Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity
- PDF / 3,078,766 Bytes
- 25 Pages / 595.276 x 793.701 pts Page_size
- 72 Downloads / 179 Views
RESEARCH
Open Access
Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity Daniel R. Utter1* , Gary G. Borisy2, A. Murat Eren3,4, Colleen M. Cavanaugh1* and Jessica L. Mark Welch3* * Correspondence: dutter@g. harvard.edu; [email protected]. edu; [email protected] 1 Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA 3 The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA Full list of author information is available at the end of the article
Abstract Background: The increasing availability of microbial genomes and environmental shotgun metagenomes provides unprecedented access to the genomic differences within related bacteria. The human oral microbiome with its diverse habitats and abundant, relatively well-characterized microbial inhabitants presents an opportunity to investigate bacterial population structures at an ecosystem scale. Results: Here, we employ a metapangenomic approach that combines public genomes with Human Microbiome Project (HMP) metagenomes to study the diversity of microbial residents of three oral habitats: tongue dorsum, buccal mucosa, and supragingival plaque. For two exemplar taxa, Haemophilus parainfluenzae and the genus Rothia, metapangenomes reveal distinct genomic groups based on shared genome content. H. parainfluenzae genomes separate into three distinct subgroups with differential abundance between oral habitats. Functional enrichment analyses identify an operon encoding oxaloacetate decarboxylase as diagnostic for the tongue-abundant subgroup. For the genus Rothia, grouping by shared genome content recapitulates species-level taxonomy and habitat preferences. However, while most R. mucilaginosa are restricted to the tongue as expected, two genomes represent a cryptic population of R. mucilaginosa in many buccal mucosa samples. For both H. parainfluenzae and the genus Rothia, we identify not only limitations in the ability of cultivated organisms to represent populations in their native environment, but also specifically which cultivar gene sequences are absent or ubiquitous. Conclusions: Our findings provide insights into population structure and biogeography in the mouth and form specific hypotheses about habitat adaptation. These results illustrate the power of combining metagenomes and pangenomes to investigate the ecology and evolution of bacteria across analytical scales. Keywords: Oral microbiome, Metagenomes, Pangenomes, Rothia, Haemophilus parainfluenzae, Population structure, Biogeography
© The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party
Data Loading...
