Shared antimicrobial resistance gene families across gut microbiomes in indigenous Orang Asli communities of Peninsular Malaysia

Abstract Introduction Indigenous groups across the world have been underrepresented in the ongoing efforts to map human microbiome diversity. This study investigates the gut microbiome and resistome diversities of three indigenous Malaysian (Orang Asli, OA) communities with different lifestyles and degree of urbanisation. We included an urban Malay group as a comparison. Methods Healthy participants over 18 years old gave were recruited from three indigenous communities, namely Temuan (urban, n=12), Temiar (semi-urban, n=9) and Jahai (rural, hunter-gatherer, n=12), and Malay (urban, non-indigenous, n=9). Stools were collected on dry ice and sequenced using shotgun metagenomics. Results Approximately 65% of the reads were classified across the dataset. Microbial alpha diversity (Shannon) decreased but antibiotic resistance genes (ARGs) diversity increased as the degree of urbanisation in the groups increased (P < 0.05). The groups contributed to 13% of the variation observed in the microbial composition (PERMANOVA, P = 0.001), and 14.5% in resistome composition (PERMANOVA, P = 0.001). Romboutsia timonensis was significantly depleted in Jahai compared to Malay (FDR = 0.04). Shared ARGs conferring resistance to beta-lactams ( cfxA ), tetracyclines ( tet ), and macrolides ( erm ) were observed across all groups, irrespective of geographical location, ethnicity and lifestyle. Conclusion This study provides initial characterisation of the gut microbiome and resistome of three underrepresented indigenous OA communities in Malaysia. Our findings offer foundational evidence of antimicrobial resistance patterns and underscores the need for broader inclusion of underrepresented populations in national surveillance and stewardship efforts.