Lissin, A. | bioRxiv Science

bioRxiv2026

The StrainDiscoveryDatabase: an open framework for standardized microbial strain data

The vast amount of existing data on microbial strains holds immense potential to revolutionize bioindustry through the application of Artificial Intelligence (AI). However, the training of robust predictive AI models requires large-scale, unified, and non-redundant microbial datasets, which is currently severely hindered by the deep fragmentation of the data and the existence of synonymous strain identifiers in different culture collections. To overcome these infrastructural bottlenecks, we have established the StrainDiscoveryDatabase (SDD), a comprehensive, machine-readable dataset encompassing over 6.2 million harmonized data points for 256,889 microbial strains. The SDD does not rely on its own data repository, but rather on existing data that is retrieved on the fly from highly curated databases. Through an automated pipeline phenotypic, genotypic, and contextual data are systematically retrieved via the Application Programming Interfaces (APIs) of the Bacterial Diversity database (BacDive), the Microbial Resource Research Infrastructure Information System (MIRRI-IS) and the catalogue of the DSMZ. In order to reliably resolve synonymous strain identifiers, the StrainInfo database and its identification tools are employed, enabling the accurate deduplication and unification of records from disparate sources. The resulting aggregated, globally unique dataset is provided in a highly standardized JSON format in strict adherence to the FAIR data principles. By bridging isolated database silos and linking distributed knowledge to discrete biological entities, the SDD provides a high-quality, foundational resource designed to accelerate trait-based strain discovery, large-scale comparative analysis, and machine learning applications, thereby supporting the translation of the extensive existing knowledge on microbial traits to bioindustrial applications.

microbiology↗

bioRxiv2024

Broad diversity of human gut bacteria accessible via a traceable strain deposition system

Numerous bacteria in the human gut microbiome remain unknown and/or have yet to be cultured. While collections of human gut bacteria have been published, few strains have been made publicly available. A major hurdle in making strains publicly available is their deposition to public culture collections. We propose a framework for the bulk-deposition of strains to culture collections, which removes many of the barriers previously identified (www.dsmz.de/bulk-deposit). Using this bulk-deposition system we have created a publicly available collection of human gut isolates. The Human intestinal Bacteria Collection (HiBC) (www.hibc.rwth-aachen.de) contains 340 strains representing 198 species within 29 families and 7 phyla, of which 29 previously unknown species are taxonomically described and named. These included two butyrate-producing species of Faecalibacterium and new dominant species associated with health and inflammatory bowel disease, Ruminococcoides intestinale and Blautia intestinihominis, respectively. Plasmids were prolific within the HiBC isolates, with almost half (46%) of strains containing plasmids, with a maximum of six within a strain. This included a broadly occurring plasmid (pBAC) that exists in three diverse forms across Bacteroidales species. Megaplasmids were identified within two strains, the pMMCAT megaplasmid is globally present within multiple Bacteroidales species. This collection of easily searchable and publicly available gut bacterial isolates will facilitate functional studies of the gut microbiome.

microbiology↗