Giant DNA chunks found inside bacteria in the oral microbiome of human saliva surprise scientists

Amazing stuff! I am scratching my head and wonder why this was never before investigated or discovered! Lack of technology/methods?

"... These ... 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 ... 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." ..."

"Researchers ... have made a surprising discovery hiding in people’s mouths: Inocles, giant DNA elements that had previously escaped detection. These appear to play a central role in helping bacteria adapt to the constantly changing environment of the mouth. The findings provide fresh insight into how oral bacteria colonize and persist in humans, with potential implications for health, disease and microbiome research. ...

“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,” ... “By exploring this, we discovered Inocles, an example of extrachromosomal DNA — chunks of DNA that exist in cells, in this case bacteria, but outside their main DNA. ..."

From the abstract:

"Survival strategy of bacteria is expanded by extrachromosomal elements (ECEs). However, their genetic diversity and functional roles for adaptability are largely unknown.

Here, we discover a novel family of intracellular ECEs using 56 saliva samples by developing an efficient microbial DNA extraction method coupled with long-read metagenomics assembly.

Even though this ECE family was not hitherto identified, our global prevalence analysis using 476 salivary metagenomic datasets elucidates that these ECEs reside in 74% of the population.

These ECEs, which we named, “Inocles”, are giant plasmid-like circular genomic elements of 395 kb in length, including Streptococcus as a host bacterium.

Inocles encode a series of genes that contribute to intracellular stress tolerance, such as oxidative stress and DNA damage, and cell wall biosynthesis and modification involved in the interactions with oral epithelial cells.

Moreover, Inocles exhibit significant positive correlations with immune cells and proteins responding to microbial infection in peripheral blood. Intriguingly, we examine and find their marked reductions among 68 patients of head and neck cancers and colorectal cancers, suggesting its potential usage for a novel biomarker of gastrointestinal cancers. Our results suggest that Inocles potentially boost the adaptive capacity of host bacteria against various stressors in the oral environment."

Huge DNA chunks found in human saliva surprise scientists

Giant DNA discovered hiding in your mouth Three-quarters of all people may host newly identified genetic material called Inocles, which could impact research on oral health, immunity, and even cancer risk (original news release)

Giant extrachromosomal element “Inocle” potentially expands the adaptive capacity of the human oral microbiome (open access)

Functional characterization of Inocle. A schematic describing what Inocles do and where they’re found. It shows the kinds of roles its genes might have, and how those jobs could be connected to things happening in the human body.

Fig. 3: Identification and characterizations of the four Inocle taxa.

Cancer May Be Driven by extrachromosomal DNA

Good news! Very recommendable! Cancer is history! Every day we learn more about this disease! This research could be a major breakthrough! Following long and well written article is actually authored by a subject matter expert and cancer researcher!

"... This work revealed the presence of [extrachromosomal DNA] ecDNA in almost every cancer type we looked at. We further found that ecDNA enabled cancers to change their genomes quickly, and even to move genes back onto chromosomes, but not in their original locations. ...

We first demonstrated that ecDNA is circular. These ecDNAs differ from the more common small extrachromosomal circular DNA particles (eccDNAs) that are found in the genomes of eukaryotes from yeast to flies to humans. For one, eccDNAs average only about 100–1,000 base pairs in length and are thus relatively unlikely to contain intact genes or other functional elements, while ecDNAs are relatively large, averaging around 1.3 million base pairs. ecDNAs are chock-full of growth-promoting oncogenes, and they contain other genes and regulatory regions that may be involved in tumor formation and progression. 

Moreover, unlike other types of small circular DNAs such as eccDNAs and ribosomal DNAs that can be found in normal cells at low levels, ecDNAs are unique to cancer, and they are highly amplified. ..."

Cancer May Be Driven by DNA Outside of Chromsomes | The Scientist Magazine® In the last decade, researchers have come to realize that tumors harbor bits of extrachromosomal DNA that can drive malignancy.