Prophages in the infant gut are largely induced, and may be functionally relevant to their hosts

Abstract

Background: Bacteriophages are the most abundant biological entity on the planet, and are key components of any ecosystem they are present in. The gut virome is increasingly being implicated in disease states although these studies largely focus on lytic phages in adults. Here we identify prophages from a large infant cohort and investigate their potential functions. Results: We identified 10645 vOTUs from 662 metagenomes. No core virome was found: the most prevalent vOTU was identified in 70% of the samples. The most abundant and prevalent group of phages are a novel group closely related to Bacteroides phage Hanky p00. Functional annotation of this group revealed the presence of genes in the dDTP-L-rhamnose pathway, possibly involved in the production of capsular polysaccharides. We also found an abundance of diversity generating retroelements in the phages. Additionally, paired virome data allowed us to show that the majority of prophages are induced in at least one sample and that this is not affected by the use of antibiotics in the 4 weeks prior to sampling. Conclusions: Prophages in the infant gut are largely unique to the individual and not shared. Most of them appear to be induced and so may be key drivers in shaping the bacterial microbiome. The most abundant group of phages are novel, and possess elements that may allow them to maintain differentially susceptible subpopulations of their host bacterium; whilst also containing diversity generating retroelements that could expand their host range. Prophages are important components of the infant gut that may have far reaching influences on the composition and function of the microbiome.

Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome

“…In support of the long-term memory role of distal CRISPR spacers, we found that the fraction of spacers targeting lysogenic phages systematically increases from the leading to the trailing end of the array (Figure 3d). Considering the high rates of lytic activity and CRISPR spacer turnover that characterize the infant gut, and the possible contribution of early phagebacteria interactions to shaping the adult gut microbiome (13,(89)(90)(91), an intriguing possibility might be that long-term memory spacers were selected during the consolidation of a coexisting community of MGE and bacteria in the first years of age.…”

Expanding known viral diversity in the healthy infant gut

“…) 49 known for its diversity-generating retroelements, and it has been extensively described in a parallel provirome study performed on the same samples 50 .…”

Genome binning of viral entities from bulk metagenomics data

“…The Copenhagen Prospective Studies on Asthma in Childhood 2010 (COPSAC) dataset consisted of 662 paired samples (refs. 33,34 ) and the Diabimmune dataset contained 112 paired samples 35 . Each of the two datasets included a list of curated viral species, 10,021 and 328 respectively, that we used here as our gold standard for training and testing our tool.…”

“…The Copenhagen Prospective Studies on Asthma in Childhood 2010 (COPSAC) dataset consisted of 662 paired samples obtained at age 1 year from an unselected childhood cohort (refs. 33,34 ). The COPSAC study was conducted in accordance with the guiding principles of the Declaration of Helsinki and was approved by the Capital Region of Denmark Local Ethics Committee (H-B-2008-093), and the Danish Data Protection Agency (2015-41-3696).…”