Streptococcal isolates from infant stool

Streptococcal species are human commensals that are known to colonize multiple body sites. Despite being early colonizers of the infant gut, we lack information about their origin and gut persistence. To gain more insight into the habitats of the streptococci present in the infant gut, we performed whole metagenome sequencing and streptococcal isolation for 100 stool samples from 10-day-old infants, characterizing the streptococci at the strain-level. We designed selective qPCR primers for 7 streptococcal strains, and these were subsequently utilized to screen samples from multiple body sites of the infants and their mothers. We found that two of the strains (one Streptococcus parasanguinis and one Streptococcus vestibularis) were prevalent in the stool samples, both from infants during their first 2 years of life and from their mothers, indicating that these strains are adapted to the gut environment. The S. parasanguinis strain was closely related to another prevalent strain, however, this close relative was mainly detected in samples from other body sites. Differences in the genomes of these strains were related to their adhesin genes, suggesting that host surface attachment could be a main factor for the observed differences in body site specificity. Our main finding is that even closely related streptococcal strains have very different distribution patterns across human body sites, and that this can potentially be related to variations in adhesins.