Assessing phage-host population dynamics by reintroducing virulent viruses to synthetic microbiomes

Cell Host Microbe. 2024 Apr 18:S1931-3128(24)00114-8. doi: 10.1016/j.chom.2024.04.001. Online ahead of print.ABSTRACTMicrobiomes 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.PMID:38653241 | DOI:10.1016/j.chom.2024.04.001

Source: Cell Host and Microbe - April 23, 2024 Category: Microbiology Authors: Jacob Wilde Randy Boyes Avery V Robinson Brendan A Daisley Alexander J Botschner Dylan J L Brettingham Christine V Macpherson Elizabeth Mallory Emma Allen-Vercoe Source Type: research