人类肠道的亚种系统发育揭示了跨细菌王国的共同进化约束。

Cell systems Pub Date : 2025-02-19 Epub Date: 2025-01-17 DOI:10.1016/j.cels.2024.12.008
Benjamin A Doran, Robert Y Chen, Hannah Giba, Vivek Behera, Bidisha Barat, Anitha Sundararajan, Huaiying Lin, Ashley Sidebottom, Eric G Pamer, Arjun S Raman
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引用次数: 0

摘要

人类肠道微生物组包含许多相同物种的细菌菌株(“菌株水平变异”),这些菌株塑造了微生物组的功能。微生物群落正在被研究的巨大规模和分子分辨率促使人们解决如何描述菌株水平变异的问题。我们介绍了“谱树”——一种根据超过7000种不同细菌的共同进化约束模式构建的推断的亲缘关系树。利用光谱树描述了我们分离的600多种不同的肠道共生菌株,进行了全基因组测序和代谢谱分析,揭示了(1)菌株水平变异中广泛存在的系统发育结构,(2)亚种系统发育的起源是人类噬菌体感染的共同历史,以及(3)人类间菌株变异在预测菌株水平代谢质量方面的关键作用。总的来说,我们的工作证明了共生肠道细菌在物种水平以下的结构系统发育的存在和代谢重要性,这促使人们根据其进化背景重新定义个体菌株。本文的透明同行评议过程记录包含在补充信息中。
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Subspecies phylogeny in the human gut revealed by co-evolutionary constraints across the bacterial kingdom.

The human gut microbiome contains many bacterial strains of the same species ("strain-level variants") that shape microbiome function. The tremendous scale and molecular resolution at which microbial communities are being interrogated motivates addressing how to describe strain-level variants. We introduce the "Spectral Tree"-an inferred tree of relatedness built from patterns of co-evolutionary constraint between greater than 7,000 diverse bacteria. Using the Spectral Tree to describe over 600 diverse gut commensal strains that we isolated, whole-genome sequenced, and metabolically profiled revealed (1) widespread phylogenetic structure among strain-level variants, (2) the origins of subspecies phylogeny as a shared history of phage infections across humans, and (3) the key role of inter-human strain variation in predicting strain-level metabolic qualities. Overall, our work demonstrates the existence and metabolic importance of structured phylogeny below the level of species for commensal gut bacteria, motivating a redefinition of individual strains according to their evolutionary context. A record of this paper's transparent peer review process is included in the supplemental information.

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