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Prophages in the infant gut are pervasively induced and may modulate the functionality of their hosts

Tamsin A Redgwell1, Jonathan Thorsen1,2, Marie-Agnès Petit3

  • 1Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Ledreborg Allé 34, DK-2820, Gentofte, Denmark.

NPJ Biofilms and Microbiomes
|March 20, 2025
PubMed

Insights

Prophages are key components of the infant gut microbiome, influencing its function. Most identified prophages were induced, regardless of environmental factors, suggesting significant host-microbe interactions.

Area of Science:

  • Microbiology
  • Virology
  • Human Gut Microbiome Research

Background:

  • The gut microbiome's role in health and disease is well-established.
  • The gut virome, particularly prophages, is increasingly recognized for its importance.
  • Prophage induction patterns in the infant gut remain largely unstudied.

Purpose of the Study:

  • To identify and characterize putative prophages in the infant gut.
  • To investigate the functional roles of these prophages.
  • To determine prophage induction patterns in infants.

Main Methods:

  • Analysis of 662 metagenomes from 1-year-old children.
  • Identification of 10645 putative prophages (virus Operational Taxonomic Units).
  • Paired analysis of viromes and metagenomes to assess prophage induction.

Main Results:

  • No core provirome was identified; the most prevalent vOTU was found in ~70% of samples.
  • The dominant prophage cluster was related to Bacteroides phage Hanky p00', carrying diversity-generating retroelements and capsular polysaccharide synthesis genes.
  • Most prophages in the infant gut were found to be induced, unaffected by environmental perturbers.

Conclusions:

  • Prophages are major, dynamic components of the infant gut microbiome.
  • Infant gut prophages possess functional genes that can influence the microbiome.
  • Prophage induction is a common phenomenon in the infant gut, potentially impacting host-microbe interactions.

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