Expanding known viral diversity in the healthy infant gut

Faecal viromes of 647 healthy infants were deeply sequenced to identify more than 230 previously undescribed gut virus families, expanding known diversity within the human infant gut virome. 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.

Automated summary

Deep sequencing of faecal viromes from 647 healthy infants identified over 230 previously unknown gut virus families, expanding our understanding of the diversity in the human infant gut virome. The findings highlight the importance of the gut microbiome in infancy for the development of the immune system and long-term protection against chronic diseases. This study provides valuable insights into the viral diversity in the infant gut virome and expands phage taxonomy, serving as a resource for future research.