While scientists are amassing a fair amount of data regarding our gut microbiomes, the oral microbiome is a bit of a new frontier. Case in point: researchers have just discovered huge pieces of DNA there that they never knew existed.
You likely already know that floating inside the nuclei of nearly every cell in the human body, strands of DNA twine around each other, acting as the blueprints that direct our existence. But what you may not have heard is that there are also chunks of DNA floating inside some cells that are not part of the double helix. These rogue genetic pieces are known as extrachromosomal DNA (ecDNA) and, while they can play a role in the development and growth of cancerous tumors, they can also help maintain our telomeres, protective caps at the ends of our chromosomes involved in the aging process.
Seeking to explore the possibility of ecDNA existing in human saliva, researchers at the University of Tokyo got a "big" surprise as they carried out a new study. Not only did they find ecDNA in the oral microbiome hidden inside bacteria known as Streptococcus salivarius, they found comparatively giant chunks of it. They named these chunks "Inocles."
"We know there are a lot of different kinds of bacteria in the oral microbiome, but many of their functions and means of carrying out those functions are still unknown," said lead study author, Yuya Kiguchi. "By exploring this, we discovered Inocles, an example of extrachromosomal DNA. It’s like finding a book with extra footnotes stapled to it, and we’re just starting to read them to find out what they do."
To spot the never-before seen genetic material, the researchers invented their own way of mapping the DNA found in the human saliva samples they used in the study. Instead of focusing on the fragmented genetic data that usually comes from such analysis, they created a way to capture much longer strands of DNA, which they termed preNuc. The method allowed them to spot the Inocles inside the oral bacteria.
"The average genome size of Inocle is 350 kilobase pairs, a measure of length for genetic sequences, so it is one of the largest extrachromosomal genetic elements in the human microbiome," said Kiguchi. "Plasmids, other forms of extrachromosomal DNA, are at most a few tens of kilobase pairs. This long length endows Inocles with genes for various functions, including resistance to oxidative stress, DNA damage repair and cell wall-related genes, possibly involved in adapting to extracellular stress response."
That being said, the researchers aren't entirely sure exactly what role the big blocks of ecDNA serve, and they plan to carry out additional work to examine them – especially the uncharacterized genes they contain. Their work may lead to an understanding of how Inocles influence overall oral health and how they may hinder or help the development of cavities and gum disease.
"What’s remarkable is that, given the range of the human population the saliva samples represent, we think 74% of all human beings may possess Inocles," concludes Kiguchi. "And even though the oral microbiome has long been studied, Inocles remained hidden all this time because of technological limitations.
"Now that we know they exist, we can begin to explore how they shape the relationship between humans, their resident microbes and our oral health. And there’s even some hints that Inocles might serve as markers for serious diseases like cancer.”
The study has been published in the journal Nature Communications.
Source: University of Tokyo
