Expanding known viral diversity in the healthy infant gut

Nature Microbiology · 26 authors, 10 centres

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TL;DR

Deep metagenomic sequencing of 647 healthy infant gut viromes revealed 248 viral family-level clusters (VFCs), 232 of which were previously unknown. The study shows temperate phages dominate the infant gut virome and that caudoviral richness exceeds bacterial host richness by an order of magnitude.

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De novo assembly and classification were used to identify viral family-level clusters (VFCs) and determine phage lifestyles. The approach uncovered 248 VFCs, of which 232 were previously unknown, predominantly belonging to the Caudoviricetes class. After systematic resolution, only 7% of virome sequences remained unaccounted. Temperate phages dominated the 1-year-old gut virome, in contrast to adult viromes where virulent phages dominate. Caudoviral richness exceeded host bacterial richness by approximately an order of magnitude, with 2,858 caudoviral genera versus 203 host genera. The study used a 30-minute short multiple-displacement amplification (sMDA) step to enable ssDNA virus detection.

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other

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biomedical research

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ORIGINAL PAPER

PMC10159846

Expanding known viral diversity in the healthy infant gut

Nature Microbiology

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ABSTRACT

Abstract 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. Subject terms: Phage biology, Translational research

CITATION EXPORT

Shiraz A Shah, Ling Deng, Jonathan Thorsen et al.. Expanding known viral diversity in the healthy infant gut. Nature Microbiology. (2023). https://doi.org/10.1038/s41564-023-01345-7

AUTHORS

26 · 10 CENTRES

Shiraz A Shah, Ling Deng, Jonathan Thorsen, Anders G Pedersen, Moïra B Dion, Josué L Castro-Mejía, Ronalds Silins, Fie O Romme, Romain Sausset, Leon E Jessen, Eric Olo Ndela, Mathis Hjelmsø, Morten A Rasmussen, Tamsin A Redgwell, Cristina Leal Rodríguez, Gisle Vestergaard, Yichang Zhang, Bo Chawes, Klaus Bønnelykke, Søren J Sørensen, Hans Bisgaard, Francois Enault, Jakob Stokholm, Sylvain Moineau, Marie-Agnès Petit, Dennis S Nielsen

1Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
2Department of Food Science, University of Copenhagen, Copenhagen, Denmark
3Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
4Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
5Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Quebec Canada
6Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Quebec Canada
7Université Paris-Saclay, INRAE, Agroparistech, Micalis institute, Jouy-en-Josas, France
8Lab de Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
9Department of Biology, University of Copenhagen, Copenhagen, Denmark
10Félix d’Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Quebec Canada