Oral bacteriophages are maintained at high levels for months in individuals but infrequently transmitted between mothers and infants

Abstract

In this work, we exploit recent advances in metagenomic assembly and bacteriophage identification to describe the phage content of saliva from 5 mother-baby pairs sampled twice 7 - 11 months apart during the first year of the babies lives. We identify 25 phage genomes that are comprised of one to 71 contigs, with 16 having a single contig. At the detectable level, phage were sparsely distributed with the most common one being present in 4 of the 20 samples, derived from two mothers and one baby. However, if they were present in the early time point sample from an individual, they were also present in the later sample from the same person more frequently than expected by chance. The nucleotide diversity ({pi}) in phage from the same sample or the same person was much lower than between different individuals, indicating dominance of one strain in each person. This was different from bacterial genomes, which had higher diversity indicating the presence of multiple strains within an individual. We identify likely bacterial hosts for 16 of the 25 phage, including an apparent inovirus that is capable of integrating in the dif site of Haemophilus species. It appears that phage in the oral cavity are sparsely distributed, but can be maintained for months once acquired.