TY - JOUR T1 - Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome JF - bioRxiv DO - 10.1101/2020.04.29.069278 SP - 2020.04.29.069278 AU - Alon Shaiber AU - Amy D. Willis AU - Tom O. Delmont AU - Simon Roux AU - Lin-Xing Chen AU - Abigail C. Schmid AU - Mahmoud Yousef AU - Andrea R. Watson AU - Karen Lolans AU - Özcan C. Esen AU - Sonny T. M. Lee AU - Nora Downey AU - Hilary G. Morrison AU - Floyd E. Dewhirst AU - Jessica L. Mark Welch AU - A. Murat Eren Y1 - 2020/01/01 UR - http://biorxiv.org/content/early/2020/05/03/2020.04.29.069278.abstract N2 - Microbial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and their intriguing patterns of site specificity amidst the lack of dispersal limitation. Yet, the determinants of niche partitioning in this habitat are yet to be fully understood, especially among the taxa that belong to recently discovered branches of microbial life. Here we assembled metagenomes from daily tongue and dental plaque samples from multiple individuals and reconstructed 790 non-redundant genomes, 43 of which resolved to TM7 that formed six monophyletic clades distinctly associated either with plaque or with tongue. Both pangenomic and phylogenomic analyses grouped tongue-specific TM7 clades with other host-associated TM7 genomes. In contrast, plaque-specific TM7 grouped together with environmental TM7 genomes. Besides offering deeper insights into the ecology, evolution, and the mobilome of the cryptic members of the oral microbiome, our study reveals an intriguing resemblance between dental plaque and non-host environments indicated by the TM7 evolution, suggesting that plaque may have served as a stepping stone for environmental microbes to adapt to host environments for some clades of human associated microbes. Additionally, we report that prophages are widespread amongst oral-associated TM7, while absent from environmental TM7, suggesting that prophages may have played a role in adaptation of TM7 to the host environment.Competing Interest StatementThe authors have declared no competing interest. ER -