Mah Jonathan C, Lohmueller Kirk E, Garud Nandita
Bioinformatics Interdepartmental Program, University of California, Los Angeles.
Department of Ecology and Evolutionary Biology, University of California, Los Angeles.
bioRxiv. 2023 Nov 13:2023.11.09.566454. doi: 10.1101/2023.11.09.566454.
Despite the importance of gut commensal microbiota to human health, there is little knowledge about their evolutionary histories, including their population demographic histories and their distributions of fitness effects (DFE) of new mutations. Here, we infer the demographic histories and DFEs of 27 of the most highly prevalent and abundant commensal gut microbial species in North Americans over timescales exceeding human generations using a collection of lineages inferred from a panel of healthy hosts. We find overall reductions in genetic variation among commensal gut microbes sampled from a Western population relative to an African rural population. Additionally, some species in North American microbiomes display contractions in population size and others expansions, potentially occurring at several key historical moments in human history. DFEs across species vary from highly to mildly deleterious, with accessory genes experiencing more drift compared to core genes. Within genera, DFEs tend to be more congruent, reflective of underlying phylogenetic relationships. Taken together, these findings suggest that human commensal gut microbes have distinct evolutionary histories, possibly reflecting the unique roles of individual members of the microbiome.
尽管肠道共生微生物群对人类健康至关重要,但人们对它们的进化历史知之甚少,包括它们的种群人口统计学历史以及新突变的适应性效应分布(DFE)。在这里,我们利用从一组健康宿主推断出的谱系集合,在超过人类世代的时间尺度上,推断了北美27种最普遍且丰富的共生肠道微生物物种的人口统计学历史和DFE。我们发现,与非洲农村人口相比,从西方人群中采样的共生肠道微生物的遗传变异总体减少。此外,北美微生物群落中的一些物种显示出种群规模的收缩,而其他物种则出现扩张,这可能发生在人类历史上的几个关键历史时刻。不同物种的DFE从高度有害到轻度有害不等,与核心基因相比,辅助基因经历了更多的漂变。在属内,DFE往往更趋一致,反映了潜在的系统发育关系。综合来看,这些发现表明人类共生肠道微生物具有独特的进化历史,可能反映了微生物群落中个体成员的独特作用。