Pangenomes of human gut microbiota uncover links between genetic diversity and stress response

IF 20.6 1区 医学 Q1 MICROBIOLOGY Cell host & microbe Pub Date : 2024-09-30 DOI:10.1016/j.chom.2024.08.017
Saar Shoer, Lee Reicher, Chunyu Zhao, Katherine S. Pollard, Yitzhak Pilpel, Eran Segal
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Abstract

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.

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人类肠道微生物群的庞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对宿主健康起着核心作用。在这里,我们为 728 个人类肠道原核生物物种创建了泛基因组,使菌株特异性基因组的基因数量翻了两番。每个菌种都有一个由一千个基因组成的核心基因组,即使是近缘菌种之间也存在差异,另外还有一个不同菌株特有的附属基因组。功能分析显示,菌株的高变异性与孢子繁殖有关,而低变异性则与抗生素耐药性有关。我们进一步绘制了整个人类肠道群体的抗生素耐药性组图,发现 237 个极端耐药性病例,甚至对最后一种抗生素也有耐药性,其中以肠杆菌科细菌为主。最后,微生物群中特定基因的存在与宿主的年龄和性别有关。我们的研究凸显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要影响。庞基因组和抗生素耐药性图谱是进一步研究的宝贵资源。
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来源期刊
Cell host & microbe
Cell host & microbe 生物-微生物学
CiteScore
45.10
自引率
1.70%
发文量
201
审稿时长
4-8 weeks
期刊介绍: Cell Host & Microbe is a scientific journal that was launched in March 2007. The journal aims to provide a platform for scientists to exchange ideas and concepts related to the study of microbes and their interaction with host organisms at a molecular, cellular, and immune level. It publishes novel findings on a wide range of microorganisms including bacteria, fungi, parasites, and viruses. The journal focuses on the interface between the microbe and its host, whether the host is a vertebrate, invertebrate, or plant, and whether the microbe is pathogenic, non-pathogenic, or commensal. The integrated study of microbes and their interactions with each other, their host, and the cellular environment they inhabit is a unifying theme of the journal. The published work in Cell Host & Microbe is expected to be of exceptional significance within its field and also of interest to researchers in other areas. In addition to primary research articles, the journal features expert analysis, commentary, and reviews on current topics of interest in the field.
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