New research shows that gut bacteria and metabolites may reveal early warning signs of multiple gastrointestinal diseases.
Scientists have uncovered biological signals in the gut that may make it easier to spot and manage several gastrointestinal diseases (GIDs), including gastric cancer (GC), colorectal cancer (CRC), and inflammatory bowel disease (IBD).
The potential biomarkers come from two sources: the microbiome, meaning the community of bacteria living in the digestive tract, and the metabolome, meaning the small molecules produced as the body and microbes break down food and carry out chemical reactions.
In the study, certain bacteria and metabolites consistently appeared alongside each condition. That pattern matters because biomarkers like these could eventually support earlier detection using approaches that are less invasive than many current tests. Some signals also showed up across more than one disease, hinting that different GIDs may share underlying biological changes.
To find those patterns, the researchers used machine learning methods and AI-based algorithms to examine microbiome and metabolome datasets from patients with GC, CRC, and IBD.
When they compared diseases directly, they found that models trained on GC data were able to identify biomarkers linked to IBD, and models built from CRC data could predict GC biomarkers with high accuracy. In other words, information learned from one condition helped reveal markers in another, which could be useful for developing tools that work across multiple gastrointestinal illnesses.
The research was led by a team from the University of Birmingham Dubai (Part of Health Data Science MSc Programme), the University of Birmingham, Birmingham, UK, and University Hospitals Birmingham NHS Foundation Trust, and the results were published in the Journal of Translational Medicine.
Toward Earlier and Less Invasive Diagnosis
Lead co-author Dr Animesh Acharjee, from the University of Birmingham, commented: “Current diagnostic methods like endoscopy and biopsies are effective but can be invasive, expensive, and sometimes miss diseases at early stages.
“Our analysis offers a better understanding of the underlying mechanisms driving disease progression and identifies key biomarkers for targeted therapies. These biomarkers could help identify diseases earlier and more accurately, leading to better, more personalised treatment.”
The study reveals that, for example, in GC bacteria from the Firmicutes, Bacteroidetes, and Actinobacteria groups were common, and changes in certain metabolites like dihydrouracil and taurine were noted. Some of these biomarkers were also relevant for IBD, suggesting overlap between the diseases but, while these markers worked well for detecting IBD, they were less effective for CRC.
For CRC, bacteria such as Fusobacterium and Enterococcus, and metabolites like isoleucine and nicotinamide, were significant – sometimes overlapping with those for GC, indicating possible shared pathways in disease development.
In IBD, bacteria from the Lachnospiraceae family and metabolites like urobilin and glycerate were important, with some of these markers also involved in cancer pathways, showing how these diseases are interconnected.
Simulating Disease-Related Metabolic Changes
The research team simulated gut microbial growth and metabolite fluxes, revealing significant metabolic differences between healthy and diseased states.
“Our study’s cross-disease analysis emphasized the potential of using microbial and metabolic biomarkers identified in one GID to predict another,” added Dr Acharjee. “This innovative approach could lead to the development of universal diagnostic tools to revolutionize the diagnosis and treatment of for multiple gastrointestinal conditions.”
The research team now plans to further explore the clinical applications of their findings, including the development of non-invasive diagnostic tests and targeted therapies based on the identified biomarkers. They also aim to validate their models in larger, diverse patient cohorts and investigate these biomarkers’ potential in predicting other related diseases.
Reference: “Deciphering microbial and metabolic influences in gastrointestinal diseases-unveiling their roles in gastric cancer, colorectal cancer, and inflammatory bowel disease” by Daryll Philip, Rebecca Hodgkiss, Swarnima Kollampallath Radhakrishnan, Akshat Sinha and Animesh Acharjee, 16 May 2025, Journal of Translational Medicine.
DOI: 10.1186/s12967-025-06552-w
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