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

Autor:	Wilde J; University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada., Boyes R; Queen's University, Department of Community Health and Epidemiology, Kingston, ON K7L 3N6, Canada., Robinson AV; University of Oxford, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Oxford OX3 7FY, UK., Daisley BA; University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada., Botschner AJ; University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada., Brettingham DJL; University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada., Macpherson CV; University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada., Mallory E; University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada., Allen-Vercoe E; University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada. Electronic address: eav@uoguelph.ca.
Jazyk:	angličtina
Zdroj:	Cell host & microbe [Cell Host Microbe] 2024 May 08; Vol. 32 (5), pp. 768-778.e9. Date of Electronic Publication: 2024 Apr 22.
DOI:	10.1016/j.chom.2024.04.001
Abstrakt:	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. Competing Interests: Declaration of interests E.A.-V. is the co-founder and CSO of NuBiyota LLC & Company that is working to commercialize human gut-derived microbial communities for medical applications. (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)
Databáze:	MEDLINE
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