Eubacterium rectale is one of the most prevalent human gut bacteria, but its diversity and population genetics are not well understood because large-scale whole-genome investigations of this microbe have not been carried out. Here, we leverage metagenomic assembly followed by a reference-based binning strategy to screen over 6500 gut metagenomes spanning geography and lifestyle and reconstruct over 1300 E. rectale high-quality genomes from metagenomes. We extend previous results of biogeographic stratification, identifying a new subspecies predominantly found in African individuals and showing that closely related non-human primates do not harbor E. rectale. Comparison of pairwise genetic and geographic distances between subspecies suggests that isolation by distance and co-dispersal with human populations might have contributed to shaping the contemporary population structure of E. rectale. We confirm that a relatively recently diverged E. rectale subspecies specific to Europe consistently lacks motility operons and that it is immotile in vitro, probably due to ancestral genetic loss. The same subspecies exhibits expansion of its carbohydrate metabolism gene repertoire including the acquisition of a genomic island strongly enriched in glycosyltransferase genes involved in exopolysaccharide synthesis. Our study provides new insights into the population structure and ecology of E. rectale and shows that shotgun metagenomes can enable population genomics studies of microbiota members at a resolution and scale previously attainable only by extensive isolate sequencing.

中文翻译：

---

对来自宏基因组的 1321 个直肠真杆菌基因组的分析揭示了复杂的系统地理种群结构和亚种功能适应

直肠真杆菌是最普遍的人类肠道细菌之一，但由于尚未对这种微生物进行大规模的全基因组研究，它的多样性和群体遗传学尚不清楚。在这里，我们利用宏基因组组装和基于参考的分箱策略筛选超过 6500 个跨越地理和生活方式的肠道宏基因组，并从宏基因组重建超过 1300 个 E.rectale 高质量基因组。我们扩展了以前的生物地理分层结果，确定了一个主要在非洲个体中发现的新亚种，并表明密切相关的非人类灵长类动物不携带 E. rectale。亚种之间成对的遗传和地理距离的比较表明，距离隔离和与人群的共同分散可能有助于塑造 E. rectale 的当代种群结构。我们证实，欧洲特有的相对最近分化的 E.rectale 亚种始终缺乏运动操纵子，并且它在体外是不动的，可能是由于祖先遗传损失。相同的亚种表现出其碳水化合物代谢基因库的扩展，包括获得一个基因组岛，该基因组岛富含参与胞外多糖合成的糖基转移酶基因。我们的研究为大肠杆菌的种群结构和生态学提供了新的见解。