The human gut microbiota varies considerably among world populations due to a variety of factors including genetic background, diet, cultural habits and socioeconomic status. Here we characterized 110 healthy Mongolian adults gut microbiota by shotgun metagenomic sequencing and compared the intestinal microbiome among Mongolians, the Hans and European cohorts. The results showed that the taxonomic profile of intestinal microbiome among cohorts revealed the Actinobaceria and Bifidobacterium were the key microbes contributing to the differences among Mongolians, the Hans and Europeans at the phylum level and genus level, respectively. Metagenomic species analysis indicated that Faecalibacterium prausnitzii and Coprococcus comeswere enrich in Mongolian people which might contribute to gut health through anti-inflammatory properties and butyrate production, respectively. On the other hand, the enriched genus Collinsella, biomarker in symptomatic atherosclerosis patients, might be associated with the high morbidity of cardiovascular and cerebrovascular diseases in Mongolian adults. At the functional level, a unique microbial metabolic pathway profile was present in Mongolian's gut which mainly distributed in amino acid metabolism, carbohydrate metabolism, energy metabolism, lipid metabolism, glycan biosynthesis and metabolism. We can attribute the specific signatures of Mongolian gut microbiome to their unique genotype, dietary habits and living environment.The gut microbiota (GM) is recognized as a human co-evolutionary partner that facilitates nutritional acquisition and immune modulation, and helps maintain host homeostasis in response to profound lifestyle changes 1-3 . Researchers have delineated the structural and functional configurations of gut metagenomes in different world populations by next generation sequencing [4][5][6][7] . The functional GM layout may represent host genotypic characteristics and reflect an adaptive ecosystem response to the host diet and cultural habits.The microbiota of the Mongolian population is of particular interest to researchers, because Mongolia encompasses a uniquely wide range of environmental conditions and ethnogeographical cohorts. Moreover, the Mongol Empire was the world's largest contiguous empire, exerted a major influence that greatly enhanced the cultural exchange between Mongolia and Europe that took place during the Middle Ages, when Mongolians intermingled with various populations in the Eurasian continent. Importantly, it has been reported that genetically, more than 20% people in the world are related to Mongolians 8 . Mongolians living in pastureland, such as Khentii Province, maintains a traditional nomadic lifestyle (Fig. 1A), whereas those in urban areas, such as Ulan Bator (the capital of Mongolia) and TUW Province (the suburbs of the capital), have adopted an urban lifestyle due to rapid modernization and economic development. Chinese Mongolians living in Hohhot and Xilingol have inter-married with ethic Han Chinese, which may generate some differences fr...