Types and characteristics of shared microbiota within families of ethnic minorities in Inner Mongolia

Gut microbial diversity is often studied from the perspective of community composition, but less is known about the genetic heterogeneity within species. The human gut microbiota exhibits substantial individual variation, influenced by numerous factors. This study characterized the gut microbial composition of 25 ethnic minority families from Inner Mongolia. We found that cohabitation within the same family was a more significant determinant of variation in both macrodiversity and microdiversity than other factors, including family role, ethnicity, sex, age, and geographical region. Based on average nucleotide identity, we identified 17 bacterial strains that were shared within families. Among these, Bifidobacterium adolescentis and Holdemanella biformis demonstrated higher average abundance, while Eubacterium rectale and Clostridiales bacterium were shared more frequently and across multiple families. Annotation against the Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed that most of these shared strains possess the genetic potential for the production or biosynthesis of short-chain fatty acids (SCFAs). Concurrently, computational analysis demonstrated that the genes of shared strains showed relatively low non-synonymous to synonymous polymorphism (pN/pS) ratios. Correlation network analysis indicated that, with the exception of Clostridiales bacterium, the shared strains generally did not occupy central nodes within the microbial interaction network. This research provides valuable insights into the patterns of gut microbiota sharing within families of Inner Mongolian ethnic minorities and offers a scientific basis for developing family-scale probiotic interventions.IMPORTANCEChina is a multi-ethnic nation with the Han ethnic group as the majority. Among its diverse ethnic groups, the populations of the Daur, Evenki, and Buryat are relatively small, with the Seventh National Population Census reporting their numbers at 132,299, 34,617, and 436,000, respectively. These minority groups often consume a diet characterized by high fat, high protein, and low fiber, primarily consisting of dairy products and meat, which may elevate their risks of obesity, diabetes, and cardiovascular diseases. Investigating the shared gut microbiota of these local ethnic minorities at both macro and micro diversity levels, using the family as a unit, is instrumental in safeguarding their health. In the future, based on this study, guidelines can be formulated to either facilitate or hinder the sharing of microbiota, depending on whether a specific shared strain is identified as beneficial or risky to health.