Given the proximity of your tongue to your teeth and your cheeks to your gums, you might expect that the microbial communities that call these niches home, would be highly similar if not identical. You would be wrong. It turns out that the microbes that live on your tongue are more likely to match those that live on another person’s tongue than those that live on your teeth.

This and other insights on the variability of the structural pattern and composition of the human oral microbiome are reported in the Genome Biology article, “Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity.”

Microbial ecologies impact our physiology from digestion to emotion. Yet, applying these insights using probiotics or clinical therapeutics is difficult due to our limited understanding of the biogeography, adaptation, and evolution of human bacterial populations in physiological and pathological conditions.

Identifying specific genes or gene sets that allow certain bacteria to adapt to a specific habitat could be the key to targeting probiotics, where an advanced understanding of the habitat requirements for specific bacterial species could allow scientists to target beneficial bacteria to specified habitats or remove harmful bacteria from their niches.

“As microbial ecologists, we are fascinated by how bacteria can seemingly divide up any habitat into various niches, but as humans ourselves, we also have this innate curiosity about how microbes pattern themselves within our bodies,” said lead author Daniel R. Utter, PhD candidate in the department of organismic and evolutionary biology, Harvard University.

One approach to studying bacterial populations is metagenomics—directly sequencing the total DNA obtained from an environmental sample. Without a need to grow bacteria, this approach offers a deep and accurate insight into microbial diversity but faces the limiting challenge of linking short sequence reads to a single organism without combining sequences from different microbial strains. Another approach that overcomes this limitation is pangenomics. This involves sequencing the sum of all genes found in a set of related bacteria.

This study combines pangenomic and metagenomic approaches (metapangenomics) to study the diversity of microbes in the inner cheek, tongue, and teeth, and gain a broader perspective into the adaptation of microbial populations to different habitats.

“The mouth is the perfect place to study microbial communities,” said co-author A. Murat Eren, PhD, assistant professor in the department of medicine at the University of Chicago. “Not only is it the beginning of the GI tract, but it’s also a very special and small environment that’s microbially diverse enough that we can really start to answer interesting questions about microbiomes and their evolution.”

The team used four species of bacteria commonly found in the mouth—Haemophilus parainfluenzae and three oral species of the genus Rothia—as references to investigate related species sampled in hundreds of volunteers’ mouths from the Human Microbiome Project.

“We used these genomes as a starting point, but quickly moved beyond them to probe the total genetic variation among the trillions of bacterial cells living in our mouths,” said Utter. “Because, at the end of the day, that’s what we’re curious about, not the arbitrary few that have been sequenced.

“We found a tremendous amount of variability,” said Utter. “But we were shocked by the patterning of that variability across the different parts of the mouth; specifically, between the tongue, cheek, and tooth surfaces.”

The authors reported that H. parainfluenzae genomes separate into three subgroups that are enriched differently in the three oral niches investigated. Microbial subgroups abundant in the tongue encoded the enzyme oxaloacetate decarboxylase. These observations indicate subgroups of a single species may prefer a specific oral habitat over others, and in some cases, a few genes can explain the choice of a specific bacteria’s habitat. The study also identified specific ways free-living oral bacteria differed from their lab-grown relatives.

“The resolution afforded by these techniques—via the direct comparison of genomes of ‘domesticated’ and ‘wild’ bacteria—allows us to dissect these differences gene by gene,” said Colleen Cavanaugh, PhD, professor of biology in the department of organismic and evolutionary biology, Harvard University. “We were also able to identify novel bacterial strains related to, but different than, those we have in culture.”

“The ability to identify specific genes behind habitat adaptation has been somewhat of a ‘holy grail’ in microbial ecology,” added Utter. “We are very excited for our contributions in this area!”