, 79. doi: 10.1186/1741-7007-7-79
  • Murphy EF, Cotter PD, Hogan A, et al. (2013). Divergent metabolic outcomes arising from targeted manipulation of the gut microbiota in diet-induced obesity. Gut, 62, 220--6
  • Nakamura YK, Omaye ST. (2012). Metabolic diseases and pro- and prebiotics, mechanistic insights. Nutr Metab (Lond), 9, 60. DOI: 10.1186/1743-7075-9-60
  • Ness RB, Hillier S, Richter HE, Soper DE, et al. (2003). Can known risk factors explain racial differences in the occurrence of bacterial vaginosis? J Natl Med Assoc, 95, 201–12
  • Neyrinck AM, Possemiers S, Druart C, et al. (2011). Prebiotic effects of wheat arabinoxylan related to the increase in bifidobacteria, Roseburia and Bacteroides/Prevotella in diet-induced obese mice. PLoS One, 6, e20944. doi: 10.1371/journal.pone.0020944
  • Nicholson JK, Holmes E, Kinross J, et al. (2012). Host-gut microbiota metabolic interactions. Science, 336, 1262–7
  • Nieminen MT, Uittamo J, Salaspuro M, Rautemaa R. (2009). Acetaldehyde production from ethanol and glucose by non-Candida albicans yeasts in vitro. Oral Oncol, 45, e245–8
  • Nohynek LJ, Alakomi HL, Kähkönen MP, et al. (2006). Berry phenolics, antimicrobial properties and mechanisms of action against severe human pathogens. Nutr Cancer, 54, 18–32
  • O’Mahony C, Scully P, O’Mahony D, et al. (2008). Commensal-induced regulatory T cells mediate protection against pathogen-stimulated NF-kappaB activation. PLoS Pathog, 4, e1000112. doi: 10.1371/journal.ppat.1000112
  • Okubo T, Ishihara N, Oura A, et al. (1992). In vivo effects of tea polyphenols intake on human intestinal microflora and metabolism. Biosci Biotechnol Biochem, 56, 588e591
  • Olszak T, An D, Zeissig S, et al. (2012). Microbial exposure during early life has persistent effects on natural killer T cell function. Science, 336, 489–93
  • Ottaviani E, Ventura N, Mandrioli M, et al. (2011). Gut microbiota as a candidate for lifespan extension, an ecological/evolutionary perspective targeted on living organisms as metaorganisms. Biogerontology, 12, 599–609
  • Paliy O, Agans R. (2012). Application of phylogenetic microarrays to interrogation of human microbiota. FEMS Microbiol Ecol, 79, 2–11
  • Perry S, de Jong BC, Solnick JV, et al. (2010). Infection with Helicobacter pylori is associated with protection against tuberculosis. PLoS ONE, 5, e8804
  • Pieper R, Jha R, Rossnagel B, et al. (2008). Effect of barley and oat cultivars with different carbohydrate compositions on the intestinal bacterial communities in weaned piglets. FEMS Microbiol Ecol, 66, 556–66
  • Putignani L, Carsetti R, Signore F, Manco M. (2010). Additional maternal and nonmaternal factors contribute to microbiota shaping in newborns. Proc Natl Acad Sci USA, 107, E159
  • Puupponen-Pimiä R, Nohynek L, Hartmann-Schmidlin S, et al. (2005). Berry phenolics selectively inhibit the growth of intestinal pathogens. J Appl Microbiol, 98, 991–1000
  • Ramirez-Farias C, Slezak K, Fuller Z, et al. (2009). Effect of inulin on the human gut microbiota, stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii. Br J Nutr, 101, 541–50
  • Round JL, Mazmanian SK. (2009). The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol, 9, 313–23
  • Rudney JD, Xie H, Rhodus NL, et al. (2010). A metaproteomic analysis of the human salivary microbiota by three-dimensional peptide fractionation and tandem mass spectrometry. Mol Oral Microbiol, 25, 38–49
  • Russell WR, Gratz SW, Duncan SH, et al. (2011). High-protein, reduced-carbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health. Am J Clin Nutr, 93, 1062–72
  • Saulnier DM, Gibson GR, Kolida S. (2008). In vitro effects of selected synbiotics on the human faecal microbiota composition. FEMS Microbiol Ecol, 66, 516–27
  • Schmidt B, Mulder IE, Musk CC, et al. (2011). Establishment of normal gut microbiota is compromised under excessive hygiene conditions. PLoS One, 6, e28284
  • Sekirov I, Russell SL, Antunes LC, Finlay BB. (2010). Gut microbiota in health and disease. Physiol Rev, 90, 859–904
  • Seksik P, Rigottier-Gois L, Gramet G, et al. (2003). Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon. Gut, 52, 237–42
  • Seok J, Warren HS, Cuenca AG, et al. (2013). Genomic responses in mouse models poorly mimic human inflammatory diseases. Proc Natl Acad Sci USA, 110, 3507–12
  • Signoretto C, Bianchi F, Burlacchini G, et al. (2010). Drinking habits are associated with changes in the dental plaque microbial community. J Clin Microbiol, 48, 347–56
  • Signoretto C, Burlacchini G, Bianchi F, et al. (2006). Differences in microbiological composition of saliva and dental plaque in subjects with different drinking habits. New Microbiol, 29, 293–302
  • Sommer MO, Dantas G, Church GM. (2009). Functional characterization of the antibiotic resistance reservoir in the human microflora. Science, 325, 1128–31
  • Sonoyama K, Ogasawara T, Goto H, et al. (2010). Comparison of gut microbiota and allergic reactions in BALB/c mice fed different cultivars of rice. Brit J Nutr, 103, 218–26
  • Spor A, Koren O, Ley R. (2011). Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol, 9, 279–90
  • Świątecka D, Narbad A, Ridgway KP, Kostyra H. (2011). The study on the impact of glycated pea proteins on human intestinal bacteria. Int J Food Microbiol, 145, 267–72
  • Talebi Bezmin Abadi A, Rafiei A, Ajami A, et al. (2011). Helicobacter pylori homB, but not cagA, is associated with gastric cancer in Iran. J Clin Microbiol, 49, 3191–7
  • Turnbaugh PJ, Ridaura VK, Faith JJ, et al. (2009). The effect of diet on the human gut microbiome, a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med, 1, 6ra14. doi: 10.1126/scitranslmed.3000322
  • Tzounis X, Vulevic J, Kuhnle GG, et al. (2008). Flavanol monomer-induced changes to the human faecal microflora. Br J Nutr, 99, 782–92
  • Uittamo J, Siikala E, Kaihovaara P, et al. (2009). Chronic candidosis and oral cancer in APECED-patients, production of carcinogenic acetaldehyde from glucose and ethanol by Candida albicans. Int J Cancer, 124, 754–6
  • Upadhayaa SD, Songa JY, Park MA, et al. (2012). Isolation, screening and identification of swine gut microbiota with ochratoxin A biodegradation ability. Asian-Aust J Anim Sci, 25, 114–21
  • van Baarlen P, Troosta F, van der Meera C, et al. (2009). Differential NF-kappaB pathways induction by Lactobacillus plantarum in the duodenum of healthy humans correlating with immune tolerance. Proc Natl Acad Sci USA, 106, 2371–6
  • van Baarlen P, Troost F, van der Meer C, et al. (2011). Human mucosal in vivo transcriptome responses to three lactobacilli indicate how probiotics may modulate human cellular pathways. Proc Natl Acad Sci USA, 108, 4562–9
  • Ventura M, Turroni F, Zomer A, et al. (2009). The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity. PLoS Genet, 5, e1000785
  • Verberkmoes NC, Russell AL, Shah M, et al. (2009). Shotgun metaproteomics of the human distal gut microbiota. ISME J, 3, 179–89
  • Vitali B, Ndagijimana M, Cruciani F, et al. (2010). Impact of a synbiotic food on the gut microbial ecology and metabolic profiles. BMC Microbiol, 10, 4. doi: 10.1186/1471-2180-10-4
  • Wacklin P, Mäkivuokko H, Alakulppi N, et al. (2011). Secretor genotype (FUT2 gene) is strongly associated with the composition of Bifidobacteria in the human intestine. PLoS One, 6, e20113
  • Waligora-Dupriet AJ, Campeotto F, Romero K, et al. (2011). Diversity of gut Bifidobacterium species is not altered between allergic and non-allergic French infants. Anaerobe, 17, 91–6
  • Wall R, Marques TM, O'Sullivan O, et al. (2012). Contrasting effects of Bifidobacterium breve NCIMB 702258 and Bifidobacterium breve DPC 6330 on the composition of murine brain fatty acids and gut microbiota. Am J Clin Nutr, 95, 1278–87
  • Wikoff WR, Anfora AT, Liu J, et al. (2009). Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc Natl Acad Sci USA, 106, 3698–703
  • Wu GD, Chen J, Hoffmann C, et al. (2011). Linking long-term dietary patterns with gut microbial enterotypes. Science, 334, 105–108
  • Yager EJ, Szaba FM, Kummer LW, et al. (2009). Gamma-Herpesvirus-induced protection against bacterial infection is transient. Viral Immunol, 22, 67–72
  • Yamakoshi J, Tokutake S, Kikuchi M, et al. (2001). Effect of proanthocyanidin-rich extract from grape seeds on human fecal flora and faecal odor. Microbial Ecol Health Disease, 13, 25e31
  • Yeşilova Y, Çalka Ö, Akdeniz N, Berktaş M. (2012). Effect of probiotics on the treatment of children with atopic dermatitis. Ann Dermatol, 24, 189–93
  • Zhao LH, Guan S, Gao X, et al. (2011). Preparation, purification and characteristics of an aflatoxin degradation enzyme from Myxococcus fulvus ANSM068. J Appl Microbiol, 110, 147–55

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