Navigating the global ocean microbiome through a web-based genome collection
Zurich Seminars in Bioinformatics - Samuel Miravet Verde (Sunagawa Lab ETHZ)
- 12:15 UZH Irchel Y55-l-06/08 and ZOOM Call
High-throughput sequencing has empowered researchers to profile taxonomic, genomic, and functional compositions of ocean microbiomes through the reconstruction of metagenome-assembled genomes (MAGs) from environmental samples. As part of an environment that is marked by vast physicochemical gradients and immense phylogenetic and functional microbial diversity, the ocean microbiome offers ample opportunities to study the ecology and evolution of microbial communities as well as gene-encoded functions in the context of its natural environment. However, this information is currently scattered across the primary literature and sequence databases and/or difficult to access, hindering the systematic analysis of large-scale metagenomic datasets at global scale.
Here we introduce the Ocean Microbiomics Database (OMD), an evolving data repository designed for the exploration of ocean microbial diversity, biogeography, and gene-encoded functions from a genomic-resolved perspective. The OMD encompasses in its second version over 12,000 marine samples, more than 275,000 MAGs and 7,900 genomes from strains isolated from marine environments. Linked to these genomes, the OMD offers access to sample-associated metadata, quality metrics and derived resources, including catalogs of genes and biosynthetic gene clusters (BGCs). The database can be accessed and interactively explored through a web interface accessible at microbiomics.io, a fast and user-friendly web application facilitating efficient mining of the OMD.
Recent demonstrations have showcased the OMD's potential in guiding the discovery of novel taxa, enzymes and bioactive compounds. In conclusion, these resources harness recent advancements in computational biology and environmental genomics, with plans for updates in future, such as providing a genome-mining based alternative to large-scale biochemical screens in the field of marine microbial ecology.