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

Abstract

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 Indigenous Orang Asli communities in Malaysia with different lifestyles and degree of urbanisation. Healthy adult participants (>18 years old) were recruited from three Indigenous communities - Temuan (urban), Temiar (semi-urban), and Jahai (rural hunter-gatherer), as well as urban Malays. Stool samples were collected on dry ice and analysed using shotgun metagenomic sequencing. 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. This study provides initial characterisation of the gut microbiome and resistome of three Indigenous Orang Asli 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. Impact statementOur study generated one of the first integrated microbiome-resistome analyses across an urbanisation gradient of Malaysian gut microbiome. Shotgun metagenomic profiling of hard-to-access Indigenous cohorts enabled taxonomic classification for most reads, supporting high-resolution microbial community and ARG analysis. Increasing urbanisation was associated with reduced microbial alpha diversity alongside increased ARG diversity, with population grouping explaining an insightful proportion of both microbiome and resistome variation. Core resistance determinants to beta-lactams (cfxA), tetracyclines (tet), and macrolides (erm) were consistently detected across lifestyles and geographies. These results establish a baseline framework for urbanisation-linked microbial shifts in the under-studied Malaysian gut microbiome and provide actionable direction for investigating national AMR drivers, surveillance design, and targeted stewardship strategies in underrepresented populations. Data summary and code availabilitySupporting data are provided in the supplementary data files. Specific accession numbers of the sequence data are provided as Supplementary Material. Codes produced for this analysis can be found at https://zenodo.org/records/18208358.