Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, 101 David L. Boren Blvd, Norman, OK, 73019, USA.
Department of Anthropology, University of Oklahoma, Norman, OK, 73019, USA.
Sci Rep. 2021 Jan 18;11(1):1724. doi: 10.1038/s41598-021-81257-w.
High taxonomic diversity in non-industrial human gut microbiomes is often interpreted as beneficial; however, it is unclear if taxonomic diversity engenders ecological resilience (i.e. community stability and metabolic continuity). We estimate resilience through genus and species-level richness, phylogenetic diversity, and evenness in short-chain fatty acid (SCFA) production among a global gut metagenome panel of 12 populations (n = 451) representing industrial and non-industrial lifestyles, including novel metagenomic data from Burkina Faso (n = 90). We observe significantly higher genus-level resilience in non-industrial populations, while SCFA production in industrial populations is driven by a few phylogenetically closely related species (belonging to Bacteroides and Clostridium), meaning industrial microbiomes have low resilience potential. Additionally, database bias obfuscates resilience estimates, as we were 2-5 times more likely to identify SCFA-encoding species in industrial microbiomes compared to non-industrial. Overall, we find high phylogenetic diversity, richness, and evenness of bacteria encoding SCFAs in non-industrial gut microbiomes, signaling high potential for resilience in SCFA production, despite database biases that limit metagenomic analysis of non-industrial populations.
非工业人类肠道微生物组中的高分类多样性通常被解释为有益的；然而，分类多样性是否会产生生态弹性（即群落稳定性和代谢连续性）尚不清楚。我们通过全球肠道宏基因组panel 中的 12 个人群（n=451）的短链脂肪酸（SCFA）产生的属和种水平丰富度、系统发育多样性和均匀度来估计弹性，该 panel 代表了工业和非工业生活方式，包括来自布基纳法索的新宏基因组数据（n=90）。我们观察到非工业人群的属水平弹性显著更高，而工业人群的 SCFA 产生则由少数系统发育上密切相关的物种（属于拟杆菌属和梭菌属）驱动，这意味着工业微生物组的弹性潜力较低。此外，数据库偏差使弹性估计变得复杂，因为与非工业微生物组相比，我们在工业微生物组中识别出编码 SCFA 的物种的可能性要高出 2-5 倍。总的来说，我们发现非工业肠道微生物组中编码 SCFA 的细菌具有高系统发育多样性、丰富度和均匀度，这表明尽管存在限制非工业人群宏基因组分析的数据库偏差，但 SCFA 产生的弹性潜力很大。
