Abstract
ABSTRACT:
The Human Microbiome Project (HMP) revealed the significance of the gut microbiome in promoting health. Disruptions in microbiome composition are associated with the pathogenesis of numerous diseases. The indigenous microflora has co-evolved with humans for millions of years and humans have preserved the inherited microbiomes through consumption of fermented foods and interactions with environmental microbes. Through modernization, traditional foods were abandoned, native food starters were substituted with industrial products, vaccines and antibiotics were used, extreme hygiene measures were taken, the rate of cesarean section increased, and breast feeding changed into formula. These factors have reduced human exposure to microbial symbionts and led to shrinkage of the core microbiome. Reduction in microbiome biodiversity can compromise the human immune system and predispose individuals to several modern diseases. This article suggests launching microbiome biobanks for archiving native microbiomes, supervising antibiotic use, probiotic design and native starter production, as well as advertising a revisit to native lifestyles.
Papers of special note have been highlighted as: • of interest; •• of considerable interest
References
- 1 . The human microbiome project. Nature 449(7164), 804–810 (2007).Crossref, Medline, CAS, Google Scholar
- 2 A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464(7285), 59–65 (2010). •• Presents a catalog containing the majority of prevalent human intestinal microbial genes that are largely shared among individuals. Furthermore, the minimal gut metagenome with regards to the functions present in all individuals is depicted.Crossref, Medline, CAS, Google Scholar
- 3 . Analyses of the microbial diversity across the human microbiome. PloS ONE 7(6), e32118 (2012).Crossref, Medline, CAS, Google Scholar
- 4 Unlocking the potential of metagenomics through replicated experimental design. Nat. Biotechnol. 30(6), 513–520 (2012).Crossref, Medline, CAS, Google Scholar
- 5 Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput. Biol. 8(6), e1002358 (2012).Crossref, Medline, CAS, Google Scholar
- 6 . Supervised classification of human microbiota. FEMS Microbiol. Rev. 35(2), 343–359 (2011).Crossref, Medline, CAS, Google Scholar
- 7 . Metabolomics: towards understanding host–microbe interactions. Future Microbiol. 5(2), 153–161 (2010).Link, CAS, Google Scholar
- 8 Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts. PLoS Biol. 9(12), e1001221 (2011).Crossref, Medline, CAS, Google Scholar
- 9 . Homeostasis and inflammation in the intestine. Cell 140(6), 859–870 (2010).Crossref, Medline, CAS, Google Scholar
- 10 . Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. Proc. Natl Acad. Sci. USA 99(24), 15451–15455 (2002).Crossref, Medline, CAS, Google Scholar
- 11 Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation. Proc. Natl Acad. Sci. USA 106(27), 11276–11281 (2009).Crossref, Medline, CAS, Google Scholar
- 12 Host genes related to paneth cells and xenobiotic metabolism are associated with shifts in human ileum-associated microbial composition. PloS ONE 7(6), e30044 (2012).Crossref, Medline, CAS, Google Scholar
- 13 . Gut–brain axis: how the microbiome influences anxiety and depression. Trends Neurosci. 36(5), 305–312 (2013).Crossref, Medline, CAS, Google Scholar
- 14 Structure, function and diversity of the healthy human microbiome. Nature 486(7402), 207–214 (2012).Crossref, Medline, CAS, Google Scholar
- 15 . Colonization resistance and microbial ecophysiology: using gnotobiotic mouse models and single-cell technology to explore the intestinal jungle. FEMS Microbiol. Rev. 37(5), 793–829 (2013).Crossref, Medline, CAS, Google Scholar
- 16 . Microbiome: pathogens and commensals fight it out. Nat. Rev. Microbiol. 10(7), 445–445 (2012).Crossref, Medline, CAS, Google Scholar
- 17 . Designing probiotics with respect to the native microbiome. Future Microbiol. 7(5), 571–575 (2012).Link, CAS, Google Scholar
- 18 . The microbiome: the forgotten organ of the astronaut's body – probiotics beyond terrestrial limits. Future Microbiol. 7(9), 1037–1046 (2012).Link, CAS, Google Scholar
- 19 . What are the consequences of the disappearing human microbiota? Nat. Rev. Microbiol. 7(12), 887–894 (2009).Crossref, Medline, CAS, Google Scholar
- 20 . Recognition of microorganisms and activation of the immune response. Nature 449(7164), 819–826 (2007).Crossref, Medline, CAS, Google Scholar
- 21 Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139(3), 485–498 (2009). •• A nice example of the immunomodulatory potential of a specific member of gut microbiota.Crossref, Medline, CAS, Google Scholar
- 22 . 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 (1992).Crossref, Medline, CAS, Google Scholar
- 23 . A primitive T cell-independent mechanism of intestinal mucosal IgA responses to commensal bacteria. Science 288(5474), 2222–2226 (2000).Crossref, Medline, CAS, Google Scholar
- 24 . Gut matters: microbe–host interactions in allergic diseases. J. Allergy Clin. Immunol. 129(6), 1452–1459 (2012).Crossref, Medline, Google Scholar
- 25 Development of immunological capacity under germfree and conventional conditions. Ann. NY Acad. Sci. 409(1), 96–113 (2006).Google Scholar
- 26 . Expansion of alpha beta T-cell receptor-bearing intestinal intraepithelial lymphocytes after microbial colonization in germ-free mice and its independence from thymus. Immunol. 79(1), 32–37 (1993).Medline, CAS, Google Scholar
- 27 . Increase in the population of duodenal immunoglobulin A plasmocytes in axenic mice associated with different living or dead bacterial strains of intestinal origin. Infect. Immun. 21(2), 532–539 (1978).Crossref, Medline, CAS, Google Scholar
- 28 . Immune adaptations that maintain homeostasis with the intestinal microbiota. Nat. Rev. Immunol. 10(3), 159–169 (2010).Crossref, Medline, CAS, Google Scholar
- 29 . Infections and autoimmune diseases. J. Autoimmun. 25(1), 74–80 (2005).Crossref, Medline, CAS, Google Scholar
- 30 . Epithelial cells and their neighbors. IV. Bacterial contributions to intestinal epithelial barrier integrity. Am. J. Physiol. Gastrointest. Liver Physiol. 289(5), G779–G784 (2005).Crossref, Medline, CAS, Google Scholar
- 31 . The immune system and the gut microbiota: friends or foes? Nat. Rev. Immunol. 10(10), 735–744 (2010).Crossref, Medline, CAS, Google Scholar
- 32 Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature 455(7216), 1109–1113 (2008).Crossref, Medline, CAS, Google Scholar
- 33 Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 328(5975), 228–231 (2010).Crossref, Medline, CAS, Google Scholar
- 34 . The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci. Transl. Med. 1(6), 6ra14 (2009).Crossref, Medline, Google Scholar
- 35 Linking long-term dietary patterns with gut microbial enterotypes. Science 334(6052), 105–108 (2011).Crossref, Medline, CAS, Google Scholar
- 36 . Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 152(1), 39–50 (2013).Crossref, Medline, CAS, Google Scholar
- 37 Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice. ISME J. 4(2), 232–241 (2009).Crossref, Medline, Google Scholar
- 38 Association of Helicobacter pylori infection and diet on the risk of gastric cancer: a case–control study in Hawaii. Cancer Causes Control 19(8), 869–877 (2008).Crossref, Medline, Google Scholar
- 39 Diet-induced metabolic improvements in a hamster model of hypercholesterolemia are strongly linked to alterations of the gut microbiota. Appl. Environ. Microbiol. 75(12), 4175–4184 (2009).Crossref, Medline, CAS, Google Scholar
- 40 . The role of protein and calorie restriction in outcome from Salmonella infection in mice. J. Parenter. Enteral Nutr. 16(6), 561–565 (1992).Crossref, Medline, CAS, Google Scholar
- 41 Meat, fish, and colorectal cancer risk: the European Prospective Investigation into cancer and nutrition. J. Natl Cancer Inst. 97(12), 906–916 (2005).Crossref, Medline, Google Scholar
- 42 . Resistant starch attenuates colonic DNA damage induced by higher dietary protein in rats. Nutr. Cancer 51(1), 45–51 (2005).Crossref, Medline, CAS, Google Scholar
- 43 . Trends in antimicrobial prescribing rates for children and adolescents. JAMA 287(23), 3096–3102 (2002).Crossref, Medline, Google Scholar
- 44 . Trends in antimicrobial drug prescribing among office-based physicians in the United States. JAMA 273(3), 214–219 (1995).Crossref, Medline, CAS, Google Scholar
- 45 . The use of antibacterials in children: a report of the Specialist Advisory Committee on Antimicrobial Resistance (SACAR) Paediatric Subgroup. J. Antimicrob. Chemother. 60(Suppl. 1), i15–i26 (2007).Crossref, Medline, CAS, Google Scholar
- 46 Reshaping the gut microbiome with bacterial transplantation and antibiotic intake. Genome Res. 20(10), 1411–1419 (2010).Crossref, Medline, CAS, Google Scholar
- 47 . Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc. Natl Acad. Sci. USA. 108(Suppl. 1), 4554–4561 (2010).Medline, Google Scholar
- 48 . Antibiotic resistance and its cost: is it possible to reverse resistance? Nat. Rev. Microbiol. 8(4), 260–271 (2010).Crossref, Medline, CAS, Google Scholar
- 49 . The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 6(11), e280 (2008).Crossref, Medline, Google Scholar
- 50 . Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PloS ONE. 5(3), e9836 (2010).Crossref, Medline, Google Scholar
- 51 Neonatal antibiotic treatment alters gastrointestinal tract developmental gene expression and intestinal barrier transcriptome. Physiol. Genomics 23(2), 235–245 (2005).Crossref, Medline, CAS, Google Scholar
- 52 Metabonomic and microbiological analysis of the dynamic effect of vancomycin-induced gut microbiota modification in the mouse. J. Proteome Res. 7(9), 3718–3728 (2008).Crossref, Medline, CAS, Google Scholar
- 53 Antibiotic-induced perturbations of the intestinal microbiota alter host susceptibility to enteric infection. Infect. Immun. 76(10), 4726–4736 (2008).Crossref, Medline, CAS, Google Scholar
- 54 Sensitivity of human strains of Oxalobacter formigenes to commonly prescribed antibiotics. Urology 79(6), 1286–1289 (2012).Crossref, Medline, Google Scholar
- 55 . Oxalobacter formigenes and its potential role in human health. Appl. Environ. Microbiol. 68(8), 3841–3847 (2002).Crossref, Medline, CAS, Google Scholar
- 56 . Enteric oxalate elimination is induced and oxalate is normalized in a mouse model of primary hyperoxaluria following intestinal colonization with Oxalobacter. Am. J. Physiol. Gastrointest. Liver Physiol. 300(3), G461–G469 (2011).Crossref, Medline, CAS, Google Scholar
- 57 . Helicobacter pylori colonization is inversely associated with childhood asthma. J. Infect. Dis. 198(4), 553–560 (2008).Crossref, Medline, Google Scholar
- 58 Helicobacter pylori infection prevents allergic asthma in mouse models through the induction of regulatory T cells. J. Clin. Invest. 121(8), 3088–3093 (2011).Crossref, Medline, CAS, Google Scholar
- 59 . Does diversity of environmental microbial exposure matter for the occurrence of allergy and asthma? J. Allergy Clin. Immunol. 130(1), 44–50 (2012).Crossref, Medline, Google Scholar
- 60 Microbial exposure of rural school children, as assessed by levels of N-acetyl-muramic acid in mattress dust, and its association with respiratory health. J. Allergy Clin. Immunol. 113(5), 860–867 (2004).Crossref, Medline, CAS, Google Scholar
- 61 Does early indoor microbial exposure reduce the risk of asthma? The Prevention and Incidence of Asthma and Mite Allergy birth cohort study. J. Allergy Clin. Immunol. 117(5), 1067–1073 (2006).Crossref, Medline, Google Scholar
- 62 . Prenatal or early-life exposure to antibiotics and risk of childhood asthma: a systematic review. Pediatrics 127(6), 1125–1138 (2011).Crossref, Medline, Google Scholar
- 63 . The risk of the hemolytic-uremic syndrome after antibiotic treatment of Escherichia coli O157: H7 infections. N. Engl. J. Med. 342(26), 1930–1936 (2000).Crossref, Medline, CAS, Google Scholar
- 64 . Association between the use of antibiotics in the first year of life and pediatric inflammatory bowel disease. Am. J. Gastroenterol. 105(12), 2687–2692 (2010).Crossref, Medline, Google Scholar
- 65 . Antibiotic exposure and IBD development among children: a population-based cohort study. Pediatrics 130(4), e794–e803 (2012).Crossref, Medline, Google Scholar
- 66 . Association between the use of antibiotics and new diagnoses of Crohn's disease and ulcerative colitis. Am. J. Gastroenterol. 106(12), 2133–2142 (2011).Crossref, Medline, Google Scholar
- 67 . Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era. Gastroenterology 136(6), 2015 (2009).Crossref, Medline, CAS, Google Scholar
- 68 . Disruption of the gut microbiome as a risk factor for microbial infections. Curr. Opin. Microbiol. 16(2), 221–227 (2013).Crossref, Medline, Google Scholar
- 69 . Innate immune recognition of the microbiota promotes host–microbial symbiosis. Nat. Immunol. 14(7), 668–675 (2013).Crossref, Medline, CAS, Google Scholar
- 70 . Antibiotic overuse: stop the killing of beneficial bacteria. Nature 476(7361), 393–394 (2011).Crossref, Medline, CAS, Google Scholar
- 71 Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature 488(7413), 621–626 (2012).Crossref, Medline, CAS, Google Scholar
- 72 . The ecology of height: the effect of microbial transmission on human height. Perspect. Biol. Med. 45(4), 475–498 (2002).Crossref, Medline, Google Scholar
- 73 . Paleolithic nutrition. N. Engl. J. Med. 312(5), 283–289 (1985).Crossref, Medline, CAS, Google Scholar
- 74 . Evolution of the human diet: linking our ancestral diet to modern functional foods as a means of chronic disease prevention. J. Med. Food 12(5), 925–934 (2009).Crossref, Medline, CAS, Google Scholar
- 75 . Nutrigenomics. Nature 468(7327), S1 (2010).Crossref, Medline, CAS, Google Scholar
- 76 . Cardiovascular disease resulting from a diet and lifestyle at odds with our Paleolithic genome: how to become a 21st-century hunter-gatherer. In: Mayo Clinic Proceedings. MN, USA (2004).Crossref, Google Scholar
- 77 . Stone agers in the fast lane: chronic degenerative diseases in evolutionary perspective. Am. J. Med. 84(4), 739–749 (1988).Crossref, Medline, CAS, Google Scholar
- 78 . Evolutionary aspects of diet: old genes, new fuels. World Rev. Nutr. Diet. 81, 26–37 (1997).Crossref, Medline, CAS, Google Scholar
- 79 . Nutrient Content of the US Food Supply, 1909–2004: a Summary Report. Center for Nutrition Policy and Promotion, US Department of Agriculture, Washington DC, USA (2007).Google Scholar
- 80 Beneficial effects of a Paleolithic diet on cardiovascular risk factors in Type 2 diabetes: a randomized cross-over pilot study. Cardiovasc. Diabetol. 8, 35 (2009).Crossref, Medline, Google Scholar
- 81 A Palaeolithic diet improves glucose tolerance more than a Mediterranean-like diet in individuals with ischaemic heart disease. Diabetologia 50(9), 1795–1807 (2007).Crossref, Medline, CAS, Google Scholar
- 82 . Effects of a short-term intervention with a paleolithic diet in healthy volunteers. Eur. J. Clin. Nutr. 62(5), 682–685 (2007).Crossref, Medline, Google Scholar
- 83 . Metabolic and physiologic improvements from consuming a paleolithic, hunter-gatherer type diet. Eur. J. Clin. Nutr. 63(8), 947–955 (2009).Crossref, Medline, CAS, Google Scholar
- 84 . Fast foods, energy density and obesity: a possible mechanistic link. Obesity Rev. 4(4), 187–194 (2003).Crossref, CAS, Google Scholar
- 85 . Effects of snacks on energy intake: an evolutionary perspective. Appetite 47(1), 18–23 (2006).Crossref, Medline, Google Scholar
- 86 . Apparent absence of stroke and ischaemic heart disease in a traditional Melanesian island: a clinical study in Kitava. J. Intern. Med. 233(3), 269–275 (2009).Crossref, Google Scholar
- 87 . The unique aspects of the nutrition transition in South Korea: the retention of healthful elements in their traditional diet. Public Health Nutr. 5(1A), 197–204 (2002).Crossref, Medline, CAS, Google Scholar
- 88 . The nutrition transition in South Korea. Am. J. Clin. Nutr. 71(1), 44–53 (2000).Crossref, Medline, CAS, Google Scholar
- 89 Mediterranean diet pyramid: a cultural model for healthy eating. Am. J. Clin. Nutr. 61(6), 1402S–1406S (1995).Crossref, Medline, CAS, Google Scholar
- 90 Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc. Natl Acad. Sci. USA 107(44), 18933–18938 (2010).Crossref, Medline, CAS, Google Scholar
- 91 . Unravelling the effects of the environment and host genotype on the gut microbiome. Nat. Rev. Microbiol. 9(4), 279–290 (2011).Crossref, Medline, CAS, Google Scholar
- 92 . The gut microbiota shapes intestinal immune responses during health and disease. Nat. Rev. Immunol. 9(5), 313–323 (2009).Crossref, Medline, CAS, Google Scholar
- 93 . Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl Acad. Sci. USA 104(34), 13780–13785 (2007).Crossref, Medline, CAS, Google Scholar
- 94 Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 55(2), 205–211 (2006).Crossref, Medline, CAS, Google Scholar
- 95 . High prevalence of Escherichia coli belonging to the B2+ D phylogenetic group in inflammatory bowel disease. Gut 56(5), 669–675 (2007).Crossref, Medline, CAS, Google Scholar
- 96 Culture independent analysis of ileal mucosa reveals a selective increase in invasive Escherichia coli of novel phylogeny relative to depletion of Clostridiales in Crohn's disease involving the ileum. ISME J. 1(5), 403–418 (2007).Crossref, Medline, CAS, Google Scholar
- 97 Human metabolic phenotype diversity and its association with diet and blood pressure. Nature 453(7193), 396–400 (2008). • Outstanding article relating the microbiota-associated metabolic phenotype diversity to human high blood pressure.Crossref, Medline, CAS, Google Scholar
- 98 Olfactory receptor responding to gut microbiota-derived signals plays a role in renin secretion and blood pressure regulation. Proc. Natl Acad. Sci. USA 110(11), 4410–4415 (2013).Crossref, Medline, CAS, Google Scholar
- 99 . Microbial influences in inflammatory bowel diseases. Gastroenterology 134(2), 577–594 (2008).Crossref, Medline, CAS, Google Scholar
- 100 . An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444(7122), 1027–1131 (2006).Crossref, Medline, Google Scholar
- 101 The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects. Gastroenterology 133(1), 24–33 (2007).Crossref, Medline, CAS, Google Scholar
- 102 . Association between composition of the human gastrointestinal microbiome and development of fatty liver with choline deficiency. Gastroenterology 140(3), 976–986 (2011).Crossref, Medline, CAS, Google Scholar
- 103 . The microbiota and allergies/asthma. PLoS Pathog. 6(5), e1000549 (2010).Crossref, Medline, Google Scholar
- 104 Term stillbirth caused by oral Fusobacterium nucleatum. Obstet. Gynecol. 115(2 Pt 2), 442 (2010).Crossref, Medline, Google Scholar
- 105 . The microbiome and rheumatoid arthritis. Nat. Rev. Rheumatol. 7(10), 569–578 (2011).Crossref, Medline, CAS, Google Scholar
- 106 Pyrosequencing study of fecal microflora of autistic and control children. Anaerobe 16(4), 444–453 (2010).Crossref, Medline, CAS, Google Scholar
- 107 . Molecular pathways: pathogenesis and clinical implications of microbiome alteration in esophagitis and Barrett esophagus. Clin. Cancer. Res. 18(8), 2138–2144 (2012).Crossref, Medline, CAS, Google Scholar
- 108 . Microbiome and malignancy. Cell Host Microbe 10(4), 324–335 (2011).Crossref, Medline, CAS, Google Scholar
- 109 . Gut bacteria in health and disease: a survey on the interface between intestinal microbiology and colorectal cancer. Biol. Rev. Camb. Philos. Soc. 87(3), 701–730 (2012).Crossref, Medline, Google Scholar
- 110 Obesity-induced gut microbial metabolite promotes liver cancer through senescence secretome. Nature 499(7456), 97–101 (2013).Crossref, Medline, CAS, Google Scholar
- 111 Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science 339(6119), 548–554 (2013).Crossref, Medline, CAS, Google Scholar
- 112 . Back to the future: rethinking the way we eat. Am. J. Med. 125(10), 947–948 (2012).Crossref, Medline, Google Scholar
- 113 Diet, Nutrition and the Prevention of Chronic Diseases: Report of a Joint WHO/FAO Expert Consultation. WHO, Geneva, Switzerland (2002).Google Scholar
- 114 . Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS ONE 5(3), e9836 (2010).Crossref, Medline, Google Scholar
- 115 . Hay fever, hygiene, and household size. BMJ 299(6710), 1259–1260 (1989).Crossref, Medline, CAS, Google Scholar
- 116 . Exposure to a social stressor alters the structure of the intestinal microbiota: implications for stressor-induced immunomodulation. Brain Behav. Immun. 25(3), 397–407 (2011).Crossref, Medline, CAS, Google Scholar
- 117 Postnatal microbial colonization programs the hypothalamic–pituitary–adrenal system for stress response in mice. J. Physiol. 558(1), 263–275 (2004).Crossref, Medline, CAS, Google Scholar
- 118 A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. PloS ONE 7(6), e36466 (2012).Crossref, Medline, CAS, Google Scholar
- 119 Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts. Genome Res. 22(10), 1974–1984 (2012).Crossref, Medline, CAS, Google Scholar
- 120 . Human nutrition, the gut microbiome and the immune system. Nature 474(7351), 327–336 (2011).Crossref, Medline, CAS, Google Scholar
- 121 . Elton revisited: a review of evidence linking diversity and invasibility. Oikos 87, 15–26 (1999).Crossref, Google Scholar
- 122 . Human nutrition, the gut microbiome and the immune system. Nature 474(7351), 327–336 (2011).Crossref, Medline, CAS, Google Scholar
- 123 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 (2010). •• Compares intestinal microbiota between western and rural children, and highlights the importance of preserving microbial diversity from ancient rural communities worldwide.Crossref, Medline, Google Scholar
- 124 . Diet, gut microbiota and immune responses. Nat. Immunol. 12(1), 5–9 (2010).Crossref, Google Scholar
- 125 . Host–bacterial mutualism in the human intestine. Science 307(5717), 1915–1920 (2005).Crossref, Medline, Google Scholar
- 126 . The host selects mucosal and luminal associations of coevolved gut microorganisms: a novel concept. FEMS Microbiol. Rev. 35(4), 681–704 (2011).Crossref, Medline, CAS, Google Scholar
- 127 An African origin for the intimate association between humans and Helicobacter pylori. Nature 445(7130), 915–918 (2007). •• Demonstrated the decrease in genetic diversity of Helicobacter pylori with increasing geographic distance from human African origin.Crossref, Medline, Google Scholar
- 128 . Detecting a bacterial protein to understand cancer risk. Clin. Chem. 57(9), 1331–1332 (2011).Crossref, Medline, CAS, Google Scholar
- 129 . Who are we? Indigenous microbes and the ecology of human diseases. EMBO Rep. 7(10), 956–960 (2006).Crossref, Medline, CAS, Google Scholar
- 130 . Helicobacter pylori infection and gastric carcinoma among Japanese Americans in Hawaii. N. Engl. J. Med. 325(16), 1132–1136 (1991).Crossref, Medline, CAS, Google Scholar
- 131 . The language used by Helicobacter pylori to regulate human cells. J. Infect. Dis. 196(1), 6–9 (2007).Crossref, Medline, CAS, Google Scholar
- 132 Opposing risks of gastric cardia and noncardia gastric adenocarcinomas associated with Helicobacter pylori seropositivity. J. Natl Cancer Inst. 98(20), 1445–1452 (2006).Crossref, Medline, Google Scholar
- 133 . Association between gastric Helicobacter pylori colonization and glycated hemoglobin levels. J. Infect. Dis. 205(8), 1195–1202 (2012).Crossref, Medline, Google Scholar
- 134 . Inverse associations of Helicobacter pylori with asthma and allergy. Arch. Intern. Med. 167(8), 821–827 (2007).Crossref, Medline, Google Scholar
- 135 Enterotypes of the human gut microbiome. Nature 473(7346), 174–180 (2011). •• Identified three robust enterotypes that are not nation or continent specific. Moreover, they have shown the diagnostic potential of microbial markers.Crossref, Medline, CAS, Google Scholar
- 136 . Worlds within worlds: evolution of the vertebrate gut microbiota. Nat. Rev. Microbiol. 6(10), 776–788 (2008).Crossref, Medline, CAS, Google Scholar
- 137 . Diversity, stability and resilience of the human gut microbiota. Nature 489(7415), 220–230 (2012).Crossref, Medline, CAS, Google Scholar
- 138 . Reconstitution of the human biome as the most reasonable solution for epidemics of allergic and autoimmune diseases. Med. Hypotheses 77(4), 494–504 (2011).Crossref, Medline, Google Scholar
- 139 . Resistance, resilience, and redundancy in microbial communities. Proc. Natl Acad. Sci. USA 105(Suppl. 1), 11512–11519 (2008).Crossref, Medline, CAS, Google Scholar
- 140 . Microorganisms should be high on DNA preservation list. Science 290(5496), 1503 (2000).Crossref, Medline, CAS, Google Scholar
- 141 . The Svalbard seed vault and crop security. BioScience 58(3), 190–191 (2008).Crossref, Google Scholar
- 142 . Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol. Rev. 32(5), 723–735 (2008).Crossref, Medline, CAS, Google Scholar
- 143 A global view of antibiotic resistance. FEMS Microbiol. Rev. 33(1), 44–65 (2009).Crossref, Medline, CAS, Google Scholar
- 144 . Genomic and phenotypic evidence for probiotic influences of Lactobacillus gasseri on human health. FEMS Microbiol. Rev. 37(6), 915–935 (2013).Crossref, Medline, CAS, Google Scholar
- 145 Consumption of fermented milk product with probiotic modulates brain activity. Gastroenterology 144(7), 1394–1401 (2013).Crossref, Medline, CAS, Google Scholar
- 146 . Microbiome: human gut microbiota can be readily cultured, manipulated and archived. Nat. Rev. Gastroenterol. Hepatol. 8(5), 241–241 (2011).Crossref, Medline, Google Scholar
- 147 Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc. Natl Acad. Sci. USA 108(15), 6252–6257 (2011). •• Shows that the transplantation of human fecal microbiota into gnotobiotic mice results in the formation of a functional microbiome in the recipient animals. The authors also demonstrate that fecal isolates from an individual can be clonally archived and taxonomically mapped to produce personalized microbiota collections.Crossref, Medline, CAS, Google Scholar
- 148 . Fecal microbiota transplantation and emerging applications. Nat. Rev. Gastroenterol. Hepatol. 9(2), 88–96 (2011).Crossref, Medline, Google Scholar
- 149 . Survival curves for microbial species stored by freeze-drying. Cryobiology 52(1), 27–32 (2006).Crossref, Medline, Google Scholar
- 150 . 'Who owns your poop?': insights regarding the intersection of human microbiome research and the ELSI aspects of biobanking and related studies. BMC Med. Genomics 4(1), 1–9 (2011).Crossref, Medline, Google Scholar

