Chen Hongju Daisy, Ma Zhanshan Sam
Department of Mathematics and Statistics, Honghe University, Yunnan, China.
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.
Evol Bioinform Online. 2022 Nov 23;18:11769343221128540. doi: 10.1177/11769343221128540. eCollection 2022.
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's multi-site neutral and Tang and Zhou's niche-neutral hybrid models to characterize the DT niches discovered by Segata et al. Here, we complement the previous study by applying Sloan's near-neural model and Ning et al's 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 () 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.
据推测，从口腔到肠道的人类消化道（DT）可分化为不同的生态位。例如，塞加塔等人发现，沿消化道不同栖息地的微生物群可分为4种类型（生态位），包括：（i）粪便；（ii）龈下菌斑（SubP）和龈上菌斑（SupP）；（iii）舌背（TD）、咽喉（TH）、腭扁桃体（PT）和唾液（Sal）；以及（iv）硬腭（HP）、颊黏膜（BM）和角化牙龈（KG）。这些生态位不仅在组成上不同，在代谢潜力上也不同。在之前的一项研究中，我们应用哈里斯等人的多位点中性模型以及唐和周的生态位中性混合模型来描述塞加塔等人发现的消化道生态位。在此，我们通过应用斯隆的近神经模型和宁等人的随机性分析框架来补充之前的研究，以量化消化道微生物群分布的生态位中性连续体，从而揭示形成该连续体的可能生态/进化机制。总体而言，除粪便部位外，中性OTU的比例（46%）略高于正选择的比例（38%），但显著高于负选择的比例（15%）。肠道（粪便）的中性度比其他消化道部位低3至12倍。该分析还交叉验证了我们之前的假设，即KG（）在消化道微生物群中具有独特的组装动态，应被视为第五个生态位。我们的研究结果为关于边缘牙周健康是否需要至少2毫米宽的KG这一长期争论提供了新的见解。
