The influence of early life exposures on the infant gut virome

Background The factors influencing the establishment of the gut bacterial community in early life are fairly well studied. However, the factors shaping the infant gut virome remain elusive. Most gut viruses are bacteriophages (phages), i.e., viruses attacking bacteria in a host specific manner, and to a lesser extent, but also widely present, eukaryotic viruses, including viruses attacking human cells. Interestingly, early life gut virome imbalances have recently been linked with increased risk of developing diseases like type 1 diabetes and asthma. We utilized the deeply phenotyped COPSAC2010 cohort to investigate how environmental factors influence the gut virome at one year age. Results We demonstrate that presence of older siblings as well as residental location (urban or rural) had the strongest impact on gut virome composition at one year of age. A total of 16,118 species-level clustered viral representative contigs (here termed viral Operational Taxonomic Units – vOTUs) were identified and of these 2105 vOTUs varied in abundance with environmental exposure. Of these vOTUs 94.1% were phages mainly predicted to infect Bacteroidaceae , Prevotellaceae , and Ruminococcaceae . Strong co-abundance of phages and their bacterial hosts was confirmed underlining the predicted phage-host connections. Furthermore, we found some gut viruses affected by environmental factors encode enzymes involved in the utilization and degradation of major dietary components, potentially affecting infant health by influencing the bacterial host metabolic capacity. Genes encoding enzymes significantly associated with early life exposures were found in a total of 42 vOTUs. Eigtheen of these vOTUs had their life styles predicted, with 17 of them having a temperate lifestyle. Conclusion Given the importance of the gut microbiome in early life for maturation of the immune system and maintenance of metabolic health, these findings provide avaluable insights for understanding early life factors that predispose to autoimmune and metabolic disorders.