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Dental Plaque Microbes Genetically More Similar to Those of Soil Than Nearby Tongue

NEW YORK – Microbes that live in dental plaque are genetically more similar to microbes found in the soil than those that live on the tongue, a new metagenomics study has found. The finding suggests new ideas about how the oral microbiome may have evolved.

A team led by researchers at the University of Chicago Medical Center examined the dental plaque and tongue microbiomes of about half a dozen people. As they reported in Genome Biology on Tuesday, they focused on an understudied class of bacteria called Saccharibacteria, or TM7. A pangenomic and phylogenetic analysis indicated that TM7 bacteria found in dental plaque were closely related to bacteria found in soil, while TM7 bacteria on the tongue were more similar to other host-associated bacteria. This suggested to the researchers that the plaque-linked bacteria may have acted as a "stepping stone" that enabled environmental microbes to adapt to living in a host.

Both plaque-associated and tongue-associated TM7s appear to have an ancient association with animal hosts, but the former are more similar to bacteria in the environment, according to first author Alon Shaiber, now a genomic data scientist at Weill Cornell Medicine. "This is not to suggest that you might find the exact same species of TM7 successfully colonizing our dental plaque and also growing in soil," he wrote in an email. "In fact, there are probably many years of evolution separating the most closely related environmental TM7 from its plaque counterpart."

The researchers collected plaque and tongue microbial samples from seven people over the course of a few days, for a total 71 samples. After assembling the plaque and tongue samples separately, they reconstructed the microbial genomes from their set of metagenomes to yield 790 non-redundant genomes. A number of these belonged to members of the Candidate Phyla Radiation (CPR), a set of bacteria that are phylogenetically similar but also lack biological pathways typically thought of as essential, and that live in a host.

Forty-three of the CPR genes in this sample belonged to the phylum Saccharibacteria, or TM7. The vast majority — 42 — of the TM7 populations were found either in plaque or in tongue samples, but not both, suggesting the populations are site specific. A phylogenomic analysis of these and nine previously published human oral TM7 genomes found that the plaque- and tongue-associated bacteria belonged to different branches. In particular, 41 of the 42 plaque-associated genomes belonged to a single clade, indicating that its niche is an ancestral trait. 

Further phylogenetic analysis based on ribosomal protein genes of these and publicly available TM7 genomes divided their set of oral TM7 populations into six monophyletic clades that were either linked to plaque or tongue regions. But these clades had sister groups consisting of genomes from non-human sources.

In particular, tongue-associated oral TM7 populations were grouped with genomes isolated from animal guts, while plaque-associated oral TM7 populations were interspersed with genomes that were isolated from environmental or soil sources. The analysis further indicated an ancient association between these TM7 bacteria and their host environments.

The researchers said their findings suggest that the plaque microbiome may have helped the oral microbiome evolve by acting as a place where bacteria could adapt to host life.

"Our hypothesis is that plaque played a role during the evolution of host-associated microbes, such as some clades of TM7, by offering this intermediary space where the bacteria don't immediately have to deal with threats from the host," senior author Murat Eren from the University of Chicago said in a statement. "Once adapted to the plaque, the microbes could then make the jump to adapt to the host entirely, in new habitats like the tongue."