The influence of early life exposures on the infant gut virome
The factors influencing the establishment of the gut bacterial community in early life are fairly well studied. However, the factors shaping the infant gut virome remain elusive. Interestingly, early life gut virome imbalances have recently been linked with increased risk of developing diseases like...
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Taylor & Francis Group
2025-12-01
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| Series: | Gut Microbes |
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| Online Access: | https://www.tandfonline.com/doi/10.1080/19490976.2025.2501194 |
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| author | Yichang Zhang Josué L. Castro-Mejía Ling Deng Shiraz A. Shah Jonathan Thorsen Cristina Leal Rodríguez Leon E. Jessen Moïra B. Dion Bo Chawes Klaus Bønnelykke Søren J. Sørensen Hans Bisgaard Sylvain Moineau Marie-Agnès Petit Jakob Stokholm Dennis S. Nielsen |
| author_facet | Yichang Zhang Josué L. Castro-Mejía Ling Deng Shiraz A. Shah Jonathan Thorsen Cristina Leal Rodríguez Leon E. Jessen Moïra B. Dion Bo Chawes Klaus Bønnelykke Søren J. Sørensen Hans Bisgaard Sylvain Moineau Marie-Agnès Petit Jakob Stokholm Dennis S. Nielsen |
| author_sort | Yichang Zhang |
| collection | DOAJ |
| description | The factors influencing the establishment of the gut bacterial community in early life are fairly well studied. However, the factors shaping the infant gut virome remain elusive. Interestingly, early life gut virome imbalances have recently been linked with increased risk of developing diseases like type 1 diabetes and asthma. We utilized the deeply phenotyped COPSAC2010 cohort to investigate how environmental factors influence the gut virome at one year age. We demonstrate that the presence of older siblings as well as residential location (urban or rural) had the strongest impact on gut virome composition at 1 year of age. A total of 16,118 species-level clustered viral representative contigs (here termed viral Operational Taxonomic Units – vOTUs) were identified and of these 2105 vOTUs varied in abundance with environmental exposures. Of these vOTUs 94.1% were phages mainly predicted to infect Bacteroidaceae, Prevotellaceae, and Ruminococcaceae. Strong co-abundance of phages and their bacterial hosts was confirmed underlining the predicted phage-host connections. Furthermore, we found some gut viruses affected by environmental factors encode enzymes involved in the utilization and degradation of major dietary components, potentially affecting infant health by influencing the bacterial host metabolic capacity. These findings provide a valuable insights for understanding the early life factors that predispose to autoimmune and metabolic disorders. |
| format | Article |
| id | doaj-art-54f088864f1e4fe1a63f0cb7e1274c13 |
| institution | DOAJ |
| issn | 1949-0976 1949-0984 |
| language | English |
| publishDate | 2025-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Gut Microbes |
| spelling | doaj-art-54f088864f1e4fe1a63f0cb7e1274c132025-08-20T03:08:16ZengTaylor & Francis GroupGut Microbes1949-09761949-09842025-12-0117110.1080/19490976.2025.2501194The influence of early life exposures on the infant gut viromeYichang Zhang0Josué L. Castro-Mejía1Ling Deng2Shiraz A. Shah3Jonathan Thorsen4Cristina Leal Rodríguez5Leon E. Jessen6Moïra B. Dion7Bo Chawes8Klaus Bønnelykke9Søren J. Sørensen10Hans Bisgaard11Sylvain Moineau12Marie-Agnès Petit13Jakob Stokholm14Dennis S. Nielsen15Department of Food Science, University of Copenhagen, Frederiksberg, DenmarkDepartment of Food Science, University of Copenhagen, Frederiksberg, DenmarkDepartment of Food Science, University of Copenhagen, Frederiksberg, DenmarkCopenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, DenmarkCopenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, DenmarkCopenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, DenmarkCopenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, DenmarkDépartement de Biochimie, de Microbiologie, et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, CanadaCopenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, DenmarkCopenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, DenmarkDepartment of Biology, University of Copenhagen, Frederiksberg, DenmarkCopenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, DenmarkDépartement de Biochimie, de Microbiologie, et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, CanadaUniversité Paris-Saclay, INRAE, AgroParis Tech, Micalis Institute, Jouy-en-Josas, FranceDepartment of Food Science, University of Copenhagen, Frederiksberg, DenmarkDepartment of Food Science, University of Copenhagen, Frederiksberg, DenmarkThe factors influencing the establishment of the gut bacterial community in early life are fairly well studied. However, the factors shaping the infant gut virome remain elusive. Interestingly, early life gut virome imbalances have recently been linked with increased risk of developing diseases like type 1 diabetes and asthma. We utilized the deeply phenotyped COPSAC2010 cohort to investigate how environmental factors influence the gut virome at one year age. We demonstrate that the presence of older siblings as well as residential location (urban or rural) had the strongest impact on gut virome composition at 1 year of age. A total of 16,118 species-level clustered viral representative contigs (here termed viral Operational Taxonomic Units – vOTUs) were identified and of these 2105 vOTUs varied in abundance with environmental exposures. Of these vOTUs 94.1% were phages mainly predicted to infect Bacteroidaceae, Prevotellaceae, and Ruminococcaceae. Strong co-abundance of phages and their bacterial hosts was confirmed underlining the predicted phage-host connections. Furthermore, we found some gut viruses affected by environmental factors encode enzymes involved in the utilization and degradation of major dietary components, potentially affecting infant health by influencing the bacterial host metabolic capacity. These findings provide a valuable insights for understanding the early life factors that predispose to autoimmune and metabolic disorders.https://www.tandfonline.com/doi/10.1080/19490976.2025.2501194Environmental exposuresinfantgut microbiotavirusphagebacterial host |
| spellingShingle | Yichang Zhang Josué L. Castro-Mejía Ling Deng Shiraz A. Shah Jonathan Thorsen Cristina Leal Rodríguez Leon E. Jessen Moïra B. Dion Bo Chawes Klaus Bønnelykke Søren J. Sørensen Hans Bisgaard Sylvain Moineau Marie-Agnès Petit Jakob Stokholm Dennis S. Nielsen The influence of early life exposures on the infant gut virome Gut Microbes Environmental exposures infant gut microbiota virus phage bacterial host |
| title | The influence of early life exposures on the infant gut virome |
| title_full | The influence of early life exposures on the infant gut virome |
| title_fullStr | The influence of early life exposures on the infant gut virome |
| title_full_unstemmed | The influence of early life exposures on the infant gut virome |
| title_short | The influence of early life exposures on the infant gut virome |
| title_sort | influence of early life exposures on the infant gut virome |
| topic | Environmental exposures infant gut microbiota virus phage bacterial host |
| url | https://www.tandfonline.com/doi/10.1080/19490976.2025.2501194 |
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