Department of Microbiology and Immunology, Montana, State University, Bozeman, MT, USA.
ISME J. 2019 Sep;13(9):2306-2318. doi: 10.1038/s41396-019-0435-7. Epub 2019 May 14.
Longitudinal human gut microbiome datasets generated using community-level, sequence-based approaches often report a sub-set of long-lived "resident" taxa that rarely, if ever, are lost. This result contrasts with population-level turnover of resident clones on the order of months to years. We hypothesized that the disconnect between these results is due to a relative lack of simultaneous discrimination of the human gut microbiome at both the community and population-levels. Here, we present results of a small, longitudinal cohort study (n = 8 participants) of healthy human adults that identifies static and dynamic members of the gut microbiome at the clone level based on cultivation/genetic discrimination and at the operational taxonomic unit/amplified sequence variant levels based on 16S rRNA sequencing. We provide evidence that there is little "stability" within resident clonal populations of the common gut microbiome bacterial family, Enterobacteriaceae. Given that clones can vary substantially in genome content and that evolutionary processes operate on the population level, these results question the biological relevance of apparent stability at higher taxonomic levels.
采用基于群落水平的序列分析方法生成的人类肠道宏基因组数据集通常报告了一小部分寿命较长的“常驻”分类群，这些分类群很少（如果有的话）会消失。这一结果与居民克隆在数月至数年的种群水平上的更替形成对比。我们假设，这些结果之间的脱节是由于相对缺乏对人类肠道微生物组在群落和种群水平上的同时区分。在这里，我们介绍了一项小型纵向队列研究（n=8 名参与者）的结果，该研究基于培养/遗传区分，在克隆水平上，以及基于 16S rRNA 测序，在操作分类单元/扩增序列变异水平上，确定了健康人类成年人肠道微生物组的静态和动态成员。我们提供的证据表明，常见肠道微生物科肠杆菌科的常驻克隆种群内几乎没有“稳定性”。鉴于克隆在基因组内容上可能有很大差异，并且进化过程发生在种群水平上，这些结果质疑了在更高分类水平上出现的明显稳定性的生物学相关性。
