Project started

Coordinated by Prof. Jan Baumbach, Institute for Computational Systems Biology, Universität Hamburg (DE).
Start: 01 April 2023 - Duration: 5 years - Total EU funding: approximately € 6 million.

What is Microb-AI-ome ?

Identifying colorectal cancer (CRC) early enables better treatment options. Screening usually entails a quantitative faecal immunological test (FIT) to predict the need for colonoscopy for the detection of colorectal lesions, an expensive and invasive procedure. Microb-AI-ome aims to predict this need with specificity increased by >20 percentage points by using metagenomic microbiomes. We hypothesise that computational microbiome profiles extracted using artificial intelligence (Al) technology will allow for optimised personal therapy stratification. However, currently, clinicians do not have access to broad microbiome data. Microb-AI-ome’s aim is to develop a novel kind of computational stratification technology to enable microbiome-enhanced precision medicine of CRC.


Why do we need a federated microbiome database?

Metagenomic microbiome data to date is distributed over many national registries, and privacy regulations are hindering its effective integration. With microb-AI-ome, we will overcome this barrier by establishing the first privacy-preserving federated big data network in CRC research. We will integrate isolated, national databases, into one international federated database network - rather than a cloud - covering metagenomes for over 5,000 individuals screened for CRC, and an expected total of 100,000 by 2026. Microb-AI-ome ensures that no sensitive patient data will leave the safe harbours of the local databases while still allowing for the classification of clinical CRC phenotypes, which we will demonstrate in clinical practice allowing regulatory bodies to adopt evidence-based guidelines.


How is the Microb-AI-ome project built?

The Microb-AI-ome research is grouped into six core Work Packages (WP): Creation of a federated database network for international colorectal cancer data (WP1) and Application and validation of federated AI models (WP4), both lead by the coordinators in the University of Hamburg in Germany; Data collection and management (WP2), lead by the Master Misericoridae University Hospital in Ireland; a Federated artificial intelligence models and patient stratification apps work package (WP3) lead by the National Research Institute for Agriculture, Food and the Environment in France; Evidence-based guidelines (WP5) lead by Public Assistance - Paris Hospital in France; and finally a Legal and ethical assessment work package (WP6) lead by the Research Institute AG & CO KG in Austria.

In addition, the University College of Cork (Ireland) as worldwide recognized experts in human gut microbial analysis, will generate the shotgun metagenomic sequencing data, and help explore the performance of the CRC stratifier and will provide access to additional gut microbial samples and associated clinical data. The company Genome Design SRL (Romania), will be responsible for the system architecture and software development of the platform and app store (WP8). Finally, tp21 GmbH (Germany) will be aiding the coordinators in management, as well as will be taking over the dissemination and communication (WP7) of results.

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