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bioRxiv · 10.1101/2023.08.07.552389

Infant gut bacteriophage strain persistence during the first three years of life

Lou, Y. C.·Chen, L.·Borges, A. L.·West-Roberts, J. A.·Firek, B. A.·Morowitz, M.·Banfield, J.
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Abstract

Bacteriophages are key components of gut microbiomes, yet the phage colonization process in the infant gut remains uncertain. Here, we established a large phage sequence database and used strain-resolved analyses to investigate phage succession in infants throughout the first three years of life. Analysis of 819 fecal metagenomes collected from 28 full-term and 24 preterm infants and their mothers revealed that early-life phageome richness increased over time and reached adult-like complexity by age three. Approximately 9% of early phage colonizers, mostly maternally transmitted and infecting Bacteroides, persisted for three years and were more prevalent in full-term than in preterm infants. Although rare, phages with stop codon reassignment were more likely to persist than non-recoded phages and generally displayed an increase in in-frame re-assigned stop codons over three years. Overall, maternal seeding, stop codon reassignment, host CRISPR-Cas locus prevalence, and diverse phage populations contribute to stable viral colonization.

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Lou, Y. C., Chen, L., Borges, A. L., West-Roberts, J. A., Firek, B. A., Morowitz, M., Banfield, J.. 2023-08-08. Infant gut bacteriophage strain persistence during the first three years of life. https://doi.org/10.1101/2023.08.07.552389

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