Distinctive Patterns of Gut Bifidobacterium Diversity in Mongolian Adults: Regional Variation and Dairy Intake Associations

Background/Objectives: Despite increasing interest in the human gut microbiome, particularly in Bifidobacterium, studies focusing on traditionally living populations with high habitual dairy consumption remain limited. This study investigated species-level diversity, abundance, and regional variation of Bifidobacterium among healthy Mongolian adults and contextualized these findings within a global comparative framework. Methods: A total of 100 healthy adults were recruited from four Mongolian regions. Fecal samples were analyzed using species-resolved shotgun metagenomics, and dietary intake was assessed through a standardized food frequency questionnaire. Alpha- and beta-diversity metrics, differential abundance tests, and diet–microbe correlations were performed on members of the Bifidobacterium species. To assess the broader significance of the Mongolian Bifidobacterium profile, Shannon diversity was further compared against a curated global dataset comprising 1286 healthy adults from 29 countries using harmonized bioinformatic and statistical pipelines. Results: Shannon diversity within the Bifidobacterium genus was significantly higher in nomadic Mongolians, particularly those from Khuvsgul and Dundgobi, and strong geographic structuring was observed in beta-diversity analyses (PERMANOVA, p < 0.001). Nomadic populations showed higher relative abundances of B. adolescentis and B. angulatum, whereas B. pseudocatenulatum predominated in Ulaanbaatar. Although overall Bifidobacterium abundance was lowest in Bulgan, B. longum remained the dominant species in this region. Spearman correlation analysis with false discovery rate correction identified significant associations between dairy intake and specific Bifidobacterium species. Homemade yogurt and traditional dairy intake were positively associated with B. angulatum. B. catenulatum was positively associated with homemade yogurt, traditional dairy, and total fermented dairy intake, whereas factory milk intake was negatively associated with B. angulatum but positively associated with B. pseudocatenulatum. Mongolia ranked among the top eight of 30 countries for Bifidobacterium Shannon diversity though total Bifidobacterium abundance showed substantial inter-individual and regional variation. Conclusions: Mongolian adults exhibit relatively high Bifidobacterium diversity at both national and global scales. Traditional dairy consumption was associated with species-specific variation in Bifidobacterium composition, supporting the contribution of dietary practices to regional gut microbiota patterns.