Researchers at University of Galway have created the world’s largest collection of digital microbes - nearly a quarter million computer models - to help revolutionise our understanding of the human microbiome and its impact on health.
This study focuses on the bacterial microbiome - the communities of bacteria living in and on our bodies.
The team created APOLLO, a collection of 247,092 advanced computer models, each representing the unique metabolic processes of a distinct microbe found within these communities.
The unprecedented database will allow scientists to use software to study how microbes function within the human body and interact with health and disease, to accelerate new health discoveries, which would otherwise solely rely on cumbersome experiments using living organisms.
Human microbiome
Spanning multiple continents, age groups and body sites, APOLLO is the most extensive computational model collection of the human microbiome created to date.
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The research project builds upon the team’s decade-long expertise, from earlier AGORA (hundreds of microbes) and AGORA2 (thousands of microbes) generations.
The team also created 14,451 computer simulations of individual microbiome communities, based on real-life samples, to reveal how microbial metabolism varies by body site, age, and health conditions. The APOLLO simulations also predicted key faecal metabolites linked to Crohn’s disease, Parkinson’s disease, and child undernutrition – insights that could help shape future diagnostic and treatment strategies.
Precision health
The work was conducted by a team of scientists at University of Galway’s Digital Metabolic Twin Centre, led by Professor Ines Thiele, a principal investigator with APC Microbiome Ireland - Research Ireland centre for the study of microbiological community, hosted by University College Cork.
Professor Thiele’s research team uses computational modelling to advance precision health.
How APOLLO will benefit society:
- Improved diagnostics - by identifying microbial metabolic markers, APOLLO could help develop non-invasive diagnostic tools, allowing earlier and more accurate diagnosis.
- Personalised treatments - simulations can predict how an individual’s microbiome interacts with their diet, medications, and health conditions. This could lead to tailored treatments that optimise gut health and improve responses to therapies.
- Drug development and probiotics - it may be possible to design targeted probiotics, prebiotics, and microbiome-based therapies to treat specific diseases more effectively.
- Public Health insights - by including diverse microbiomes, APOLLO provides a global perspective, helping address how modern lifestyles impact microbiome health. This knowledge shall guide public health policies, such as around antibiotic use, diet, and disease prevention.
Dr Cyrille Thinnes, project scientist, said: “APOLLO marks a major milestone in personalised microbiome modelling on a global scale. Our microbiome plays crucial roles in digestion, immune function, and overall health. Studying these microbes is essential for understanding how they influence various conditions, from gut health to neurological diseases, and for developing new diagnostic tools, treatments, and personalise healthcare solutions.
“APOLLO captures an unprecedented diversity of microbes across continents, demographics and body sites, filling critical gaps in global health research. It addresses pressing concerns about the impact of westernised lifestyles, characterised by sedentary habits, processed diets and antibiotic overuse, on microbial diversity and functions. By including understudied non-westernised populations and body sites beyond the gut, APOLLO provides a vital resource for advancing microbiome research and its applications.”
Vital player in health
Professor Ines Thiele, study lead on the project, said: “The human microbiome is a vital player in health and disease, dynamically interacting with its host. Understanding these complex interactions requires cutting-edge technology. Our research integrates digital models of both microbes and humans, enabling us to explore the microbiome’s role in health in unprecedented detail.
“APOLLO takes this innovation further by incorporating microbiome communities on a dimension to now enable personalisation on a global scale.
“Over the past decade, we have gone from a single generic human model to detailed models that account for sex, physiology, and individual organs. Similarly, we started with models of a few microbes and have now expanded to cover hundreds of thousands. These models can further incorporate information on dietary habits and health conditions, helping to generate testable hypotheses and personalised health recommendations. APOLLO represents a major step in the shift towards digital twin-enabled precision healthcare, moving us closer to tailoring health solutions for individuals worldwide.”
The research was published in Cell Systems and is available at https://www.cell.com/cell-systems/fulltext/S2405-4712(25)00029-8
This work was led by University of Galway in collaboration with colleagues in Ireland, France, and Italy, at University College Cork, University College Dublin, APC Microbiome Ireland, University of Lorraine, and University of Padova.
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