The deep-sea marine environment presents one of the most extreme habitats on Earth, characterized by high hydrostatic pressure, low temperatures, anoxia, and scarce nutrient availability. Despite these hostile conditions, highly specialized microbial communities flourish within deep-sea sediments. Traditional bioprospecting has historically relied on cultivation-dependent methods; however, more than 99% of marine sediment microbes remain unculturable under standard laboratory conditions. Furthermore, the biosynthetic potential of the culturable minority often remains silent outside their natural habitats and environmental conditions. To fully tap into these resources, culture-independent approaches such as metagenomics and metabolomics are essential.

Recent advancements in high-throughput, cost-effective next-generation sequencing (NGS) have revolutionized access to this uncultured biosphere. By employing shotgun metagenomic sequencing, genomic DNA extracted directly from deep-sea sediments can be sequenced, assembled and analysed, completely bypassing the cultivation bottleneck. Concurrently, untargeted metabolomics enables comprehensive profiling of the total in situ metabolite pool within the sediment matrix.

By coupling metagenomics and untargeted metabolomics, this integrated multi-omics approach effectively bridges the gap between genetic blueprints and phenotypic metabolic outputs. Ultimately, this framework provides a powerful toolkit for uncovering novel biosynthetic pathways and unearthing next-generation natural products from the marine microbiome. This presentation will highlight ongoing research on deep-sea sediment core samples retrieved from the South China Sea, alongside current initiatives driving innovation within the laboratory.