The genetic diversity of the gut microbiota has a central role in host health. Here, we created pangenomes for 728 human gut prokaryotic species, quadrupling the genes of strain-specific genomes. Each of these species has a core set of a thousand genes, differing even between closely related species, and an accessory set of genes unique to the different strains. Functional analysis shows high strain variability associates with sporulation, whereas low variability is linked with antibiotic resistance. We further map the antibiotic resistome across the human gut population and find 237 cases of extreme resistance even to last-resort antibiotics, with a predominance among Enterobacteriaceae. Lastly, the presence of specific genes in the microbiota relates to host age and sex. Our study underscores the genetic complexity of the human gut microbiota, emphasizing its significant implications for host health. The pangenomes and antibiotic resistance map constitute a valuable resource for further research.

中文翻译：

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人类肠道微生物群的泛基因组揭示了遗传多样性与应激反应之间的联系


肠道微生物群的遗传多样性在宿主健康中起着核心作用。在这里，我们为 728 种人类肠道原核物种创建了泛基因组，将菌株特异性基因组的基因增加了四倍。这些物种中的每一个都有一组由一千个基因组成的核心集，甚至在密切相关的物种之间也有所不同，以及一组不同菌株独有的附属基因。功能分析表明，高菌株变异性与孢子形成有关，而低变异性与抗生素耐药性有关。我们进一步绘制了人类肠道人群的抗生素耐药组图谱，发现 237 例甚至对最后的抗生素也存在极端耐药性，其中肠杆菌科以肠杆菌科为主。最后，微生物群中特定基因的存在与宿主年龄和性别有关。我们的研究强调了人类肠道微生物群的遗传复杂性，强调了其对宿主健康的重大影响。泛基因组和抗生素耐药性图谱构成了进一步研究的宝贵资源。