人类微生物群中普遍存在的噬菌体家族的鉴定和时空追踪

A. Tadmor, Gita Mahmoudabadi, Helen Foley, R. Phillips
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摘要

病毒是人类微生物组的主要组成部分,但其多样性、生活方式、时空动态和功能影响尚未得到很好的了解。由于噬菌体具有调节共生细菌丰度和表型的潜在能力,阐明人类相关噬菌体的生态学可能对人类健康产生重大影响。研究人员分析了来自18个栖息地103名受试者的690个人类微生物组计划宏基因组,发现尽管在人类病毒组中观察到巨大的人际多样性,但人类拥有不同的噬菌体家族,其特征是它们共享的保守标志基因,即大端酶亚基(TerL)基因。对这些噬菌体家族的系统发育分析表明,口腔和肠道中不同的栖息地具有独特的噬菌体群落结构。在大约7个月的时间尺度上,这些噬菌体家族中的大多数在口腔和肠道中持续存在,然而,在某些口腔栖息地中的存在似乎是短暂的,可能是由于宿主在口腔内的迁移。有趣的是,某些噬菌体家族被发现与致病性、携带和疾病相关的分离物高度相关,并且可能作为疾病的新生物标志物。我们的发现揭示了人类核心病毒组的新亮点,并提供了一种独立于宏基因组的方法,利用广泛共享的保守噬菌体标记来探测核心病毒组。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Identification and spatio-temporal tracking of ubiquitous phage families in the human microbiome
Viruses are a major component of the human microbiome, yet their diversity, lifestyles, spatiotemporal dynamics, and functional impact are not well understood. Elucidating the ecology of human associated phages may have a major impact on human health due to the potential ability of phages to modulate the abundance and phenotype of commensal bacteria. Analyzing 690 Human Microbiome Project metagenomes from 103 subjects sampled across up to 18 habitats, we found that despite the great interpersonal diversity observed among human viromes, humans harbor distinct phage families characterized by their shared conserved hallmark genes known as large terminase subunit (TerL) genes. Phylogenetic analysis of these phage families revealed that different habitats in the oral cavity and gut have unique phage community structures. Over a ~7-month timescale most of these phage families persisted in the oral cavity and gut, however, presence in certain oral habitats appeared to be transitory, possibly due to host migration within the oral cavity. Interestingly, certain phage families were found to be highly correlated with pathogenic, carriage and disease-related isolates, and may potentially serve as novel biomarkers for disease. Our findings shed new light on the core human virome and offer a metagenomic-independent way to probe the core virome using widely shared conserved phage markers.
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