{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,23]],"date-time":"2026-01-23T12:14:18Z","timestamp":1769170458628,"version":"3.49.0"},"reference-count":36,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2019,6,14]],"date-time":"2019-06-14T00:00:00Z","timestamp":1560470400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"University of Malaya-Ministry of Education under High Impact Research (HIR) Grant UM.C\/625\/1\/HIR\/MoE\/CHAN\/13\/3","award":["H-50001-A000030"],"award-info":[{"award-number":["H-50001-A000030"]}]},{"name":"Shenzhen\u2019s Sanming Project","award":["SZSM201510050"],"award-info":[{"award-number":["SZSM201510050"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>The present study explored the differences in gastric microbiome between three distinct populations of Southeast Asia. These include the isolated Orang Asli population and modern Malaysians, as well as patients from Myanmar, the least developed country in the region. All 79 subjects recruited in this study had Helicobacter pylori infection. Based on alpha diversity analysis, Orang Asli had the richest and most diverse gastric microbiome, followed by Myanmar and modern Malaysian groups. Beta diversity analysis revealed significant separation of samples between different populations. These observations are likely to be associated with the level of modernization of each population. Our data further suggested increased bacterial species richness and diversity of the gastric microbiome in individuals who were less modernized, particularly in the Orang Asli group, could suppress the growth of H. pylori. In addition, there were significant variations in the gastric microbiome between modern Malaysians with different types of gastric diseases. Notably, Cutibacterium acnes was present at significantly greater abundance level in patients with non-ulcerative dyspepsia than those with peptic-ulcer diagnosis. This suggests that C. acnes may also play a role in gastritis besides H. pylori, which merits further investigation.<\/jats:p>","DOI":"10.3390\/microorganisms7060174","type":"journal-article","created":{"date-parts":[[2019,6,14]],"date-time":"2019-06-14T11:19:58Z","timestamp":1560511198000},"page":"174","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["The Influence of Modernization and Disease on the Gastric Microbiome of Orang Asli, Myanmars and Modern Malaysians"],"prefix":"10.3390","volume":"7","author":[{"given":"Eng Guan","family":"Chua","sequence":"first","affiliation":[{"name":"The Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, WA 6009, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3554-5313","authenticated-orcid":false,"given":"Mun Fai","family":"Loke","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, University of Malaya, Kuala Lumpur 50603, Malaysia"},{"name":"School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Singapore 599489, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Selva Perumal","family":"Gunaletchumy","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, University of Malaya, Kuala Lumpur 50603, Malaysia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Han Ming","family":"Gan","sequence":"additional","affiliation":[{"name":"School of Science, Monash University Malaysia, Selangor 47500, Malaysia"},{"name":"Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Melbourne, VIC 3216, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kavitha","family":"Thevakumar","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, University of Malaya, Kuala Lumpur 50603, Malaysia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9705-4010","authenticated-orcid":false,"given":"Chin Yen","family":"Tay","sequence":"additional","affiliation":[{"name":"The Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, WA 6009, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sylvia","family":"Young","sequence":"additional","affiliation":[{"name":"Harry Perkins Institute of Medical Research, The Centre for Medical Research at the University of Western Australia, Perth, WA 6009, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Than Than","family":"Aye","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology, Thingangyun Sanpya General Hospital, Yangon 11071, Myanmar"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Win Win","family":"Maw","sequence":"additional","affiliation":[{"name":"Microbiology Department, University of Medicine 2, Yangon 11031, Myanmar"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mya Mya","family":"Aye","sequence":"additional","affiliation":[{"name":"University of Medical Technology, Mandalay 05071, Myanmar"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alex Hwong-Ruey","family":"Leow","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3265-6445","authenticated-orcid":false,"given":"Ahmad Najib","family":"Azmi","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sri Ganesh","family":"Kalimuthu","sequence":"additional","affiliation":[{"name":"CliniPath Malaysia Sdn Bhd, Kuala Lumpur 55100, Malaysia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haji Mohd Akmal Bin Dato","family":"Dahlan","sequence":"additional","affiliation":[{"name":"Hospital Orang Asli Gombak, Selangor 53100, Malaysia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Khean Lee","family":"Goh","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jamuna","family":"Vadivelu","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, University of Malaya, Kuala Lumpur 50603, Malaysia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2019,6,14]]},"reference":[{"key":"ref_1","first-page":"8","article-title":"\u2018Ome Sweet \u2018Omics-A Genealogical Treasury of Words","volume":"15","author":"Lederberg","year":"2001","journal-title":"Scientist"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"4250","DOI":"10.1073\/pnas.0306398101","article-title":"Bacterial biota in the human distal esophagus","volume":"101","author":"Pei","year":"2004","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"5721","DOI":"10.1128\/JCM.43.11.5721-5732.2005","article-title":"Defining the normal bacterial flora of the oral cavity","volume":"43","author":"Aas","year":"2005","journal-title":"J. Clin. Microbiol."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Verhelst, R., Verstraelen, H., Claeys, G., Verschraegen, G., Delanghe, J., Van Simaey, L., De Ganck, C., Temmerman, M., and Vaneechoutte, M. (2004). Cloning of 16S rRNA genes amplified from normal and disturbed vaginal microflora suggests a strong association between Atopobium vaginae, Gardnerella vaginalis and bacterial vaginosis. BMC Microbiol., 4.","DOI":"10.1186\/1471-2180-4-16"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1177\/2050640614566846","article-title":"The human gastric microbiota: Is it time to rethink the pathogenesis of stomach diseases?","volume":"3","author":"Nardone","year":"2015","journal-title":"United Eur. Gastroenterol. J."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1311","DOI":"10.1016\/S0140-6736(84)91816-6","article-title":"Unidentified curved bacilli in the stomach of patients with gastritis and peptic ulceration","volume":"1","author":"Marshall","year":"1984","journal-title":"Lancet"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"18594","DOI":"10.1038\/srep18594","article-title":"Different gastric microbiota compositions in two human populations with high and low gastric cancer risk in Colombia","volume":"6","author":"Yang","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1038\/nature11053","article-title":"Human gut microbiome viewed across age and geography","volume":"486","author":"Yatsunenko","year":"2012","journal-title":"Nature"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"14691","DOI":"10.1073\/pnas.1005963107","article-title":"Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa","volume":"107","author":"Cavalieri","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"3654","DOI":"10.1038\/ncomms4654","article-title":"Gut microbiome of the Hadza hunter-gatherers","volume":"5","author":"Schnorr","year":"2014","journal-title":"Nat. Commun."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"20131037","DOI":"10.1098\/rsbl.2013.1037","article-title":"Geographical variation of human gut microbial composition","volume":"10","author":"Suzuki","year":"2014","journal-title":"Biol. Lett."},{"key":"ref_12","unstructured":"(2019, January 31). The World Factbook, Available online: https:\/\/www.cia.gov\/library\/publications\/the-world-factbook\/."},{"key":"ref_13","unstructured":"UNICEF (2017). Drinking Water, Sanitation and Hygiene Database, The WHO\/UNICEF."},{"key":"ref_14","unstructured":"Nicholas, C., International Work Group for Indigenous Affairs (IWGIA), and Center for Orang Asli Concerns (COAC) (2000). The Orang Asli and the Contest for Resources: Indigenous Politics, Development, and Identity in Peninsular Malaysia, Center for Orang Asli Concerns."},{"key":"ref_15","first-page":"20","article-title":"Preliminary Exploration of a Semai Musician\u2019s Transmission of Indigenous Musical Traditions in Peninsular Malaysia","volume":"23","author":"Ching","year":"2015","journal-title":"Pertanika J. Soc. Sci. Humanit."},{"key":"ref_16","first-page":"75","article-title":"Orang Asli in Peninsular Malaysia: Population, Spatial Distribution and Socio-Economic Condition","volume":"6","author":"Masron","year":"2013","journal-title":"J. Ritsumeikan Soc. Sci. Hum."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.1093\/nar\/gks808","article-title":"Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies","volume":"41","author":"Klindworth","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"3846","DOI":"10.1128\/AEM.02772-10","article-title":"Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads","volume":"77","author":"Bartram","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_19","unstructured":"(2019, January 31). 16S Metagenomic Sequencing Library Preparation. Available online: https:\/\/support.illumina.com\/documents\/documentation\/chemistry_documentation\/16s\/16s-metagenomic-library-prep-guide-15044223-b.pdf."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Parikh, H.I., Koparde, V.N., Bradley, S.P., Buck, G.A., and Sheth, N.U. (2016). MeFiT: Merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing. BMC Bioinform., 17.","DOI":"10.1186\/s12859-016-1358-1"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"9743","DOI":"10.1038\/srep09743","article-title":"MICCA: A complete and accurate software for taxonomic profiling of metagenomic data","volume":"5","author":"Albanese","year":"2015","journal-title":"Sci Rep."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Gao, X., Lin, H., Revanna, K., and Dong, Q. (2017). A Bayesian taxonomic classification method for 16S rRNA gene sequences with improved species-level accuracy. BMC Bioinform., 18.","DOI":"10.1186\/s12859-017-1670-4"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data","volume":"7","author":"Caporaso","year":"2010","journal-title":"Nat. Methods"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"29123","DOI":"10.1038\/srep29123","article-title":"PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets","volume":"6","author":"Dabdoub","year":"2016","journal-title":"Sci Rep."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Iwai, S., Weinmaier, T., Schmidt, B.L., Albertson, D.G., Poloso, N.J., Dabbagh, K., and DeSantis, T.Z. (2016). Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0166104"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/j.chom.2008.02.015","article-title":"Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome","volume":"3","author":"Turnbaugh","year":"2008","journal-title":"Cell Host Microbe"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1022","DOI":"10.1038\/4441022a","article-title":"Microbial ecology: Human gut microbes associated with obesity","volume":"444","author":"Ley","year":"2006","journal-title":"Nature"},{"key":"ref_29","first-page":"1","article-title":"Energy and Nutrient Intakes: Findings from the Malaysian Adult Nutrition Survey (MANS)","volume":"14","author":"Mirnalini","year":"2008","journal-title":"Malays. J. Nutr."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"R1053","DOI":"10.1152\/ajpregu.00003.2012","article-title":"Arginine plus proline supplementation elicits metabolic adaptation that favors wound healing in diabetic rats","volume":"303","author":"Belabed","year":"2012","journal-title":"Am. J. Physiol. Regul. Integr. Comp. Physiol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1007\/s00726-011-1200-z","article-title":"Effects of beta-alanine supplementation on exercise performance: A meta-analysis","volume":"43","author":"Hobson","year":"2012","journal-title":"Amino Acids"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.nmni.2016.01.001","article-title":"Noncontiguous finished genome sequence and description of Nocardioides massiliensis sp. nov. GD13(T)","volume":"10","author":"Dubourg","year":"2016","journal-title":"New Microbes New Infect."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1328","DOI":"10.1126\/science.284.5418.1328","article-title":"Helicobacter pylori virulence and genetic geography","volume":"284","author":"Covacci","year":"1999","journal-title":"Science"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"4422","DOI":"10.1099\/ijsem.0.001367","article-title":"The natural history of cutaneous propionibacteria, and reclassification of selected species within the genus Propionibacterium to the proposed novel genera Acidipropionibacterium gen. nov., Cutibacterium gen. nov. and Pseudopropionibacterium gen. nov","volume":"66","author":"Scholz","year":"2016","journal-title":"Int J. Syst. Evol. Microbiol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1002\/path.4782","article-title":"Propionibacterium acnes overabundance and natural killer group 2 member D system activation in corpus-dominant lymphocytic gastritis","volume":"240","author":"Wurm","year":"2016","journal-title":"J. Pathol."},{"key":"ref_36","first-page":"222","article-title":"The Diagnosis and Treatment of Functional Dyspepsia","volume":"115","author":"Madisch","year":"2018","journal-title":"Dtsch Arztebl. Int."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/7\/6\/174\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T12:58:38Z","timestamp":1760187518000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/7\/6\/174"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,6,14]]},"references-count":36,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2019,6]]}},"alternative-id":["microorganisms7060174"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms7060174","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,6,14]]}}}