Expanding known viral diversity in the healthy infant gut.

Autor: Shah SA; Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark. shiraz.shah@dbac.dk., Deng L; Department of Food Science, University of Copenhagen, Copenhagen, Denmark., Thorsen J; Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark.; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark., Pedersen AG; Department of Health Technology, Technical University of Denmark, Lyngby, Denmark., Dion MB; Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Quebec, Canada.; Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Quebec, Canada., Castro-Mejía JL; Department of Food Science, University of Copenhagen, Copenhagen, Denmark., Silins R; Department of Food Science, University of Copenhagen, Copenhagen, Denmark., Romme FO; Department of Food Science, University of Copenhagen, Copenhagen, Denmark., Sausset R; Université Paris-Saclay, INRAE, Agroparistech, Micalis institute, Jouy-en-Josas, France., Jessen LE; Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark.; Department of Health Technology, Technical University of Denmark, Lyngby, Denmark., Ndela EO; Lab de Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France., Hjelmsø M; Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark., Rasmussen MA; Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark.; Department of Food Science, University of Copenhagen, Copenhagen, Denmark., Redgwell TA; Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark., Leal Rodríguez C; Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark., Vestergaard G; Department of Health Technology, Technical University of Denmark, Lyngby, Denmark., Zhang Y; Department of Food Science, University of Copenhagen, Copenhagen, Denmark., Chawes B; Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark., Bønnelykke K; Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark., Sørensen SJ; Department of Biology, University of Copenhagen, Copenhagen, Denmark., Bisgaard H; Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark., Enault F; Lab de Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France., Stokholm J; Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark.; Department of Food Science, University of Copenhagen, Copenhagen, Denmark., Moineau S; Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Quebec, Canada.; Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Quebec, Canada.; Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Quebec, Canada., Petit MA; Université Paris-Saclay, INRAE, Agroparistech, Micalis institute, Jouy-en-Josas, France., Nielsen DS; Department of Food Science, University of Copenhagen, Copenhagen, Denmark. dn@food.ku.dk.
Jazyk: angličtina
Zdroj: Nature microbiology [Nat Microbiol] 2023 May; Vol. 8 (5), pp. 986-998. Date of Electronic Publication: 2023 Apr 10.
DOI: 10.1038/s41564-023-01345-7
Abstrakt: The gut microbiome is shaped through infancy and impacts the maturation of the immune system, thus protecting against chronic disease later in life. Phages, or viruses that infect bacteria, modulate bacterial growth by lysis and lysogeny, with the latter being especially prominent in the infant gut. Viral metagenomes (viromes) are difficult to analyse because they span uncharted viral diversity, lacking marker genes and standardized detection methods. Here we systematically resolved the viral diversity in faecal viromes from 647 1-year-olds belonging to Copenhagen Prospective Studies on Asthma in Childhood 2010, an unselected Danish cohort of healthy mother-child pairs. By assembly and curation we uncovered 10,000 viral species from 248 virus family-level clades (VFCs). Most (232 VFCs) were previously unknown, belonging to the Caudoviricetes viral class. Hosts were determined for 79% of phage using clustered regularly interspaced short palindromic repeat spacers within bacterial metagenomes from the same children. Typical Bacteroides-infecting crAssphages were outnumbered by undescribed phage families infecting Clostridiales and Bifidobacterium. Phage lifestyles were conserved at the viral family level, with 33 virulent and 118 temperate phage families. Virulent phages were more abundant, while temperate ones were more prevalent and diverse. Together, the viral families found in this study expand existing phage taxonomy and provide a resource aiding future infant gut virome research.
(© 2023. The Author(s).)
Databáze: MEDLINE
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