Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

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

View ORCID ProfileAlon Shaiber, View ORCID ProfileAmy D. Willis, View ORCID ProfileTom O. Delmont, View ORCID ProfileSimon Roux, Lin-Xing Chen, View ORCID ProfileAbigail C. Schmid, View ORCID ProfileMahmoud Yousef, View ORCID ProfileAndrea R. Watson, View ORCID ProfileKaren Lolans, View ORCID ProfileÖzcan C. Esen, View ORCID ProfileSonny T. M. Lee, Nora Downey, View ORCID ProfileHilary G. Morrison, View ORCID ProfileFloyd E. Dewhirst, View ORCID ProfileJessica L. Mark Welch, View ORCID ProfileA. Murat Eren
doi: https://doi.org/10.1101/2020.04.29.069278
Alon Shaiber
1Department of Medicine, University of Chicago, Chicago, IL 60637, USA
2Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Alon Shaiber
Amy D. Willis
3Department of Biostatistics, University of Washington, Seattle WA 98195, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Amy D. Willis
Tom O. Delmont
4Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Tom O. Delmont
Simon Roux
5Department of Energy Joint Genome Institute, Berkeley CA 94720, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Simon Roux
Lin-Xing Chen
6Department of Earth and Planetary Sciences, University of California, CA 94720, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Abigail C. Schmid
7Undergraduate Student, Computational and Applied Mathematics, University of Chicago, Chicago, IL 60637, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Abigail C. Schmid
Mahmoud Yousef
8Undergraduate Student, Computer Science, University of Chicago, Chicago, IL 60637, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Mahmoud Yousef
Andrea R. Watson
1Department of Medicine, University of Chicago, Chicago, IL 60637, USA
9Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Andrea R. Watson
Karen Lolans
1Department of Medicine, University of Chicago, Chicago, IL 60637, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Karen Lolans
Özcan C. Esen
1Department of Medicine, University of Chicago, Chicago, IL 60637, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Özcan C. Esen
Sonny T. M. Lee
10Division of Biology, Kansas State University, Manhattan, KS 66506, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Sonny T. M. Lee
Nora Downey
11Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Hilary G. Morrison
11Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Hilary G. Morrison
Floyd E. Dewhirst
12Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142, USA
13Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA 02115, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Floyd E. Dewhirst
Jessica L. Mark Welch
11Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jessica L. Mark Welch
  • For correspondence: meren@uchicago.edu jmarkwelch@mbl.edu
A. Murat Eren
1Department of Medicine, University of Chicago, Chicago, IL 60637, USA
2Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
9Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
11Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for A. Murat Eren
  • For correspondence: meren@uchicago.edu jmarkwelch@mbl.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Data/Code
  • Preview PDF
Loading

Abstract

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 Statement

The authors have declared no competing interest.

Footnotes

  • https://figshare.com/projects/Data_for_Oral_TM7s_by_Shaiber_et_al_2020_/74301

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted May 03, 2020.
Download PDF
Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome
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
bioRxiv 2020.04.29.069278; doi: https://doi.org/10.1101/2020.04.29.069278
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome
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
bioRxiv 2020.04.29.069278; doi: https://doi.org/10.1101/2020.04.29.069278

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Microbiology
Subject Areas
All Articles
  • Animal Behavior and Cognition (3609)
  • Biochemistry (7585)
  • Bioengineering (5533)
  • Bioinformatics (20825)
  • Biophysics (10344)
  • Cancer Biology (7995)
  • Cell Biology (11653)
  • Clinical Trials (138)
  • Developmental Biology (6617)
  • Ecology (10224)
  • Epidemiology (2065)
  • Evolutionary Biology (13639)
  • Genetics (9557)
  • Genomics (12856)
  • Immunology (7930)
  • Microbiology (19568)
  • Molecular Biology (7675)
  • Neuroscience (42182)
  • Paleontology (308)
  • Pathology (1259)
  • Pharmacology and Toxicology (2208)
  • Physiology (3271)
  • Plant Biology (7058)
  • Scientific Communication and Education (1295)
  • Synthetic Biology (1953)
  • Systems Biology (5433)
  • Zoology (1119)