The virota and its transkingdom interactions in the healthy infant gut

Virome and 16/18S analyses were performed on 304 longitudinal fecal samples of eight infants. The gut virota—the collection of all viruses present in the gut—was dominated by bacteriophages, which were nearly absent at birth and emerged rapidly within the first weeks after birth. Over 85% of phage reads correspond to 305 near-complete genomes, most of which (70.5%) were individual infant–specific, including two crAssphages, whereas 7.8% of phages were present in at least 50% of infants. Bacterial hosts could be predicted for 80% of phages, mainly infecting Firmicutes. Strong temporal correlations between phages and their predicted bacterial hosts were identified for >40% of our phages, and together with the observation of a decreasing fraction of phages with a temperate lifestyle further suggest that phages are induced from early-colonizing bacteria. The vast majority (>86%) of identified eukaryotic viruses, known to cause gastroenteritis, occurred without clinical signs, and an increase in the rate of infection occurred after day-care entrance. On average, 112 genomic contigs of distinct anelloviruses could be identified per infant, some of which were shed at >1 y. The identified plant viruses reflected the infant diet. Finally, the sporadic identification of fungi and parasites argues against the presence of such stable communities in the study population. Overall, this work provides a very high temporal resolution on how the different members of the infant gut microbiota, and especially the virome, develop over time in the gut of healthy infants, and might serve as valuable baseline knowledge for further studies investigating the effect of perturbations in the infant gut microbiota.