Scientists at the University of Galway have created APOLLO, the largest-ever digital microbiome collection, with 247,092 models to revolutionize health research.
Researchers at the University of Galway have developed APOLLO, the world’s largest digital collection of microbial models, comprising 247,092 computer-generated representations of bacteria from the human microbiome. This groundbreaking resource aims to advance our understanding of how microbial communities influence health and disease.
Focusing on the bacterial microbiome—the diverse populations of bacteria that live in and on the human body—APOLLO provides detailed models of each microbe’s metabolic processes.
By enabling scientists to study microbial functions through computational simulations rather than relying solely on complex lab experiments, this database has the potential to accelerate medical discoveries and improve disease research.
Spanning multiple continents, age groups and body sites, APOLLO is the most extensive computational model collection of the human microbiome created to date.
The research project builds upon the team’s decade-long expertise, from earlier AGORA (hundreds of microbes) and AGORA2 (thousands of microbes) generations.
Simulating Real-World Microbiome Communities
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 fecal metabolites linked to Crohn’s disease, Parkinson’s disease, and child undernutrition – insights that could help shape future diagnostic and treatment strategies.
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 modeling 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.
- Personalized treatments – simulations can predict how an individual’s microbiome interacts with their diet, medications, and health conditions. This could lead to tailored treatments that optimize 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.
Expert Perspectives on APOLLO’s Significance
Dr Cyrille Thinnes, project scientist, said: “APOLLO marks a major milestone in personalized microbiome modeling 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 personalize 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 westernized lifestyles, characterized by sedentary habits, processed diets, and antibiotic overuse, on microbial diversity and functions. By including understudied non-westernized populations and body sites beyond the gut, APOLLO provides a vital resource for advancing microbiome research and its applications.”
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 personalization 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 personalized 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.”
Reference: “A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites” by Almut Heinken, Timothy Otto Hulshof, Bram Nap, Filippo Martinelli, Arianna Basile, Amy O’Brolchain, Neil Francis O’Sullivan, Celine Gallagher, Eimer Magee, Francesca McDonagh, Ian Lalor, Maeve Bergin, Phoebe Evans, Rachel Daly, Ronan Farrell, Rose Mary Delaney, Saoirse Hill, Saoirse Roisin McAuliffe, Trevor Kilgannon, Ronan M.T. Fleming, Cyrille C. Thinnes and Ines Thiele, 12 February 2025, Cell Systems.
DOI: 10.1016/j.cels.2025.101196
