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Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

التفاصيل البيبلوغرافية
العنوان: Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome
المؤلفون: Alon Shaiber, Amy D. Willis, Tom O. Delmont, Simon Roux, Lin-Xing Chen, Abigail C. Schmid, Mahmoud Yousef, Andrea R. Watson, Karen Lolans, Özcan C. Esen, Sonny T. M. Lee, Nora Downey, Hilary G. Morrison, Floyd E. Dewhirst, Jessica L. Mark Welch, A. Murat Eren
المصدر: Genome Biology, Vol 21, Iss 1, Pp 1-35 (2020)
بيانات النشر: BMC, 2020.
سنة النشر: 2020
المجموعة: LCC:Biology (General)
LCC:Genetics
مصطلحات موضوعية: Metagenomics, Metapangenomics, Niche partitioning, Human oral cavity, Candidate phyla radiation, Saccharibacteria, Biology (General), QH301-705.5, Genetics, QH426-470
الوصف: Abstract Introduction Microbial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and intriguing patterns of site specificity amidst the lack of dispersal limitation. However, the determinants of niche partitioning in this habitat are yet to be fully understood, especially among taxa that belong to recently discovered branches of microbial life. Results Here, we assemble metagenomes from tongue and dental plaque samples from multiple individuals and reconstruct 790 non-redundant genomes, 43 of which resolve to TM7, a member of the Candidate Phyla Radiation, forming six monophyletic clades that distinctly associate with either plaque or tongue. Both pangenomic and phylogenomic analyses group tongue-specific clades with other host-associated TM7 genomes. In contrast, plaque-specific TM7 group with environmental TM7 genomes. Besides offering deeper insights into the ecology, evolution, and mobilome of 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 microbes. Additionally, we report that prophages are widespread among oral-associated TM7, while absent from environmental TM7, suggesting that prophages may have played a role in adaptation of TM7 to the host environment. Conclusions Our data illuminate niche partitioning of enigmatic members of the oral cavity, including TM7, SR1, and GN02, and provide genomes for poorly characterized yet prevalent members of this biome, such as uncultivated Flavobacteriaceae.
نوع الوثيقة: article
وصف الملف: electronic resource
اللغة: English
تدمد: 1474-760X
Relation: https://doaj.org/toc/1474-760X
DOI: 10.1186/s13059-020-02195-w
URL الوصول: https://doaj.org/article/a6fb499471734e1d8c8eb15a4b66f129
رقم الأكسشن: edsdoj.6fb499471734e1d8c8eb15a4b66f129
قاعدة البيانات: Directory of Open Access Journals
الوصف
تدمد:1474760X
DOI:10.1186/s13059-020-02195-w