Fig. 3

Gut archaeome variations with geography, ethnicity, and rural versus urban residency. The archaeomes were analyzed and plotted via principal component analysis (PCA) based upon the itchison distance between species-level archaeome compositions. a, b Archaeome variations with geographic region and ethnicity respectively. Comparisons of subject archaeome distribution on PC1 between the base mean of each group of interest (region or ethnicity) and that of all groups. Statistical significance was determined by Wilcoxon rank sum test with Holm-Bonferroni adjustment of p values, *p < 0.05, **p < 0.01, ***p < 0.001. c Archaeome variations between rural and urban subjects. Comparison of subject archaeome distributions on PC1 between rural and urban residents and statistical significance were determined by t test, *p < 0.05. For box plots, the boxes extend from the 1st to 3rd quartile (25th to 75th percentiles), with the median depicted by a horizontal line. d, e Differentially enriched gut archaeal taxa between rural and urban residents were determined by LefSE analysis (only those differential taxa with FDR adjusted p values < 0.05 and LDA effect size > 2 are shown). In d, taxa color-coated in red denote taxa enriched in rural subjects, while those color-coated in green denote taxa enriched in urban subjects. e The discriminatory species between rural and urban archaeomes