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Wilde J, Boyes R, Robinson AV, Daisley BA, Botschner AJ, Brettingham DJL, Macpherson CV, Mallory E, Allen-Vercoe E. Assessing phage-host population dynamics by reintroducing virulent viruses to synthetic microbiomes. Cell Host Microbe 2024:S1931-3128(24)00114-8. [PMID: 38653241 DOI: 10.1016/j.chom.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/31/2024] [Accepted: 04/01/2024] [Indexed: 04/25/2024]
Abstract
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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Affiliation(s)
- Jacob Wilde
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada
| | - Randy Boyes
- Queen's University, Department of Community Health and Epidemiology, Kingston, ON K7L 3N6, Canada
| | - Avery V Robinson
- University of Oxford, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Oxford OX3 7FY, UK
| | - Brendan A Daisley
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada
| | - Alexander J Botschner
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada
| | - Dylan J L Brettingham
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada
| | - Christine V Macpherson
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada
| | - Elizabeth Mallory
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada
| | - Emma Allen-Vercoe
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, ON N1G 2W1, Canada.
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Elder R, Vancuren SJ, Botschner AJ, Josephy PD, Allen-Vercoe E. Metabolism of azo food dyes by bacterial members of the human gut microbiome. Anaerobe 2023; 83:102783. [PMID: 37769703 DOI: 10.1016/j.anaerobe.2023.102783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/08/2023] [Accepted: 09/17/2023] [Indexed: 10/03/2023]
Abstract
OBJECTIVES We set out to survey the capacities of bacterial isolates from the human gut microbiome to reduce common azo food dyes in vitro. METHODS A total of 206 strains representative of 124 bacterial species and 6 phyla were screened in vitro using a simple azo dye decolorization assay. Strains which showed azoreductive activity were characterized by studies of azoreduction kinetics and bacterial growth. RESULTS Several groups of gut bacteria, including ones not previously associated with azoreduction, reduced one or more of the four azo food dyes commonly used in Canada: Allura Red, Amaranth, Sunset Yellow, and Tartrazine. Strains within some species differed in their azoreductive capabilities. Some strains displayed evidence of effects on growth related to the presence of azo dyes and/or the products of their azoreduction. CONCLUSION The continued widespread use of food azo dyes requires re-evaluation in light of the potential for disturbance of the gut microbial ecosystem resulting from azoreduction and the possibility of consequences for human health.
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Affiliation(s)
- Riley Elder
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, N1G 2W1, Guelph, Ontario, Canada
| | - Sarah J Vancuren
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, N1G 2W1, Guelph, Ontario, Canada
| | - Alexander J Botschner
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, N1G 2W1, Guelph, Ontario, Canada
| | - P David Josephy
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, N1G 2W1, Guelph, Ontario, Canada
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, N1G 2W1, Guelph, Ontario, Canada.
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Goetz JA, Kuehfuss NM, Botschner AJ, Zhu S, Thompson LK, Cox G. Exploring functional interplay amongst Escherichia coli efflux pumps. Microbiology (Reading) 2022; 168. [PMID: 36318669 DOI: 10.1099/mic.0.001261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Bacterial efflux pumps exhibit functional interplay that can translate to additive or multiplicative effects on resistance to antimicrobial compounds. In diderm bacteria, two different efflux pump structural types - single-component inner membrane efflux pumps and cell envelope-spanning multicomponent systems - cooperatively export antimicrobials with cytoplasmic targets from the cell. Harnessing our recently developed efflux platform, which is built upon an extensively efflux-deficient strain of Escherichia coli, here we explore interplay amongst a panel of diverse E. coli efflux pumps. Specifically, we assessed the effect of simultaneously expressing two efflux pump-encoding genes on drug resistance, including single-component inner membrane efflux pumps (MdfA, MdtK and EmrE), tripartite complexes (AcrAB, AcrAD, MdtEF and AcrEF), and the acquired TetA(C) tetracycline resistance pump. Overall, the expression of two efflux pump-encoding genes from the same structural type did not enhance resistance levels regardless of the antimicrobial compound or efflux pump under investigation. In contrast, a combination of the tripartite efflux systems with single-component pumps sharing common substrates provided multiplicative increases to antimicrobial resistance levels. In some instances, resistance was increased beyond the product of resistance provided by the two pumps individually. In summary, the developed efflux platform enables the isolation of efflux pump function, facilitating the identification of interactions between efflux pumps.
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Affiliation(s)
- James A Goetz
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Noah M Kuehfuss
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Alexander J Botschner
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Shawna Zhu
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Laura K Thompson
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Georgina Cox
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
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