Geography, Ethnicity or Subsistence-Specific Variations in Human Microbiome Composition and Diversity

Adlerberth, 2009, Establishment of the gut microbiota in Western infants, Acta Paediatr., 98, 229, 10.1111/j.1651-2227.2008.01060.x

Albert, 2015, A study of the vaginal microbiome in healthy canadian women utilizing cpn60-based molecular profiling reveals distinct gardnerella subgroup community state types, PLoS ONE, 10, e0135620, 10.1371/journal.pone.0135620

Allen, 2014, Characterization of the nasopharyngeal microbiota in health and during rhinovirus challenge, Microbiome, 2, 22, 10.1186/2049-2618-2-22

Anderson, 2011, Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47, Nat. Genet., 43, 246, 10.1038/ng.764

Armougom, 2009, Monitoring bacterial community of human gut microbiota reveals an increase in Lactobacillus in obese patients and Methanogens in anorexic patients, PLoS ONE, 4, e7125, 10.1371/journal.pone.0007125

Arumugam, 2011, Enterotypes of the human gut microbiome, Nature, 473, 174, 10.1038/nature09944

Bassis, 2015, Analysis of the upper respiratory tract microbiotas as the source of the lung and gastric microbiotas in healthy individuals, MBio, 6, e00037, 10.1128/mBio.00037-15

Bengtsson-Palme, 2015, The human gut microbiome as a transporter of antibiotic resistance genes between continents, Antimicrob. Agents Chemother., 59, 6551, 10.1128/AAC.00933-15

Blaser, 2008, Does Helicobacter pylori protect against asthma and allergy?, Gut, 57, 561, 10.1136/gut.2007.133462

Blaser, 2013, Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents, ISME J., 7, 85, 10.1038/ismej.2012.81

Blekhman, 2015, Host genetic variation impacts microbiome composition across human body sites, Genome Biol., 16, 191, 10.1186/s13059-015-0759-1

Bonder, 2016, The influence of a short-term gluten-free diet on the human gut microbiome, Genome Med., 8, 45, 10.1186/s13073-016-0295-y

Botero, 2014, Respiratory tract clinical sample selection for microbiota analysis in patients with pulmonary tuberculosis, Microbiome, 2, 29, 10.1186/2049-2618-2-29

Brooks, 2015, The truth about metagenomics. quantifying and counteracting bias in 16S rRNA studies, BMC Microbiol., 15, 66, 10.1186/s12866-015-0351-6

Castellarin, 2011, Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma, Genome Res., 22, 299, 10.1101/gr.126516.111

Charlson, 2011, Topographical continuity of bacterial populations in the healthy human respiratory tract, Am. J. Respir. Crit. Care Med., 184, 957, 10.1164/rccm.201104-0655OC

Chen, 2013, The skin microbiome: current perspectives and future challenges, J. Am. Acad. Dermatol., 69, 143, 10.1016/j.jaad.2013.01.016

Chiller, 2001, Skin microflora and bacterial infections of the skin, J. Investig. Dermatol. Symp. Proc., 6, 170, 10.1046/j.0022-202x.2001.00043.x

Clemente, 2012, The impact of the gut microbiota on human health: an integrative view, Cell, 148, 1258, 10.1016/j.cell.2012.01.035

Cogen, 2008, Skin microbiota: a source of disease or defence?, Br. J. Dermatol., 158, 442, 10.1111/j.1365-2133.2008.08437.x

Consortium, 2012, Structure, function and diversity of the healthy human microbiome, Nature, 486, 207, 10.1038/nature11234

Cruz, 2009, The association of immigration and acculturation attributes with oral health among immigrants in New York City, Am. J. Public Health, 99, S474, 10.2105/ajph.2008.149799

De Filippo, 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, 14691, 10.1073/pnas.1005963107

de Jongh, 2005, High expression levels of keratinocyte antimicrobial proteins in psoriasis compared with atopic dermatitis, J. Invest. Dermatol., 125, 1163, 10.1111/j.0022-202X.2005.23935.x

de Steenhuijsen Piters, 2016, Dysbiosis of upper respiratory tract microbiota in elderly pneumonia patients, ISME J., 10, 97, 10.1038/ismej.2015.99

Dewhirst, 2010, The human oral microbiome, J. Bacteriol., 192, 5002, 10.1128/JB.00542-10

Dickson, , Spatial variation in the healthy human lung microbiome and the adapted Island model of lung biogeography, Ann. Am. Thorac. Soc., 12, 821, 10.1513/AnnalsATS.201501-029OC

Dickson, , The microbiome and the respiratory tract, Annu. Rev. Physiol., 78, 481, 10.1146/annurev-physiol-021115-105238

Ellis, 2013, Comparison of the distal gut microbiota from people and animals in Africa, PLoS ONE, 8, e54783, 10.1371/journal.pone.0054783

Fallani, 2010, Intestinal microbiota of 6-week-old infants across Europe: geographic influence beyond delivery mode, breast-feeding, and antibiotics, J. Pediatr. Gastroenterol. Nutr., 51, 77, 10.1097/MPG.0b013e3181d1b11e

Falony, 2016, Population-level analysis of gut microbiome variation, Science, 352, 560, 10.1126/science.aad3503

Feng, 2015, Gut microbiome development along the colorectal adenoma-carcinoma sequence, Nat. Commun., 6, 6528, 10.1038/ncomms7528

Fettweis, 2014, Differences in vaginal microbiome in African American women versus women of European ancestry, Microbiology, 160, 2272, 10.1099/mic.0.081034-0

Fredricks, 2001, Microbial ecology of human skin in health and disease, J. Investig. Dermatol. Symp. Proc., 6, 167, 10.1046/j.0022-202x.2001.00039.x

Gao, 2008, Substantial alterations of the cutaneous bacterial biota in psoriatic lesions, PLoS ONE, 3, e2719, 10.1371/journal.pone.0002719

Garrett, 2010, Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis, Cell Host Microbe, 8, 292, 10.1016/j.chom.2010.08.004

Gerasimidis, 2016, The effect of DNA extraction methodology on gut microbiota research applications, BMC Res. Notes, 9, 365, 10.1186/s13104-016-2171-7

Gomez, 2016, Gut microbiome of coexisting BaAka pygmies and bantu reflects gradients of traditional subsistence patterns, Cell Rep., 14, 2142, 10.1016/j.celrep.2016.02.013

Goodrich, 2016, Genetic determinants of the gut microbiome in UK twins, Cell Host Microbe, 19, 731, 10.1016/j.chom.2016.04.017

Greenhill, 2015, Characterization of the gut microbiota of Papua New Guineans using reverse transcription quantitative PCR, PLoS ONE, 10, e0117427, 10.1371/journal.pone.0117427

Grice, 2011, The skin microbiome, Nat. Rev. Microbiol., 9, 244, 10.1038/nrmicro2537

Grzeskowiak, 2012, Distinct gut microbiota in southeastern African and northern European infants, J. Pediatr. Gastroenterol. Nutr., 54, 812, 10.1097/MPG.0b013e318249039c

Gudjonsson, 2009, Global gene expression analysis reveals evidence for decreased lipid biosynthesis and increased innate immunity in uninvolved psoriatic skin, J. Invest. Dermatol., 129, 2795, 10.1038/jid.2009.173

Hehemann, 2010, Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota, Nature, 464, 908, 10.1038/nature08937

Hospodsky, 2014, Hand bacterial communities vary across two different human populations, Microbiology, 160, 1144, 10.1099/mic.0.075390-0

Hyman, 2005, Microbes on the human vaginal epithelium, Proc. Natl. Acad. Sci. U.S.A., 102, 7952, 10.1073/pnas.0503236102

Islami, 2008, Helicobacter pylori and esophageal cancer risk: a meta-analysis, Cancer Prev. Res., 1, 329, 10.1158/1940-6207.CAPR-08-0109

Kao, 2016, Indian women of childbearing age do not metabolically conserve arginine as do American and Jamaican women, J. Nutr., 145, 884, 10.3945/jn.114.208231

Karlsson, 2013, Gut metagenome in European women with normal, impaired and diabetic glucose control, Nature, 498, 99, 10.1038/nature12198

Kemppainen, 2015, Early childhood gut microbiomes show strong geographic differences among subjects at high risk for type 1 diabetes, Diabetes Care, 38, 329, 10.2337/dc14-0850

Kostic, 2012, Genomic analysis identifies association of Fusobacterium with colorectal carcinoma, Genome Res., 22, 292, 10.1101/gr.126573.111

Lavelle, 1970, Crowding and spacing within the human dental arch of different racial groups, Arch. Oral Biol., 15, 1101, 10.1016/0003-9969(70)90123-8

Lavelle, 1971, Mandibular molar tooth configurations in different racial groups, J. Dent. Res., 50, 1353, 10.1177/00220345710500054501

Leung, 2015, Insights into the pan-microbiome: skin microbial communities of Chinese individuals differ from other racial groups, Sci. Rep., 5, 11845, 10.1038/srep11845

Ley, 2005, Obesity alters gut microbial ecology, Proc. Natl. Acad. Sci. U.S.A., 102, 11070, 10.1073/pnas.0504978102

Li, 2014, Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa, BMC Microbiol., 14, 316, 10.1186/s12866-014-0316-1

Mardanov, 2013, Metagenomic analysis of the dynamic changes in the gut microbiome of the participants of the MARS-500 experiment, simulating long term space flight, Acta Nat., 5, 116, 10.32607/20758251-2013-5-3-116-125

Martin, 2015, Host-microbe interactions in distal airways: relevance to chronic airway diseases, Eur. Respir. Rev., 24, 78, 10.1183/09059180.00011614

Martinez, 2015, The gut microbiota of rural papua new guineans. composition, diversity patterns, and ecological processes, Cell Rep., 11, 527, 10.1016/j.celrep.2015.03.049

Mason, 2013, Deep sequencing identifies ethnicity-specific bacterial signatures in the oral microbiome, PLoS ONE, 8, e77287, 10.1371/journal.pone.0077287

Moossavi, 2014, The necessity for an Iranian gut microbiome initiative, Middle East J. Dig. Dis., 6, 109

Morris, 2013, Comparison of the respiratory microbiome in healthy nonsmokers and smokers, Am. J. Respir. Crit. Care Med., 187, 1067, 10.1164/rccm.201210-1913OC

Morton, 2015, Variation in rural african gut microbiota is strongly correlated with colonization by entamoeba and subsistence, PLoS Genet., 11, e1005658, 10.1371/journal.pgen.1005658

Nam, 2011, Comparative analysis of Korean human gut microbiota by barcoded pyrosequencing, PLoS ONE, 6, e22109, 10.1371/journal.pone.0022109

Nasidze, 2009, Global diversity in the human salivary microbiome, Genome Res., 19, 636, 10.1101/gr.084616.108

Nasidze, 2011, High diversity of the saliva microbiome in Batwa Pygmies, PLoS ONE, 6, e23352, 10.1371/journal.pone.0023352

Nishijima, 2016, The gut microbiome of healthy Japanese and its microbial and functional uniqueness, DNA Res., 23, 125, 10.1093/dnares/dsw002

Noble, 1984, Skin microbiology: coming of age, J. Med. Microbiol., 17, 1, 10.1099/00222615-17-1-1

Nomura, , Distinct patterns of gene expression in the skin lesions of atopic dermatitis and psoriasis: a gene microarray analysis, J. Allergy Clin. Immunol., 112, 1195, 10.1016/j.jaci.2003.08.049

Nomura, , Cytokine milieu of atopic dermatitis, as compared to psoriasis, skin prevents induction of innate immune response genes, J. Immunol., 171, 3262, 10.4049/jimmunol.171.6.3262

Obregon-Tito, 2015, Subsistence strategies in traditional societies distinguish gut microbiomes, Nat. Commun., 6, 6505, 10.1038/ncomms7505

O'Keefe, 2007, Why do African Americans get more colon cancer than Native Africans?, J. Nutr., 137, 175S, 10.1093/jn/137.1.175S

O'Keefe, 2015, Fat, fibre and cancer risk in African Americans and rural Africans, Nat. Commun., 6, 6342, 10.1038/ncomms7342

Ong, 2002, Endogenous antimicrobial peptides and skin infections in atopic dermatitis, N. Engl. J. Med., 347, 1151, 10.1056/NEJMoa021481

Ou, 2013, Diet, microbiota, and microbial metabolites in colon cancer risk in rural Africans and African Americans, Am. J. Clin. Nutr., 98, 111, 10.3945/ajcn.112.056689

Peek, 2002, Helicobacter pylori and gastrointestinal tract adenocarcinomas, Nat. Rev. Cancer, 2, 28, 10.1038/nrc703

Qin, 2010, A human gut microbial gene catalogue established by metagenomic sequencing, Nature, 464, 59, 10.1038/nature08821

Qin, 2012, A metagenome-wide association study of gut microbiota in type 2 diabetes, Nature, 490, 55, 10.1038/nature11450

Rampelli, 2015, Metagenome sequencing of the hadza hunter-gatherer gut microbiota, Curr. Biol., 25, 1682, 10.1016/j.cub.2015.04.055

Ravel, 2011, Vaginal microbiome of reproductive-age women, Proc. Natl. Acad. Sci. U.S.A., 108, 4680, 10.1073/pnas.1002611107

Rehman, 2016, Geographical patterns of the standing and active human gut microbiome in health and IBD, Gut, 65, 238, 10.1136/gutjnl-2014-308341

Roth, 1989, Microbiology of the skin: resident flora, ecology, infection, J. Am. Acad. Dermatol., 20, 367, 10.1016/S0190-9622(89)70048-7

Sankaranarayanan, 2015, Gut microbiome diversity among cheyenne and arapaho individuals from Western Oklahoma, Curr. Biol., 25, 3161, 10.1016/j.cub.2015.10.060

Schnorr, 2014, Gut microbiome of the Hadza hunter-gatherers, Nat. Commun., 5, 3654, 10.1038/ncomms4654

Stearns, 2015, Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age, ISME J., 9, 1246, 10.1038/ismej.2014.250

Tagami, 2008, Location-related differences in structure and function of the stratum corneum with special emphasis on those of the facial skin, Int. J. Cosmet. Sci., 30, 413, 10.1111/j.1468-2494.2008.00459.x

Tana, 2010, Altered profiles of intestinal microbiota and organic acids may be the origin of symptoms in irritable bowel syndrome, Neurogastroenterol. Motil., 22, e114, 10.1111/j.1365-2982.2009.01427.x

Tarabichi, 2015, The administration of intranasal live attenuated influenza vaccine induces changes in the nasal microbiota and nasal epithelium gene expression profiles, Microbiome, 3, 74, 10.1186/s40168-015-0133-2

Turnbaugh, 2007, The human microbiome project, Nature, 449, 804, 10.1038/nature06244

Turnbaugh, 2006, An obesity-associated gut microbiome with increased capacity for energy harvest, Nature, 444, 1027, 10.1038/nature05414

Tyakht, 2013, Human gut microbiota community structures in urban and rural populations in Russia, Nat. Commun., 4, 2469, 10.1038/ncomms3469

Van Treuren, 2015, Variation in the microbiota of ixodes ticks with regard to geography, species, and sex, Appl. Environ. Microbiol., 81, 6200, 10.1128/AEM.01562-15

Vebo, 2016, Bead-beating artefacts in the Bacteroidetes to Firmicutes ratio of the human stool metagenome, J. Microbiol. Methods, 129, 78, 10.1016/j.mimet.2016.08.005

Verstraelen, 2016, Characterisation of the human uterine microbiome in non-pregnant women through deep sequencing of the V1-2 region of the 16S rRNA gene, PeerJ, 4, e1602, 10.7717/peerj.1602

Wade, 2013, The oral microbiome in health and disease, Pharmacol. Res., 69, 137, 10.1016/j.phrs.2012.11.006

Walker, 2015, 16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice, Microbiome, 3, 26, 10.1186/s40168-015-0087-4

Wang, 2011, Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease, Nature, 472, 57, 10.1038/nature09922

Yap, 2011, Evaluation of stool microbiota signatures in two cohorts of Asian (Singapore and Indonesia) newborns at risk of atopy, BMC Microbiol., 11, 193, 10.1186/1471-2180-11-193

Yatsunenko, 2012, Human gut microbiome viewed across age and geography, Nature, 486, 222, 10.1038/nature11053

Yi, 2014, Profiling bacterial community in upper respiratory tracts, BMC Infect. Dis., 14, 583, 10.1186/s12879-014-0583-3

Ying, 2015, The influence of age and gender on skin-associated microbial communities in urban and rural human populations, PLoS ONE, 10, e0141842, 10.1371/journal.pone.0141842

Zeller, 2014, Potential of fecal microbiota for early-stage detection of colorectal cancer, Mol. Syst. Biol., 10, 766, 10.15252/msb.20145645

Zhernakova, 2016, Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity, Science, 352, 565, 10.1126/science.aad3369

Zhou, 2007, Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women, ISME J., 1, 121, 10.1038/ismej.2007.12

Zhou, 2010, The vaginal bacterial communities of Japanese women resemble those of women in other racial groups, FEMS Immunol. Med. Microbiol., 58, 169, 10.1111/j.1574-695X.2009.00618.x