Background The gut microbiota is known to have substantial impacts on human health. Although urbanization has been documented to modify the composition of the gut microbiota, limited attention has been given to the highly diverse Chinese populations.

Methods We collected stool and saliva samples from six representative ethnic groups within the Yunnan province, with individuals of each ethnicity living in remote villages with traditional lifestyles and in the provincial capital, Kunming. Through metagenomic sequencing, de novo assembling, and subsequent analyses, marked diversity and differences in the gut microbiota among these populations were unveiled, with associations to genetic factors and lifestyles.

Results Our findings reveal substantial variations in gut microbiota among different ethnic groups, and demonstrate that the effects of urbanization on gut microbiota differ across ethnicities.

Conclusions This highlights the complexity of the relationship between socioeconomic factors and the gut microbiota, and the limitations of generalizing findings from a limited number of communities.