Dynamics of tongue microbial communities with single-nucleotide resolution using oligotyping
Mark Welch, Jessica L.
Utter, Daniel R.
Rossetti, Blair J.
Mark Welch, David B.
Eren, A. Murat
Borisy, Gary G.
MetadataShow full item record
KeywordHuman microbiome; Oral microbiota; 16S ribosomal RNA; Haemophilus; Neisseria; Streptococcus; Veillonella
The human mouth is an excellent system to study the dynamics of microbial communities and their interactions with their host. We employed oligotyping to analyze, with single-nucleotide resolution, oral microbial 16S ribosomal RNA (rRNA) gene sequence data from a time course sampled from the tongue of two individuals, and we interpret our results in the context of oligotypes that we previously identified in the oral data from the Human Microbiome Project. Our previous work established that many of these oligotypes had dramatically different distributions between individuals and across oral habitats, suggesting that they represented functionally different organisms. Here we demonstrate the presence of a consistent tongue microbiome but with rapidly fluctuating proportions of the characteristic taxa. In some cases closely related oligotypes representing strains or variants within a single species displayed fluctuating relative abundances over time, while in other cases an initially dominant oligotype was replaced by another oligotype of the same species. We use this high temporal and taxonomic level of resolution to detect correlated changes in oligotype abundance that could indicate which taxa likely interact synergistically or occupy similar habitats, and which likely interact antagonistically or prefer distinct habitats. For example, we found a strong correlation in abundance over time between two oligotypes from different families of Gamma Proteobacteria, suggesting a close functional or ecological relationship between them. In summary, the tongue is colonized by a microbial community of moderate complexity whose proportional abundance fluctuates widely on time scales of days. The drivers and functional consequences of these community dynamics are not known, but we expect they will prove tractable to future, targeted studies employing taxonomically resolved analysis of high-throughput sequencing data sampled at appropriate temporal intervals and spatial scales.
.© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 5 (2014): 568, doi:10.3389/fmicb.2014.00568.
Suggested CitationFrontiers in Microbiology 5 (2014): 568
The following license files are associated with this item:
Showing items related by title, author, creator and subject.
Huse, Susan M.; Dethlefsen, Les; Huber, Julie A.; Mark Welch, David B.; Relman, David A.; Sogin, Mitchell L. (Public Library of Science, 2008-11-21)Massively parallel pyrosequencing of hypervariable regions from small subunit ribosomal RNA (SSU rRNA) genes can sample a microbial community two or three orders of magnitude more deeply per dollar and per hour than capillary ...
On the calculation of wind stress curl over open ocean areas from synoptic meteorological data with application to time dependent ocean circulation Welch, Christopher Slocombe (Woods Hole Oceanographic Institution, 1972-02)The method used by N. P. Fofonoff for estimating wind stress curl from surface atmospheric pressure maps is developed for use with the National Meterological Center analysis grid. A formula is developed relating the wind ...
Teif, Vladimir B.; Mallm, Jan-Philipp; Sharma, Tanvi; Mark Welch, David B.; Rippe, Karsten; Eils, Roland; Langowski, Jörg; Olins, Ada L.; Olins, Donald E. (Taylor & Francis, 2017-02-23)Cell differentiation is associated with changes in chromatin organization and gene expression. In this study, we examine chromatin structure following differentiation of the human myeloid leukemia cell line (HL-60/S4) ...