Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes
Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes
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DOI：
10.1016/j.cell.2023.05.046
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发表时间：
2023-07-06
期刊：
影响因子：
64.5
通讯作者：
Sonnenburg, Justin L.
中科院分区：
文献类型：
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作者：
Carter, Matthew M.;Olm, Matthew R.;Sonnenburg, Justin L.
肠道微生物组调节免疫和代谢健康。人类微生物组数据偏向于工业化人群，限制了我们对非工业化微生物组的理解。在这里，我们对来自坦桑尼亚哈扎狩猎采集者以及尼泊尔和加利福尼亚的比较人群的 351 个粪便样本进行了超深度宏基因组测序。我们恢复了 91,662 个细菌、古细菌、噬菌体和真核生物的基因组，其中 44% 不存在于现有的统一数据集中。我们发现了 124 个在工业化人群中消失的肠道驻留物种，并强调了哈扎肠道微生物组与原位复制率、选择特征和菌株共享相关的独特方面。人们发现工业化肠道微生物富含与氧化应激相关的基因，这可能是微生物组适应炎症过程的结果。这种对哈扎人肠道微生物组的无与伦比的看法提供了宝贵的资源，扩大了我们对能够在人类肠道定殖的微生物的理解，并澄清了工业化生活方式引起的广泛扰动。
The gut microbiome modulates immune and metabolic health. Human microbiome data are biased toward industrialized populations, limiting our understanding of non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing on 351 fecal samples from the Hadza hunter-gatherers of Tanzania and comparative populations in Nepal and California. We recovered 91,662 genomes of bacteria, archaea, bacteriophages, and eukaryotes, 44% of which are absent from existing unified datasets. We identified 124 gut-resident species vanishing in industrialized populations and highlighted distinct aspects of the Hadza gut microbiome related to in situ replication rates, signatures of selection, and strain sharing. Industrialized gut microbes were found to be enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource, expands our understanding of microbes capable of colonizing the human gut, and clarifies the extensive perturbation induced by the industrialized lifestyle.