Researchers take a closer look at the genomes of microbial communities in the human mouth

The amazing, volatile bacteria that live in your mouth

Micrograph showing Rothia cells (light blue) in their native habitat, a bacterial biofilm scraped from the human tongue. Credit: Jessica Mark Welch, Marine Biology Laboratory.

Bacteria often show a strong biochemistry – some bacteria are abundant in certain places while away from others – leading to big questions when adding microbiology to medicine or probiotics : how did the bacteria get into the wrong place? How do we put the right bacteria in the right place when biochemistry has escaped whack?

However, there is one major obstacle to these questions, bacteria are so tiny and numerous with very diverse and complex numbers that pose significant challenges in understanding which subgroups of bacteria that live where and what genes or metabolic capabilities allow them to thrive in these ‘wrong’ places. .

In a new study published in Genome Biology researchers led by Harvard University studied human microorganisms and found an impressive variation in bacterial subunits living in specific areas of the mouth.

“As microbial ecologists, we are fascinated by how bacteria can divide any habitat into different areas, but as humans ourselves, we also have this innate curiosity about how microbes become patterning themselves within our bodies, ”said lead author Daniel R. Utter, Ph.D. candidate in the Department of Organic Biology and Evolution, Harvard University.

Recent developments in prescribing and bioinformatic methods have offered new ways to solve the complexity of bacterial communities. Utter and Colleen Cavanaugh, Edward C. Jeffrey Professor of Biology in the Department of Organic and Evolutionary Biology, Harvard University, joined researchers at a marine biology laboratory, Woods Hole, University of Chicago , and the Forsyth Institute to apply these states- modern ordering and monitoring methods to get a better picture of the oral midge.

“The mouth is the perfect place to study microbial communities,” says co-author A. Murat Eren, an assistant professor in the Department of Medicine at the University of Chicago. “Not only is it the beginning of the GI pathway, but it is also a very unique and small microbially diverse environment that we can begin to answer interesting questions about microbiomes and how they grow. “

In the mouth there are an incredible amount of site-specific microbes in various areas. For example, the microbes found on the tongue are very different from the microbes found on the plug on teeth. “Your tongue microbes are more like the ones that live on someone else’s tongue than they are the ones that live in your throat or on your gums!” said Eren.

The team scrapped public databases and downloaded 100 genomes representing four species of bacteria commonly found in the mouth, Haemophilus parainfluenzae and the three oral species of the genus Rothia, and used them as references to study their relatives sampled in the mouths of hundreds of volunteers from the Human Microbiome Project (HMP).

“We used these genomes as a starting point, but we quickly moved past them to study the overall genetic difference among the trillions of bacterial cells that live in our mouth,” Utter said. “Because, at the end of the day, that’s what we’re curious about, not the little irregularities that were ordered.”

Using this recently developed approach called metapangenomics, which combines pangenomes (the sum of each gene found in a set of related bacteria) with metagenomics (a study of the total DNA originating from all bacteria in a community), the researchers allowed the in – depth study of the genomes of microbes that led to a horrific discovery.

“We got a huge amount of variability,” Utter said. “But it surprised us with the patterning of that variability across different parts of the mouth; in particular, between the tongue, the cheek, and the surface of teeth.”

For example, within one microbe species the researchers found specific genetic forms that had a strong association with one different site in the mouth. In many cases, the team was able to identify a handful of genes that may explain the specific habitat of a bacterial group. By applying metapangenomics the researchers were able to identify specific ways in which bacteria lived in human mouths different from their laboratory-growing relatives.

The purpose of these techniques – by directly comparing genomes of “domestic” and “wild” bacteria – allows us to separate these differences by gene, “notes Cavanaugh.” We were also able to identify novel bacterial strains related to, but different from, those we have in culture. “

“Having identified some strong bacterial candidates that may justify adaptation to a particular habitat, we would like to test these hypotheses,” Cavanaugh said. These findings could be a key way to solve targeted probiotics, where scientists could use what they have learned about the habitat requirements of each microbe to inject beneficial microbes to land in a designated environment.

“The mouth is so easily accessible that humans have been working on bacteria from the mouth for a long time,” said co-author Jessica Mark Welch, associate scientist at a marine biology laboratory.

“In every environment we look at there are these complex complex communities of bacteria, but why is that?” said Mark Welch. “Understanding why these communities are so complex and how the different bacteria interact can help us understand how to repair a bacterial community that is damaging our communities. health, telling us which microbes need to be removed or replaced. “

This study and others like it can provide new insights into the role of oral microbes in human health. “The ability to identify specific genes behind habitat change has been largely a‘ sacred grave ’in microbial ecology,” Utter said. “We’re really excited about our contribution in this area!”

Microbes in dental plaque look more like relatives in soil than those on the tongue

Further information:
Daniel R. Utter et al. Metapangenomics of the oral microbiome provide insight into habitat change and cultivar diversity, Genome Biology (2020). DOI: 10.1186 / s13059-020-02200-2

Presented by Harvard University

Citation: Researchers take a closer look at the genomes of microphone communities in the human mouth (2020, December 19) retrieved December 19, 2020 from closer-genomes-microbial-human-mouth .html

This document is subject to copyright. Other than any fair treatment for the purpose of scrutiny or private investigation, no part may be reproduced without written permission. The content is provided for informational purposes only.