Browsing by Author "Galperina, Anastasia"

The infant gut microbiota maturation is central to infant health and well-being and has been suggested to have important health impacts in adulthood. While most of the previous research and description of the dynamics of the gut microbiota acquisition and maturation focused on the prokaryotic community; recent studies have suggested the importance of other microbial members in the community. Viruses, specifically bacteriophages (phages), are found in high abundances in the gut microbiota, and may influence prokaryotic composition and the microbiota’s trajectory during infancy. Phages can shape the bacterial community by killing their cellular host but also by modulating their bacterial host fitness in the ecosystem. Additionally, phages can carry genes which have no role in the viral replication machinery, but instead modulate the cellular host metabolism. These genes, termed auxiliary metabolic genes (AMGs), are largely uncharacterized in the human gut, in particular in the context of the infant gut microbiota maturation. In this thesis, we explored the diversity and persistence of AMGs in infant gut microbiota from 3 months to 2 years old and identified and characterized changes in the AMGs repertoire during the infant gut microbiota maturation. This project utilized a subset of the broader Finnish Health and Early Life Microbiota (HELMi) birth cohort study, a Finnish prospective cohort on early life microbiota and health. In this study, we leveraged whole genome shotgun metagenomes from faecal samples of 475 infants collected at four time points, as well as samples from their mothers (n = 304) and fathers (n = 123). The viral sequences in these metagenomes were then identified, annotated, and characterized, allowing us to build a large catalogue of bacteriophage sequences, called the HELMi Bacteriophage Catalogue (HBaC). Next, we assessed the presence of putative AMGs in this phage collection and determined their prevalence in the viral community and dynamics during the gut microbiota maturation. The HBaC contains 145,818 unique species-like viral OTUs (vOTUs) of which a majority are temperate phages, classified as Caudoviricetes. Notably, we observed an increase in phage diversity and richness during the infant gut microbiota maturation and an increase in relative abundance of virulent phages. Further, the viral community composition strongly associated with the observed prokaryotic faecal community types (FCTs). In our phage catalogue, 8 % of the vOTUs carried at least one putative AMGs and the Demerecviridae, Autographiviridae and Herelleviridae families proportionally carried the most. The most common metabolic pathways encoded by these putative AMGs found in HBaC were organic nitrogen metabolism, transport functions and carbon utilization. Interestingly, we observed a change in putative AMGs abundance and function during the infant gut microbiota maturation. In the future, additional analysis exploring the influence of early life exposures on phage and AMGs prevalence and dynamics could help unravel the complex interaction between phages and their bacterial host in the dynamic infant gut microbiota.