生物
毒力
微生物群
寄主(生物学)
人口
微生物学
病毒学
遗传学
基因
人口学
社会学
作者
Jacob Wilde,Randy Boyes,Avery Robinson,Brendan A. Daisley,Alexander J. Botschner,Dylan J. L. Brettingham,Cheryl C. Macpherson,Elizabeth P. Mallory,Emma Allen‐Vercoe
标识
DOI:10.1016/j.chom.2024.04.001
摘要
Microbiomes feature complex interactions between diverse bacteria and bacteriophages. Synthetic microbiomes offer a powerful way to study these interactions; however, a major challenge is obtaining a representative bacteriophage population during the bacterial isolation process. We demonstrate that colony isolation reliably excludes virulent viruses from sample sources with low virion-to-bacteria ratios such as feces, creating "virulent virus-free" controls. When the virulent dsDNA virome is reintroduced to a 73-strain synthetic gut microbiome in a bioreactor model of the human colon, virulent viruses target susceptible strains without significantly altering community structure or metabolism. In addition, we detected signals of prophage induction that associate with virulent predation. Overall, our findings indicate that dilution-based isolation methods generate synthetic gut microbiomes that are heavily depleted, if not devoid, of virulent viruses and that such viruses, if reintroduced, have a targeted effect on community assembly, metabolism, and prophage replication.
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