An Integrated Multi-omics Platform for Marine Microbial Discovery and Ecosystem Analysis

NewAtlantis Labs (NAL) utilizes advanced science and meta-omics data processing to transform molecular insights into a comprehensive understanding of marine ecosystems, enabling us to assess their health and resilience while informing conservation strategies. Our innovative approach can also provide the foundation for the creation of new financial products, such as ecosystem service bonds and biodiversity credits, which can generate revenue to support local conservation efforts through a benefit-sharing model compliant with the Nagoya Protocol. To achieve this, NAL is building a scientific platform optimized for marine microbes, protists, and fungi that leverages a highly interoperable toolkit ecosystem with curated structured genomics databases. Our platform is designed not only as a resource for processing metagenomics and metatranscriptomics data, but also as a contextualized knowledge base for exploring specific research areas such as predictive ecological modeling, bioprospecting for natural products, pathogenicity screening, and examining links between environmental conditions and genes, metabolic pathways, and genomes of interest. Key components of our interoperable platform include: 1) VEBA, our open-source modular end-to-end multi-omics software suite; 2) Leviathan, our open-source taxonomic and functional profiling software; 3) the Metabolic Niche Space, our open-source framework for data-driven analysis of metabolic/ecological niches; 4) our genome-resolved NAL Genomics Database, which includes >70k well-curated bacterial, protist, and fungal genomes representing over 250M proteins; 5) Clairvoyance, our open source AutoML biomarker discovery algorithm; and 6) our marine biodiversity Knowledge Graph, which integrates and contextualizes outputs from our toolkits. To demonstrate the platform's utility, here we present a case study analyzing time-series multi-omics data collected during an algal bloom event in Monterey Bay. This application illustrates how our integrated approach can reveal complex ecological dynamics and functional interactions within marine microbial communities, which provide advanced marine ecosystem analytics that can support policy making, coastal protection and conservation efforts.