Expanding known viral diversity in the healthy infant gut

Area of Science:

• Microbiology
• Virology
• Immunology

Background:

• The infant gut microbiome influences immune system maturation and long-term health.
• Bacteriophages (phages) are key regulators of gut bacterial populations, particularly in infants.
• Analyzing viral metagenomes (viromes) is challenging due to extensive unknown viral diversity and lack of standardized methods.

Purpose of the Study:

• To systematically characterize the viral diversity in infant faecal viromes.
• To identify novel viral species and their hosts within the infant gut.
• To expand phage taxonomy and provide a resource for infant gut virome research.

Main Methods:

• Analysis of faecal viromes from 647 1-year-olds in the Copenhagen Prospective Studies on Asthma in Childhood cohort.
• Assembly and curation of viral sequences to identify viral species and virus family-level clades (VFCs).
• Host prediction using clustered regularly interspaced short palindromic repeat (CRISPR) spacers from co-sampled bacterial metagenomes.

Main Results:

• Discovery of approximately 10,000 viral species across 248 VFCs, with 232 VFCs being previously unknown, primarily within the Caudoviricetes class.
• Host attribution for 79% of identified phages, revealing novel phage families targeting Clostridiales and Bifidobacterium, outnumbering crAssphages.
• Characterization of phage lifestyles, identifying 33 virulent and 118 temperate phage families, with virulent phages being more abundant and temperate phages more prevalent and diverse.

Conclusions:

• The study significantly expands known phage taxonomy and reveals extensive previously unrecognized viral diversity in the infant gut.
• Identified novel phage-host interactions and distributions provide critical insights into phage roles in infant gut ecology.
• This comprehensive resource aids future research into the infant gut virome and its impact on health and disease.