Shotgun Metagenomic Analysis of Gut Microbiome and Resistome Diversity in Indigenous Orang Asli Communities of Peninsular Malaysia

This study presents a comparative shotgun metagenomic analysis of gut microbiome and resistome profiles from 42 healthy adult individuals across three indigenous Orang Asli (OA) communities—Jahai (rural), Temiar (semi-urban), and Temuan (urban)—and urban Malays in Peninsular Malaysia. High-throughput sequencing on the Illumina NovaSeq platform revealed that the rural Jahai exhibited the highest gut microbial diversity, whereas urban Malays showed the lowest. Notably, butyrate-producing genera such as Blautia, Clostridium, and Mediterraneibacter were significantly depleted in the Jahai microbiome. The semi-urban Temiar microbiomes were enriched in Bifidobacterium species. Functional pathway analysis indicated major differences in sugar metabolism and fatty acid biosynthesis pathways, driven largely by microbial compositional shifts. Gut resistome analysis, performed using KMA and ResFinder, showed that urban Temuan and Malay individuals harbored the highest abundance and diversity of antimicrobial resistance genes (ARGs), especially against beta-lactams, tetracyclines, and macrolides. Conversely, the Jahai resistome exhibited the lowest ARG diversity, consistent with reduced antibiotic exposure. These findings highlight the impact of urbanisation on gut microbiome structure and antimicrobial resistance burden, offering valuable insights into microbial transitions in underrepresented Indigenous populations.