{"id":8434,"date":"2025-09-11T00:31:10","date_gmt":"2025-09-11T00:31:10","guid":{"rendered":"https:\/\/www.newsbeep.com\/il\/8434\/"},"modified":"2025-09-11T00:31:10","modified_gmt":"2025-09-11T00:31:10","slug":"giant-dna-discovered-hiding-in-your-mouth","status":"publish","type":"post","link":"https:\/\/www.newsbeep.com\/il\/8434\/","title":{"rendered":"Giant DNA discovered hiding in your mouth"},"content":{"rendered":"

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\"Functional<\/p>\n

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image:\u00a0<\/p>\n

A schematic describing what Inocles do and where they\u2019re 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.<\/p>\n

view more\u00a0<\/a><\/p>\n

Credit: \u00a92025 Kiguchi et al. CC-BY-ND<\/p>\n

Researchers including those at the University of Tokyo have made a surprising discovery hiding in people\u2019s 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.<\/p>\n

You might think that modern medical science knows everything there is to know about the human body. But even within the last decade, small, previously unknown organs have been discovered, and there\u2019s one area of human biology that is currently going through a research renaissance, the microbiome. This includes familiar areas such as the gut microbiome, but also the oral microbiome. Inspired in part by recent discoveries of extraneous DNA in the microbiome of soil, Project Research Associate Yuya Kiguchi and his team turned their sights to a large set of saliva samples collected by the Yutaka Suzuki Lab of the Graduate School of Frontier Sciences at the University of Tokyo. They wondered if they might find something similar in human saliva.<\/p>\n

\u201cWe 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,\u201d said Kiguchi. \u201cBy exploring this, we discovered Inocles, an example of extrachromosomal DNA \u2014 chunks of DNA that exist in cells, in this case bacteria, but outside their main DNA. It\u2019s like finding a book with extra footnotes stapled to it, and we\u2019re just starting to read them to find out what they do.\u201d<\/p>\n

Detecting Inocles was not easy, as conventional sequencing methods fragment genetic data, making it impossible to reconstruct large elements. To overcome this, the team applied advanced long-read sequencing techniques, which can capture much longer stretches of DNA. A key breakthrough came from co-first author Nagisa Hamamoto, who developed a method called preNuc to selectively remove human DNA from saliva samples, greatly improving the quality of sequencing long sections of other DNA. This allowed the researchers to assemble for the first time complete Inocle genomes, which turned out were hosted by the bacteria Streptococcus salivarius, though identifying the host itself was a difficult matter.<\/p>\n

\u201cThe 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,\u201d said Kiguchi. \u201cThis 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.\u201d<\/p>\n

The team aims to develop stable methods for culturing Inocle containing bacteria. This will allow them to investigate how Inocles function, whether they can spread between individuals, and how they might influence oral health conditions such as cavities and gum disease. Since many Inocle genes remain uncharacterized, researchers will use a mixture of laboratory experiments and also computational simulations such as AlphaFold to predict and model the roles Inocles may play.<\/p>\n

\u201cWhat\u2019s 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,\u201d said Kiguchi. \u201cNow 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\u2019s even some hints that Inocles might serve as markers for serious diseases like cancer.\u201d<\/p>\n

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Journal: Yuya Kiguchi, Nagisa Hamamoto, Yukie Kashima, Lucky R. Runtuwene, Aya Ishizaka,<\/p>\n

Yuta Kuze, Tomohiro Enokida, Nobukazu Tanaka, Makoto Tahara, Shun-Ichiro Kageyama, Takao Fujisawa, Riu Yamashita, Akinori Kanai, Josef S. B. Tuda, Taketoshi Mizutani, Yutaka Suzuki, \u201cGiant extrachromosomal element \u201cInocle\u201d potentially expands the adaptive capacity of the human oral microbiome\u201d, Nature Communications, https:\/\/doi.org\/10.1038\/s41467-025-62406-5<\/a><\/p>\n

Funding: This study was supported by grants from the Institute for Fermentation, Osaka (Y-2022-1-010), the Japan Agency for Medical Research and Development (AMED) (22fk0108538s0201), and the JSPS KAKENHI (24K18092) to Y.Kiguchi, a grant from the JSPS KAKENHI (22K15833) to T.E., and a grant from the Platform for Advanced Genome Science (22H04925) to Y.S.<\/p>\n

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Useful links:<\/p>\n

Graduate School of Frontier Sciences<\/p>\n

https:\/\/www.k.u-tokyo.ac.jp\/en\/<\/a><\/p>\n

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Department of Computational Biology and Medical Sciences<\/p>\n

https:\/\/www.cbms.k.u-tokyo.ac.jp\/en\/<\/a><\/p>\n

Research Contact:<\/p>\n

Project Research Associate Yuya Kiguchi<\/p>\n

Graduate School of Frontier Sciences, The University of Tokyo,<\/p>\n

5-1-5, Kashiwa-no-ha, Kashiwa City, Chiba 277-8561, JAPAN
yuya.kiguchi@edu.k.u-tokyo.ac.jp<\/a><\/p>\n

Press contact:
Mr. Rohan Mehra
Public Relations Group, The University of Tokyo,
7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
press-releases.adm@gs.mail.u-tokyo.ac.jp<\/a>
\u00a0<\/p>\n

About The University of Tokyo:<\/p>\n

The University of Tokyo is Japan’s leading university and one of the world’s top research universities. The vast research output of some 6,000 researchers is published in the world’s top journals across the arts and sciences. Our vibrant student body of around 15,000 undergraduate and 15,000 graduate students includes over 5,000 international students. Find out more at www.u-tokyo.ac.jp\/en\/ or follow us on X (formerly Twitter) at @UTokyo_News_en.<\/p>\n

Journal<\/p>\n

Nature Communications<\/p>\n

Method of Research<\/p>\n

Experimental study<\/p>\n

Subject of Research<\/p>\n

Human tissue samples<\/p>\n

Article Title<\/p>\n

Giant extrachromosomal element \u201cInocle\u201d potentially expands the adaptive capacity of the human oral microbiome<\/p>\n

Article Publication Date<\/p>\n

11-Aug-2025<\/p>\n","protected":false},"excerpt":{"rendered":"image:\u00a0 A schematic describing what Inocles do and where they\u2019re found. It shows the kinds of roles its…\n","protected":false},"author":2,"featured_media":8435,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[25],"tags":[377,85,46,141],"class_list":["post-8434","post","type-post","status-publish","format-standard","has-post-thumbnail","category-genetics","tag-genetics","tag-il","tag-israel","tag-science"],"_links":{"self":[{"href":"https:\/\/www.newsbeep.com\/il\/wp-json\/wp\/v2\/posts\/8434","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.newsbeep.com\/il\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.newsbeep.com\/il\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/il\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/il\/wp-json\/wp\/v2\/comments?post=8434"}],"version-history":[{"count":0,"href":"https:\/\/www.newsbeep.com\/il\/wp-json\/wp\/v2\/posts\/8434\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/il\/wp-json\/wp\/v2\/media\/8435"}],"wp:attachment":[{"href":"https:\/\/www.newsbeep.com\/il\/wp-json\/wp\/v2\/media?parent=8434"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.newsbeep.com\/il\/wp-json\/wp\/v2\/categories?post=8434"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.newsbeep.com\/il\/wp-json\/wp\/v2\/tags?post=8434"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}