Human Phageprints: A high-resolution exploration of oral phages reveals globally-distributed phage families with individual-specific and temporally-stable community compositions

Abstract

1Metagenomic studies have revolutionized the study of novel phages. However these studies 2 trade the depth of coverage for breadth. In this study we show that the targeted sequencing of a 3 phage genomic region as small as 200-300 base pairs, can provide sufficient sequence diversity to 4 serve as an individual-specific barcode or "Phageprint". The targeted approach reveals a high-5 resolution view of phage communities that is not available through metagenomic datasets. By 6 creating instructional videos and collection kits, we enabled citizen scientists to gather ~700 oral 7 samples spanning ~100 individuals residing in different parts of the world. In examining phage 8 communities at 6 different oral sites, and by comparing phage communities of individuals living 9 across the globe, we were able to study the effect of spatial separation, ranging from several 10 millimeters to thousands of kilometers. We found that the spatial separation of just a few 11 centimeters (the distance between two oral sites) can already result in highly distinct phage 12 community compositions. For larger distances, spanning the phage communities of different 13 individuals living in different parts of the world, we did not observe any correlation between spatial 14 distance and phage community composition as individuals residing in the same city did not have any 15 more similar phage communities than individuals living on different continents. Additionally, we 16 found that neither genetics nor cohabitation seem to play a role in the relatedness of phage 17 community compositions across individuals. Cohabitating siblings and even identical twins did not 18 have phage community compositions that were any more similar than those of unrelated individuals. 19The primary factor contributing to phage community composition relatedness is direct contact 20 between two habitats, as is demonstrated by the similarity between oral phage community 21 compositions of partners. Furthermore, by exploring phage communities across the span of a 22 month, and in some cases several years, we observed highly stable community compositions. These 23 3 studies consistently point to the existence of remarkably diverse and personal phage families that are 24 stable in time and apparently present in people around the world. 25 26 Due to the immense sequence diversity of phage genomes (48-50), an in-depth view of their 78 communities through a targeted sequencing approach could provide novel insights. As such, the 79 overarching aim of this study was to explore oral phage communities and their inter-and intra-80 personal diversity, their spatial patterns of distribution, as well as temporal dynamics in a large-scale 81 and high-resolution fashion. Towards this aim, we first had to choose regions within phage genomes 82 on which to perform targeted sequencing. Because of the vast diversity of uncultured phages, we 83 relied on oral metagenomic datasets to identify candidate marker sequences from such phages. 84We have described the methods for phage marker dis...

The human oral phageome

“…An earlier study by the same research group described transient salivary phage populations but may have overestimated the number of phage genotypes 5 . A 30‐day study of tongue phages showed a generally stable phage community, although some major phage phylotypes reappeared in cycles that appeared to be unrelated to diet and oral hygiene efforts 91 . The apparent stability of major oral phage groups ensures a continuous phage effect on oral microorganisms.…”

“…Oral bacteria tend to be site specialists, 156 and oral phages follow a similar pattern. 157 By correlating phage phylotypes and oral niche presence, 91 some Haemophilus and Aggregatibacter phages were found to exhibit a generalized oral distribution (eg, SuMu-like transposable phage was prevalent at tongue, buccal mucosa, and gingiva), whereas other phage phylotypes showed a clear niche specificity (eg, cluster 19 and cluster 20 of MhaA1-like phages were linked to buccal mucosa and tongue, respectively). 4 Phage generalists, which can infect strains of multiple subspecies or different species, possess a mode of infection that carries low fitness cost advantageously with low abundance of host cells.…”

“…5 A 30day study of tongue phages showed a generally stable phage community, although some major phage phylotypes reappeared in cycles that appeared to be unrelated to diet and oral hygiene efforts. 91 The apparent stability of major oral phage groups ensures a continuous phage effect on oral microorganisms.…”

“…176,178 Transmission of oral phages can take place between mother and children, family members, couples with intimate contact and people in the same household. 91,179,181 A study of couples demonstrated common features in the tongue phage population. 91 People who are sharing or have shared households in the past also harbor many phages of same sequences.…”

“…91,179,181 A study of couples demonstrated common features in the tongue phage population. 91 People who are sharing or have shared households in the past also harbor many phages of same sequences. 179 Neither a genetic relationship nor a spousal relationship seem to be required to share oral phages, and even relatively brief contact may lead to transmission.…”