{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T02:15:14Z","timestamp":1777601714522,"version":"3.51.4"},"reference-count":34,"publisher":"SAGE Publications","license":[{"start":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T00:00:00Z","timestamp":1667260800000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"},{"start":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T00:00:00Z","timestamp":1667260800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"funder":[{"DOI":"10.13039\/501100001809","name":"national natural science foundation of china","doi-asserted-by":"publisher","award":["31970116"],"award-info":[{"award-number":["31970116"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100011239","name":"state key laboratory of genetic resources and evolution","doi-asserted-by":"publisher","award":["GREKF19-07"],"award-info":[{"award-number":["GREKF19-07"]}],"id":[{"id":"10.13039\/501100011239","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["Evol Bioinform Online"],"published-print":{"date-parts":[[2022,11]]},"abstract":"<jats:p>\n                    It is postulated that the human digestive tract (DT) from mouth to intestine is differentiated into diverse niches. For example, Segata et al. discovered that the microbiomes of diverse habitats along the DT could be distinguished as 4 types (niches) including (i) stool; (ii) sub-gingival plaques (SubP) and supra-gingival plaques (SupP); (iii) tongue dorsum (TD), throat (TH), palatine tonsils (PT), and saliva (Sal); and (iv) hard palate (HP) and buccal mucosa (BM), and keratinized gingiva (KG). These niches are different not only in composition, but also in metabolic potentials. In a previous study, we applied Harris et al\u2019s multi-site neutral and Tang and Zhou\u2019s niche-neutral hybrid models to characterize the DT niches discovered by Segata et al. Here, we complement the previous study by applying Sloan\u2019s near-neural model and Ning et al\u2019s stochasticity analysis framework to quantify the niche-neutral continuum of the DT microbiome distribution to shed light on the possible ecological\/evolutionary mechanism that shapes the continuum. Overall but excluding the stool site, the proportion of neutral OTUs (46%) is slightly higher than that of the positive selection (38%), but significantly higher than negative selection (15%). The gut (stool) exhibited 3 to 12 times lower neutrality than other DT sites. The analysis also cross-verified our previous hypothesis that the KG (\n                    <jats:italic toggle=\"yes\">keratinized gingiva<\/jats:italic>\n                    ) is of distinct assembly dynamics in the DT microbiome, should be treated as a fifth niche. Our findings offer new insight on the long-standing debate concerning whether a minimum of 2-mm of KG width is necessary for marginal periodontal health.\n                  <\/jats:p>","DOI":"10.1177\/11769343221128540","type":"journal-article","created":{"date-parts":[[2022,11,23]],"date-time":"2022-11-23T05:32:48Z","timestamp":1669181568000},"update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":0,"title":["Further Quantifying the Niche-Neutral Continuum of Human Digestive Tract Microbiomes with Near Neutral Model and Stochasticity Analysis"],"prefix":"10.1177","volume":"18","author":[{"given":"Hongju (Daisy)","family":"Chen","sequence":"first","affiliation":[{"name":"Department of Mathematics and Statistics, Honghe University, Yunnan, China"},{"name":"Computational Biology and Medical Ecology Lab, State Key Lab of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, Yunnan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhanshan (Sam)","family":"Ma","sequence":"additional","affiliation":[{"name":"Computational Biology and Medical Ecology Lab, State Key Lab of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, Yunnan, China"},{"name":"Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"179","published-online":{"date-parts":[[2022,11,23]]},"reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature11209"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2012-13-6-r42"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1111\/eva.13116"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.633429"},{"key":"e_1_3_3_6_2","volume-title":"The Unified Neutral Theory of Biodiversity and Biogeography","author":"Hubbell SP.","year":"2001","unstructured":"Hubbell SP. 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Ecological drift and the distribution of species diversity. 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