1. Avershina E, Lundgård K, Sekelja M, Dotterud C, Storrø O, Øien T, Johnsen R, Rudi K (2016) Transition from infant- to adult-like gut microbiota. Environ Microbiol. doi:10.1111/1462-2920.13248

2. Aviles-Jimenez F, Vazquez-Jimenez F, Medrano-Guzman R, Mantilla A, Torres J (2014) Stomach microbiota composition varies between patients with non-atrophic gastritis and patients with intestinal type of gastric cancer. Sci Rep 4:4202. doi:10.1038/srep04202

3. Belizário JE, Napolitano M (2015) Human microbiomes and their roles in dysbiosis, common diseases, and novel therapeutic approaches. Front Microbiol 6:1050. doi:10.3389/fmicb.2015.01050

4. Bik EM, Eckburg PB, Gill SR, Nelson KE, Purdom EA, Francois F, Perez-Perez G, Blaser MJ, Relman DA (2006) Molecular analysis of the bacterial microbiota in the human stomach. Proc Natl Acad Sci USA 103:732–737. doi:10.1073/pnas.0506655103

5. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336. doi:10.1038/nmeth.f.303

6. Collado MC, Rautava S, Aakko J, Isolauri E, Salminen S (2016) Human gut colonization may be initiated in utero by distinct microbial communities in the placenta andamniotic fluid. Sci Rep 6:23129. doi:10.1038/srep23129

7. Del Chierico F, Vernocchi P, Petrucca A, Paci P, Fuentes S, Praticò G, Capuani G, Masotti A, Reddel S, Russo A, Vallone C, Salvatori G, Buffone E, Signore F, Rigon G, Dotta A, Miccheli A, de Vos WM, Dallapiccola B, Putignani L (2015) Phylogenetic and metabolic tracking of gut microbiota during perinatal development. PLoS ONE 10:e0137347. doi:10.1371/journal.pone.0137347

8. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200. doi:10.1093/bioinformatics/btr381

9. Eun CS, Kim BK, Han DS, Kim SY, Kim KM, Choi BY, Song KS, Kim YS, Kim JF (2014) Differences in gastric mucosal microbiota profiling in patients with chronic gastritis, intestinal metaplasia, and gastric cancer using pyrosequencing methods. Helicobacter 19:407–416. doi:10.1111/hel.12145

10. Forsythe SJ, Dolby JM, Webster AD, Cole JA (1988) Nitrate- and nitrite-reducing bacteria in the achlorhydric stomach. J Med Microbiol 25:253–259. doi:10.1099/00222615-25-4-253

11. Grazul H, Kanda LL, Gondek D (2016) Impact of probiotic supplements on microbiome diversity following antibiotic treatment of mice. Gut Microbes 7:101–114. doi:10.1080/19490976.2016.1138197

12. Hamady M, Lozupone C, Knight R (2010) Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 4:17–27. doi:10.1038/ismej.2009.97

13. Hansen R, Scott KP, Khan S, Martin JC, Berry SH, Stevenson M, Okpapi A, Munro MJ, Hold GL (2015) First-pass meconium samples from healthy term vaginally-delivered neonates: an analysis of the microbiota. PLoS ONE 10:e0133320. doi:10.1371/journal.pone.0133320

14. Homan M, Hojsak I, Kolaček S (2012) Helicobacter pylori in pediatrics. Helicobacter 17:43–48. doi:10.1111/j.1523-5378.2012.00982.x

15. Ibarbalz FM, Pérez MV, Figuerola EL, Erijman L (2014) The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics. PLoS One. 9:e99722. doi:10.1371/journal.pone.0099722

16. Kashtanova DA, Popenko AS, Tkacheva ON, Tyakht AB, Alexeev DG, Boytsov SA (2016) Association between the gut microbiota and diet: fetal life, early childhood and further life. Nutrition 32:620–627. doi:10.1016/j.nut.2015.12.037

17. Khanna S, Pardi DS (2016) Clinical implications of antibiotic impact on gastrointestinal microbiota and Clostridium difficile infection. Expert Rev Gastroenterol Hepatol 16:1–8. doi:10.1586/17474124.2016.1158097

18. Kirpich IA, Petrosino J, Ajami N, Feng W, Wang Y, Liu Y, Beier JI, Barve SS, Yin X, Wei X, Zhang X, McClain CJ (2016) Saturated and unsaturated dietary fats differentially modulate ethanol-induced changes in gut microbiome and metabolome in a mouse model of alcoholic liver disease. Am J Pathol 186:765–776. doi:10.1016/j.ajpath.2015.11.017

19. Lang D, MAL-ED Network Investigators (2015) Opportunities to assess factors contributing to the development of the intestinal microbiota in infants living in developing countries. Microb Ecol Health Dis 26:28316. doi:10.3402/mehd.v26.28316

20. Lee JE, Lee S, Lee H, Song YM, Lee K, Han MJ, Sung J, Ko G (2013) Association of the vaginal microbiota with human papillomavirus infection in a Korean twin cohort. PLoS ONE 8:e63514. doi:10.1371/journal.pone.0063514

21. Lee S, Sung J, Lee J, Ko G (2011) Comparison of the gut microbiotas of healthy adult twins living in South Korea and the United States. Appl Environ Microbiol 77:7433–7437. doi:10.1128/AEM.05490-11

22. Lee SA, Lim JY, Kim BS, Cho SJ, Kim NY, Kim OB, Kim Y (2015) Comparison of the gut microbiota profile in breast-fed and formula-fed Korean infants using pyrosequencing. Nutr Res Pract 9:242–248. doi:10.4162/nrp.2015.9.3.242

23. Lertpiriyapong K, Whary MT, Muthupalani S, Lofgren JL, Gamazon ER, Feng Y, Wang TC, Ge Z, Fox JG (2014) Gastric colonisation with a restricted commensal microbiota replicates the promotion of neoplastic lesions by diverse intestinal microbiota in the Helicobacter pylori INS-GAS mouse model of gastric carcinogenesis. Gut 63:54–63. doi:10.1136/gutjnl-2013-305178

24. Lim ES, Zhou Y, Zhao G, Bauer IK, Droit L, Ndao IM, Warner BB, Tarr PI, Wang D, Holtz LR (2015) Early life dynamics of the human gut virome and bacterial microbiome in infants. Nat Med 21:1228–1234. doi:10.1038/nm.3950

25. Maldonado-Contreras A, Goldfarb KC, Godoy-Vitorino F, Karaoz U, Contreras M, Blaser MJ, Brodie EL, Dominguez-Bello MG (2011) Structure of the human gastric bacterial community in relation to Helicobacter pylori status. ISME J 5:574–579. doi:10.1038/ismej.2010.149

26. McKenna P, Hoffmann C, Minkah N, Aye PP, Lackner A, Liu Z, Lozupone CA, Hamady M, Knight R, Bushman FD (2008) The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis. PLoS Pathog 4:e20. doi:10.1371/journal.ppat.0040020

27. Martin ME, Bhatnagar S, George MD, Paster BJ, Canfield DR, Eisen JA, Solnick JV (2013) The impact of Helicobacter pylori infection on the gastric microbiota of the rhesus macaque. PLoS ONE 8:e76375. doi:10.1371/journal.pone.0076375

28. Mason KL, Erb Downward JR, Falkowski NR, Young VB, Kao JY, Huffnagle GB (2012) Interplay between the gastric bacterial microbiota and Candida albicans during post antibiotic recolonization and gastritis. Infect Immun 80:150–158. doi:10.1128/IAI.05162-11

29. Papapostolou A, Kroffke B, Tatakis DN, Nagaraja HN, Kumar PS (2011) Contribution of host genotype to the composition of health-associated supragingival and subgingival microbiomes. J Clin Periodontol 38:517–524. doi:10.1111/j.1600-051X.2011.01718.x

30. Rolig AS, Cech C, Ahler E, Carter JE, Ottemann KM (2013) The degree of Helicobacter pylori-triggered inflammation is manipulated by preinfection host microbiota. Infect Immun 81:1382–1389. doi:10.1128/IAI.00044-13

31. Schanche M, Avershina E, Dotterud C, Øien T, Storrø O, Johnsen R, Rudi K (2015) High-resolution analyses of overlap in the microbiota between mothers and their children. Curr Microbiol 71:283–290. doi:10.1007/s00284-015-0843-5

32. Schloss PD, Handelsman J (2006) Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures. Appl Environ Microbiol 72:6773–6779. doi:10.1128/AEM.00474-06

33. Si J, Lee S, Park JM, Sung J, Ko G (2015) Genetic associations and shared environmental effects on the skin microbiome of Korean twins. BMC Genom 16:992. doi:10.1186/s12864-015-2131-y

34. Simões CD, Maukonen J, Kaprio J, Rissanen A, Pietiläinen KH, Saarela M (2013) Habitual dietary intake is associated with stool microbiota composition in monozygotic twins. J Nutr 143:417–423. doi:10.3945/jn.112.166322

35. Stearns JC, Lynch MD, Senadheera DB, Tenenbaum HC, Goldberg MB, Cvitkovitch DG, Croitoru K, Moreno-Hagelsieb G, Neufeld JD (2011) Bacterial biogeography of the human digestive tract. Sci Rep 1:170. doi:10.1038/srep00170

36. Wang L, Zhou J, Xin Y, Geng C, Tian Z, Yu X, Dong Q (2016) Bacterial overgrowth and diversification of microbiota in gastric cancer. Eur J Gastroenterol Hepatol 28:261–266. doi:10.1097/MEG.0000000000000542

37. Wang LL, Yu XJ, Zhan SH, Jia SJ, Tian ZB, Dong QJ (2014) Participation of microbiotain the development of gastric cancer. World J Gastroenterol 20:4948–4952. doi:10.3748/wjg.v20.i17.4948

38. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267. doi:10.1128/AEM.00062-0

39. Whary MT, Muthupalani S, Ge Z, Feng Y, Lofgren J, Shi HN, Taylor NS, Correa P, Versalovic J, Wang TC, Fox JG (2014) Helminth co-infection in Helicobacter pylori infected INS-GAS mice attenuates gastric premalignant lesions of epithelial dysplasia and glandular atrophy and preserves colonization resistance of the stomach to lower bowel microbiota. Microbes Infect 16:345–355. doi:10.1016/j.micinf.2014.01.005

40. Yang I, Woltemate S, Piazuelo MB, Bravo LE, Yepez MC, Romero-Gallo J, Delgado AG, Wilson KT, Peek RM, Correa P, Josenhans C, Fox JG, Suerbaum S (2016) Different gastric microbiota compositions in two human populations with high and low gastric cancer risk in Colombia. Sci Rep 6:18594. doi:10.1038/srep18594