Microbial Diversity and Ecological Structure of the Gut Microbiota in Children and Adults from an Indigenous Mexican Community

Gut microbiota composition is shaped by environmental factors such as lifestyle, diet, socioeconomic and cultural context, as well as host-related factors like age and sex. Although microbiota research has expanded rapidly in recent years, most current paradigms are based on data from individuals in high-income, industrialized countries, particularly in Europe and North America. As a result, microbiota profiles from non-Westernized populations—especially those from Indigenous communities—remain underrepresented in global studies, limiting our understanding of the full ecological and evolutionary diversity of human gut microbial communities. In this study, we characterized the bacterial gut microbiota of Me’phaa individuals, a pre-Columbian Indigenous group from the south-central region of México. This rural community maintains a subsistence lifestyle centered on high-fiber, plant-based diets and limited exposure to industrialized foods. Using high-throughput 16S rRNA gene sequencing, we analyzed microbial profiles from 62 individuals aged 5 to 60 years, examining differences across age and sex to explore patterns of diversity and community structure. Despite sharing similar life conditions, noticeable differences in gut microbiota were observed; alpha and beta diversities revealed significant variation across age and sex. Children exhibited greater microbial richness and inter-individual variability, consistent with dynamic colonization processes that begin in early life. In contrast, adults showed more taxonomically uniform communities, with a higher abundance of taxa such as Prevotellaceae, Succinivibrio, and Dialister, which are associated with fiber fermentation and complex carbohydrate metabolism. Additionally, sex-related differences were evident, with adult males displaying the highest relative abundance of Prevotellaceae. Finally, the presence of taxonomic groups rarely observed in urban Western populations suggests that indigenous lifestyles may preserve microbial diversity with potential metabolic relevance. Our findings advance the ecological and evolutionary understanding of human gut microbiota and highlight the importance of integrating non-Westernized populations into microbiome research to better elucidate host-microbe coadaptation and its implications for health.