Multiomic spatial analysis reveals a distinct mucosa-associated virome
ABSTRACTThe human gut virome has been increasingly explored in recent years. However, nearly all virome-sequencing efforts rely solely on fecal samples and few studies leverage multiomic approaches to investigate phage–host relationships. Here, we combine metagenomics, metaviromics, and metatranscri...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2023-12-01
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| Series: | Gut Microbes |
| Subjects: | |
| Online Access: | https://www.tandfonline.com/doi/10.1080/19490976.2023.2177488 |
| _version_ | 1797236664752406528 |
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| author | Austin Yan James Butcher Laetitia Schramm David R. Mack Alain Stintzi |
| author_facet | Austin Yan James Butcher Laetitia Schramm David R. Mack Alain Stintzi |
| author_sort | Austin Yan |
| collection | DOAJ |
| description | ABSTRACTThe human gut virome has been increasingly explored in recent years. However, nearly all virome-sequencing efforts rely solely on fecal samples and few studies leverage multiomic approaches to investigate phage–host relationships. Here, we combine metagenomics, metaviromics, and metatranscriptomics to study virome-bacteriome interactions at the colonic mucosal-luminal interface in a cohort of three individuals with inflammatory bowel disease; non-IBD controls were not included in this study. We show that the mucosal viral population is distinct from the stool virome and houses abundant crAss-like phages that are undetectable by fecal sampling. Through viral protein prediction and metatranscriptomic analysis, we explore viral gene transcription, prophage activation, and the relationship between the presence of integrase and temperate phages in IBD subjects. We also show the impact of deep sequencing on virus recovery and offer guidelines for selecting optimal sequencing depths in future metaviromic studies. Systems biology approaches such as those presented in this report will enhance our understanding of the human virome and its interactions with our microbiome and our health. |
| first_indexed | 2024-03-11T14:19:25Z |
| format | Article |
| id | doaj.art-8f21b1192f6b4d76a7cb7edeb747ed87 |
| institution | Directory Open Access Journal |
| issn | 1949-0976 1949-0984 |
| language | English |
| last_indexed | 2024-04-24T17:07:27Z |
| publishDate | 2023-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Gut Microbes |
| spelling | doaj.art-8f21b1192f6b4d76a7cb7edeb747ed872024-03-28T22:38:20ZengTaylor & Francis GroupGut Microbes1949-09761949-09842023-12-0115110.1080/19490976.2023.2177488Multiomic spatial analysis reveals a distinct mucosa-associated viromeAustin Yan0James Butcher1Laetitia Schramm2David R. Mack3Alain Stintzi4Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, CanadaOttawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, CanadaOttawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, CanadaDepartment of Pediatrics, Faculty of Medicine, University of Ottawa, Ottawa, ON, CanadaOttawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, CanadaABSTRACTThe human gut virome has been increasingly explored in recent years. However, nearly all virome-sequencing efforts rely solely on fecal samples and few studies leverage multiomic approaches to investigate phage–host relationships. Here, we combine metagenomics, metaviromics, and metatranscriptomics to study virome-bacteriome interactions at the colonic mucosal-luminal interface in a cohort of three individuals with inflammatory bowel disease; non-IBD controls were not included in this study. We show that the mucosal viral population is distinct from the stool virome and houses abundant crAss-like phages that are undetectable by fecal sampling. Through viral protein prediction and metatranscriptomic analysis, we explore viral gene transcription, prophage activation, and the relationship between the presence of integrase and temperate phages in IBD subjects. We also show the impact of deep sequencing on virus recovery and offer guidelines for selecting optimal sequencing depths in future metaviromic studies. Systems biology approaches such as those presented in this report will enhance our understanding of the human virome and its interactions with our microbiome and our health.https://www.tandfonline.com/doi/10.1080/19490976.2023.2177488Viromebacteriophagesgut microbiomephageomegut mucosa |
| spellingShingle | Austin Yan James Butcher Laetitia Schramm David R. Mack Alain Stintzi Multiomic spatial analysis reveals a distinct mucosa-associated virome Gut Microbes Virome bacteriophages gut microbiome phageome gut mucosa |
| title | Multiomic spatial analysis reveals a distinct mucosa-associated virome |
| title_full | Multiomic spatial analysis reveals a distinct mucosa-associated virome |
| title_fullStr | Multiomic spatial analysis reveals a distinct mucosa-associated virome |
| title_full_unstemmed | Multiomic spatial analysis reveals a distinct mucosa-associated virome |
| title_short | Multiomic spatial analysis reveals a distinct mucosa-associated virome |
| title_sort | multiomic spatial analysis reveals a distinct mucosa associated virome |
| topic | Virome bacteriophages gut microbiome phageome gut mucosa |
| url | https://www.tandfonline.com/doi/10.1080/19490976.2023.2177488 |
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