Despite extensive efforts to address it, the vastness of uncharacterized "dark matter" microbial genetic diversity can impact short-read sequencing based metagenomic studies. Population specific biases in genomic reference databases can further compound this problem. Leveraging advances in long-read and Hi-C technologies, we deeply characterized 109 gut microbiomes from three ethnicities in Singapore to comprehensively reconstruct 4,497 medium and high-quality metagenome assembled genomes, 1,708 of which were missing in short-read only analysis and with >28x N50 improvement. Species-level clustering identified 70 (>10% of total) novel gut species out of 685, improved reference genomes for 363 species (53% of total), and discovered 3,413 strains that are unique to these populations. Among the top 10 most abundant gut bacteria in our study, one of the species and >80% of all strains were not represented in existing databases. Annotation of biosynthetic gene clusters (BGCs) uncovered more than 27,000 BGCs with a large fraction (36-88%) not represented in current databases, and with several unique clusters predicted to produce bacteriocins that could significantly alter microbiome community structure. These results reveal the significant uncharacterized gut microbial diversity in Southeast Asian populations and highlight the utility of hybrid metagenomic references for bioprospecting and disease-focused studies.