Prophages in the infant gut are pervasively induced and may modulate the functionality of their hosts
Gut microbiome (GM) composition and function is pivotal for human health and disease, of which the virome's importance is increasingly recognised. However, prophages and their induction patterns in the infant gut remain understudied. Here, we identified 10645 putative prophages in 662 metagenomes from 1-year-old children in the COPSAC2010 mother-child cohort and investigated their potential functions. No core provirome was found as the most prevalent vOTU was identified in only ~70% of the samples. The most dominant cluster of vOTUs in the cohort was related to Bacteroides phage Hanky p00', and it carried both diversity generating retroelements and genes involved in capsular polysaccharide synthesis. Paired analysis of viromes and metagenomes from the same samples revealed that most prophages within the infant gut were induced and that induction was unaffected by a range of environmental perturbers. In summary, prophages are major components of the infant gut that may have far reaching influences on the microbiome and its host.
Authors
- Jonathan Thorsen (ORCID: https://orcid.org/0000-0003-0200-0461)
- Shiraz A. Shah (ORCID: https://orcid.org/0000-0002-4665-577X)
- Klaus Bønnelykke (ORCID: https://orcid.org/0000-0003-2003-1018)
- Marie‐Agnès Petit (ORCID: https://orcid.org/0000-0003-2242-2768)
- Bo Chawes (ORCID: https://orcid.org/0000-0001-6846-6243)
- Hans Bisgaard (ORCID: https://orcid.org/0000-0003-4131-7592)
- Søren Johannes Sørensen (ORCID: https://orcid.org/0000-0001-6227-9906)
- Jakob Stokholm (ORCID: https://orcid.org/0000-0003-4989-9769)
- Jakob Russel (ORCID: https://orcid.org/0000-0002-0565-3161)
- Gisle Vestergaard (ORCID: https://orcid.org/0000-0003-2541-4974)
- Tamsin Redgwell (ORCID: https://orcid.org/0000-0001-5835-2699)
- Ling Deng (ORCID: https://orcid.org/0000-0002-2190-9788)
- Dennis Sandris Nielsen (ORCID: https://orcid.org/0000-0001-8121-1114)
Institutions
- University of Copenhagen (DK)
- Maersk (Denmark) (DK)
- AgroParisTech (FR)
- Université Paris-Saclay (FR)
- Novo Nordisk Foundation (DK)
- Copenhagen University Hospital (DK)
- Microbiologie de l’alimentation au service de la santé (FR)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Copenhagen Prospective Studies on Asthma in Childhood (DK)
- Novo Nordisk Foundation Center for Basic Metabolic Research
- Technical University of Denmark (DK)
Publication Details
- Journal
- npj Biofilms and Microbiomes
- Published
- 2025-03-19
- DOI
- https://doi.org/10.1038/s41522-025-00674-1
- Citations
- 5
- Primary Topic
- Bacteriophages and microbial interactions
- Type
- article
- Field-Weighted Citation Impact
- 8.58
Funders
- Velux Fonden
- Joint Programming Initiative A healthy diet for a healthy life
- Novo Nordisk
- Novo Nordisk Fonden