There is usually one bit of genomic DNA in a bacterial cell that encodes for most of its functions, but bacteria can carry other bits of genetic material like plasmids, which could carry a gene for drug-resistance, for example. Scientists have identified other so-called extrachromosomal elements in bacteria as well, such as ‘Borgs’ and now, ‘Inocles.’
Reporting in Nature Communications, researchers were investigating the community of microbes in the human mouth, or the oral microbiome. This work revealed giant DNA elements the researchers called Inocles in Streptococcus salivarius bacteria. The study suggested that Inocles have a close connection to how bacteria adapt to conditions in the mouth, which are constantly changing.
“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 first study author Yuya Kiguchi, a Project Research Associate at the University of Tokyo.
In this work, the researchers analyzed a huge group of saliva samples collected from volunteers. They applied sophisticated genetic sequencing techniques to these samples to reveal Inocles; since these genetic elements are large, they have to be detected with special sequencing methods that maintain long stretches of DNA, instead of chopping them into bits like some conventional sequencing methods.
The tool was also used with preNuc, a technique that can remove the human DNA from saliva samples so that the focus is on the microbial DNA. It also helps the investigators apply long-read sequencing.
“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. Plasmids, other forms of extrachromosomal DNA, are at most a few tens of kilobase pairs,” noted Kiguchi.
The long length of Inocles allows them to potentially carry various genes. Some might encode for resistance to oxidative stress; others may be for DNA damage repair; functions in the cell wall; or aiding in adaptation, added Kiguchi.
The researchers want to create ways to grow bacteria that host Inocles, to learn more about how they might function, transmit from one cell to another, or affect human health. Many of the genes that are found on Inocles are still mysteries.
“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. And even though the oral microbiome has long been studied, Inocles remained hidden all this time because of technological limitations,” said Kiguchi. “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.”
Sources: University of Tokyo, Nature Communications