(Press-News.org)
Gut bacteria are known to be a key factor in many health-related concerns. However, the number and variety of them is vast, as are the ways in which they interact with the body’s chemistry and each other. For the first time, researchers from the University of Tokyo used a special kind of artificial intelligence called a Bayesian neural network to probe a dataset on gut bacteria in order to find relationships that current analytical tools could not reliably identify.
The human body comprises about 30 trillion to 40 trillion cells, but your intestines contain about 100 trillion gut bacteria. Technically, you’re carrying around more cells that aren’t you than are. Food for thought. And speaking of food, these gut bacteria are of course responsible for some aspects of digestion, though what’s surprising to some is how they can relate to many other aspects of human health as well. The bacteria are incredibly varied and also produce and modify a bewildering number of different chemicals called metabolites. These act like molecular messengers, permeating your body, affecting everything from your immune system and metabolism to your brain function and mood. Needless to say, there’s much to gain by understanding gut bacteria.
“The problem is that we’re only beginning to understand which bacteria produce which human metabolites and how these relationships change in different diseases,” said Project Researcher Tung Dang from the Tsunoda lab in the Department of Biological Sciences. “By accurately mapping these bacteria-chemical relationships, we could potentially develop personalized treatments. Imagine being able to grow a specific bacterium to produce beneficial human metabolites or designing targeted therapies that modify these metabolites to treat diseases.”
This sounds good, so what’s the problem? As mentioned, there are uncountably many and varied bacteria and metabolites, and therefore far more relationships between these things. Gathering data on this alone is a monumental undertaking but unpicking that data to find interesting patterns that might betray some useful function is even more so. To do this, Dang and his team decided to explore the use of state-of-the art artificial intelligence (AI) tools.
“Our system, VBayesMM, automatically distinguishes the key players that significantly influence metabolites from the vast background of less relevant microbes, while also acknowledging uncertainty about the predicted relationships, rather than providing overconfident but potentially wrong answers,” said Dang. “When tested on real data from sleep disorder, obesity and cancer studies, our approach consistently outperformed existing methods and identified specific bacterial families that align with known biological processes, giving confidence that it discovers real biological relationships rather than meaningless statistical patterns.”
As VBayesMM can handle and communicate issues of uncertainty, it gives researchers more confidence than a tool which does not. Even though the system is optimized to cope with heavy analytical workloads, mining such huge datasets still comes with high computational cost; however, as time goes on, this will become less and less of a barrier to those wishing to use it. Other limitations at present include that the system benefits from having more data about the gut bacteria than the metabolites they produce; when there’s insufficient bacteria data, the accuracy drops. Also, VBayesMM assumes the microbes act independently, but in reality, gut bacteria interact in an incredibly complex number of ways.
“We plan to work with more comprehensive chemical datasets that capture the complete range of bacterial products, though this creates new challenges in determining whether chemicals come from bacteria, the human body or external sources like diet,” said Dang. “We also aim to make VBayesMM more robust when analyzing diverse patient populations, incorporating bacterial ‘family tree’ relationships to make better predictions, and further reducing the computational time needed for analysis. For clinical applications, the ultimate goal is identifying specific bacterial targets for treatments or dietary interventions that could actually help patients, moving from basic research toward practical medical applications.”
###
Journal: Tung Dang, Artem Lysenko, Keith A. Boroevich and Tatsuhiko Tsunoda, “VBayesMM: Variational Bayesian neural network to prioritize important relationships of high-dimensional microbiome multiomics data”, Briefings in Bioinformatics, DOI: 10.1093/bib/bbaf300
Funding: This work was partly supported by JSPS KAKENHI Grant Numbers JP20H03240 and JP24K15175, and JST CREST Grant Number JPMJCR2231.
Useful links:
Graduate School of Science - https://www.s.u-tokyo.ac.jp/en/
Tsunoda Lab - https://mesm.bs.s.u-tokyo.ac.jp/index_Eng.html
Research Contacts:
Professor Tatsuhiko Tsunoda
Department of Biological Sciences, The University of Tokyo,
7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, JAPAN
tsunoda@bs.s.u-tokyo.ac.jp
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
About The University of Tokyo:
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.
END
The peer-reviewed study, The Earth4All Scenarios: Human Wellbeing on a Finite Planet Towards 2100, uses a system dynamics-based modelling approach to explore two future scenarios: Too Little Too Late, and the Giant Leap. The model presented in the paper provides the scientific basis for the analysis and policy recommendations of Earth for All: A Survival Guide for Humanity, published in 2022.
The model’s findings show that under our current ‘business as usual’ conditions – the Too Little Too Late scenario – ...
Villages, often separated from larger towns and cities, consist of clusters of households and a few public buildings. Despite their long history, the biodiversity of European villages has been understudied compared to urban areas, forests, grasslands, or agricultural fields. A new study reveals their biodiversity potential and how nearby landscapes influence biodiversity patterns and human well-being.
This research was led by an international team from the HUN-REN Centre for Ecological Research with 20 other institutes contributing from Hungary, Romania, Germany, and Italy. Published in Nature Sustainability, ...
As hydrogen infrastructure is rolled out in the EU, refuelling stations must be distributed according to the same principle in all countries. But now a study from Chalmers University of Technology in Sweden points to shortcomings in EU regulations. Using an advanced model, the researchers show that the distribution of refuelling stations may both be incorrectly dimensioned and lead to losses of tens of millions of euros a year in some countries.
By 2030, EU countries must have built hydrogen refuelling stations at least every ...
Children born by planned C-section have an increased risk of developing acute lymphoblastic leukaemia (ALL) later in life. This is shown by a study conducted by researchers at Karolinska Institutet. The researchers emphasise that the risk remains low.
The study, published in The International Journal of Cancer, covers nearly 2.5 million children born in Sweden during two periods, 1982 to 1989 and 1999 to 2015. Of these, 15.5 per cent were born by C-section, i.e. nearly 376,000 children. In the entire group, 1,495 children later developed leukaemia.
Using the Medical Birth Register, the ...
People who have survived cancer as children are at higher risk of developing severe COVID-19, even decades after their diagnosis. This is shown by a new study from Karolinska Institutet published in the journal The Lancet Regional Health – Europe.
Thanks to medical advances, more and more children are surviving cancer. However, even long after treatment has ended, health risks may remain. In a new registry study, researchers investigated how adult childhood cancer survivors in Sweden and Denmark were affected by the COVID-19 pandemic.
The ...
New research has revealed alarming coral mortality rates of 92 per cent after last year’s bleaching event at Lizard Island on Queensland’s Great Barrier Reef, marking one of the highest coral mortality rates ever documented globally.
The team assessed the impact of the Fourth Global Coral Bleaching Event, declared by the National Oceanic and Atmospheric Administration (NOAA) in April 2024, which caused extensive bleaching and mortality across the reef system.
Lead author Dr Vincent Raoult from Griffith University’s School of Environment, ...
Researchers at Zhejiang University School of Medicine have identified a single point mutation in the normal PML gene that can block the effect of arsenic trioxide, a frontline drug for acute promyelocytic leukemia. This discovery uncovers a hidden cause of treatment failure and suggests a new target for genetic screening in relapsed patients. This work addresses the urgent issue of why some patients relapse despite a therapy that otherwise greatly improves survival.
Mutation Explains Why a Small Portion of Leukemia Patients Relapse on Arsenic Therapy
Arsenic trioxide cures most acute promyelocytic leukemia patients, but some patients relapse without an ...
The future of smashed avocado might depend on patches of native vegetation preserved alongside farmland, as new Curtin research reveals the hidden role of these habitats in supporting the insects that keep crops - and brunch menus - thriving.
The research, published this week, found that insect communities in avocado orchards adjacent to native remnant vegetation foraged on more than twice as many plant species at times when crop flowering was limited, compared to those in orchards bordered by pasture.
Insects with more diverse food sources are more likely to survive and pollinate crops so this finding offers a potential clue to safeguarding ...
University of Sydney researchers have harnessed human-made lightning to develop a more efficient method of generating ammonia – one of the world’s most important chemicals. Ammonia is also the main ingredient of fertilisers that account for almost half of all global food production.
The team have successfully developed a more straightforward method to produce ammonia (NH3) in gas form. Previous efforts by other laboratories produced ammonia in a solution (ammonium, NH4+), which requires more energy and processes to transform it into the final gas product.
The current method to generate ammonia, the Haber-Bosch process, comes at great ...
Some of the most encouraging results for reaction-enhancing catalysts come from one material in particular: tin (Sn). While Sn's overall utility as a catalyst is well-known, its underlying structure-performance relationship is poorly understood, which limits our ability to maximize its potential. To address this knowledge gap, researchers at Tohoku University's Advanced Institute for Materials Research (WPI-AIMR) used machine learning to characterize Sn catalyst activity. The highly accurate simulations could be a game-changer that helps researchers swiftly and simply ...
