Kuzub, N. | bioRxiv Science

bioRxiv2024

Negativeome in Early-Life Virome Studies: Characterization and Decontamination

Environmental contamination complicates the study of low-biomass microbial communities like the human gut virome. In 1,321 early-life gut viromes and 55 negative controls (NCs) from four datasets, we identified viral contaminants and their prevalence across studies. Samples and NCs were indistinguishable in genomic and ecological features, with 71.5% of samples sharing at least one identical strain with NCs. This work demonstrates the efficacy of strain-aware decontamination for preserving biological signals.

bioinformatics↗

bioRxiv2024

Dynamics and determinants of the gut mobilome in early life

As mobile genetic elements (MGE) are critical yet understudied determinants of gut microbiome composition, we characterized the gut virome and plasmidome in 195 samples from 28 mother-infant dyads delivered by caesarean section. Infant mobilome increased in richness over the first 6 postnatal weeks, demonstrating high individual-specificity and temporal stability, establishing a personal persistent mobilome. Formula-fed infants exhibited greater mobilome richness than breastfed infants, with plasmid composition influenced by antibiotic exposure and birth weight. Plasmids constituted a significant reservoir of antibiotic resistance genes (ARG), with around 5% of infant gut plasmid taxonomic units carrying ARG. Notably, ARG profiles did not differ with antibiotic exposure at birth. We found that mother-infant sharing of viral and plasmid strains primarily occurred after 6 months of age. Overall, our integrative analysis offers novel insights into the dynamics, modulation, origin, and clinical implications of MGE in the developing gut microbiome.

genomics↗

bioRxiv2023

Mother-Infant Gut Viruses and their Bacterial Hosts: Transmission Patterns and Dynamics during Pregnancy and Early Life

Early development of the gut ecosystem is crucial for lifelong health. While infant gut bacterial communities have been studied extensively, the infant gut virome remains under-explored. We longitudinally assessed the composition of gut viruses and their bacterial hosts in 322 total metagenomes and 205 metaviromes from 30 mothers during and after pregnancy and from their 32 infants during their first year of life. While the maternal gut virome composition remained stable during late pregnancy and after birth, the infant gut virome was dynamic in the first year of life and contained a higher abundance of active temperate phages compared to the maternal gut viromes. The infant gut virome composition was also influenced by infant feeding mode and place of delivery. Lastly, we provide evidence of viral-bacterial strains co-transmission from mothers to infants, demonstrating that infants acquire some of their virome from their mothers gut. Highlights- Longitudinal characterisation of the gut microbiome and virome in 30 mothers during pregnancy, at birth and 3 months after birth and in 32 infants from birth across the first year of life. - The maternal gut bacteriome changes from the first to the second trimester and then remains stable through birth and the first 3 months after birth. - The maternal gut virome remains stable during late pregnancy, birth and the first 3 months after birth. - The infant gut virome is highly dynamic during the first year of life and is shaped by infant feeding mode and place of delivery. - The infant gut harbours more temperate bacteriophages than the maternal gut, but their relative abundance decreases with increasing infant age. - Gut viral strains and their bacterial host strains are co-transmitted from mothers to their infants. - Gut viral strains are transferred from mother to infant around birth directly or via transfer of their bacterial hosts followed by the induction of prophages.

microbiology↗