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

Abstract Background Gut microbiome (GM) composition and function plays a pivotal role in human health and disease. The gut virome is increasingly being recognised as an important GM player and has been implicated in disease states. However, these studies largely focus on free phages in adults. Here we identify prophages from the Copenhagen Prospective Studies on Asthma in Childhood 2010 (COPSAC₂₀₁₀) mother-child cohort and investigate their potential functions. Results We identified 10645 putative prophages as viral Operational Taxonomic Units (vOTUs) from 662 assembled metagenomes. No core provirome was found: the most prevalent vOTU was identified in ~ 70% of the samples. The most abundant and second most prevalent group of vOTUs in the cohort was a novel cluster closely related to Bacteroides phage Hanky p00’. Functional annotation of this cluster revealed the presence of genes in the dTDP-L-rhamnose pathway, possibly involved in the production of capsular polysaccharides. We also found an abundance of diversity generating retroelements in this cluster. Additionally, paired shotgun virome data allowed us to show that most prophages are induced in at least one sample and that induction is not affected by antibiotics in the 4 weeks prior to sampling. Conclusions Prophages in the infant gut are largely unique to the individual and generally not shared. Most of them appear to be induced and so may be key drivers in shaping the bacterial microbiome. The most abundant cluster of prophages in the infant gut is novel and possesses elements that may allow maintaining differentially susceptible subpopulations of their host bacterium; whilst also containing diversity generating retroelements that could expand their host range. In summary, prophages are important components of the infant gut that may have far reaching influences on the composition and function of the microbiome.