A data hub for the functional annotation and exploration of genomes from the human microbiome

• Applicant: Professor Rob Finn
• Subject Area: Bioinformatics and Theoretical Biology
• Term: since 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 564425905

The DFG Priority Program SPP 2474 seeks to explore the genomes of the human gut microbiome at unprecedented depth, utilising a range of molecular techniques to characterise functions at the levels of individual genes, functional complexes, whole genomes, and representative microbial communities. A key aspect of these experimental approaches is the generation of data that must be systematically collected and integrated, enabling the international scientific community to extract novel mechanistic insights into the gut microbiome’s role in human health and disease. However, a key challenge in data integration is the linking of different omics data types submitted to different biological databases, thereby allowing effective presentation of the data. Additionally, while investigations may focus on individual organisms or synthetic communities, it remains crucial to contextualise these findings within the broader, global diversity of the human gut microbiome to ensure comprehensive and meaningful interpretation. This Z-project focuses on resolving key data management issues through the following objectives: Data Submission and Integration – Facilitate the submission and integration of data into archival databases and develop approaches to provide integrated data visualisation. This will involve expanding the Gut-Microbes Data Hub to incorporate additional species, data types and facilitate interlinking of services. Expansion of the UHGG – Broaden the content of the Unified Human Gastrointestinal Genome (UHGG) by incorporating the latest metagenomic datasets, and genomes being produced from isolation efforts, thereby improving the representation of different prokaryotic species found in the human gut. Species Annotation and Contextualisation – Provide rich genome annotations for species investigated within the SPP 2474 research projects. This includes contextualising isolate genomes against the UHGG to determine pangenomes. Enhanced Functional Annotation – Leverage the latest bioinformatics tools, including those developed within the SPP, to improve the functional annotation of genes. Additionally, create interfaces that enable the acquisition of machine learning-ready datasets, enhancing data accessibility and usability. In summary, this project aims to streamline data management workflows, ensuring that insights derived from SPP 2474 research are effectively integrated and maximised for the broader scientific community.

• DFG Programme: Priority Programmes
• Subproject of: SPP 2474: Illuminating gene functions in the human gut microbiome
• International Connection: United Kingdom