PMC

Enriched and depleted genes in the acetogenesis, methanogenesis, and dissimilatory sulfate reduction in the JPGM. Relative abundances of KOs involved in the pathways for hydrogen metabolism in acetogenesis, methanogenesis, and dissimilatory sulfate reduction among the 12 countries are shown. Asterisks indicate adjusted P < 0.01 compared with the abundances of the other 11 countries (Student's t-test).

Enriched and depleted functions in the JPGM. Functional categories of the KOs most enriched and depleted in the JPGM compared with those of the other 11 countries are shown. The vertical axis represents the proportion of KOs assigned to the category. Asterisks indicate adjusted P < 0.01 (Fisher's exact test).

Taxonomic comparison of gut microbiomes of populations from the 12 countries. Relative abundances of the four dominant phyla (A), the five genera most enriched and depleted in the JPGM (B), and M. smithii (C) in the 12 countries are shown. Vertical axes represent the relative abundance of the species calculated from the number of mapped reads to the reference genomes.

Comparison of the prevalence of NOG gene families between the JP and the other nine populations. The frequency of NOGs in the JP individuals plotted against those in the other nine countries. Each circle represents a NOG. The vertical axis represents the frequency of NOGs detected in the JP individuals. The horizontal axis represents the average frequency of NOGs detected in the individuals of the nine countries. Fifty-two NOGs significantly highly prevalent in the JP cohort compared with the others (the JP >0.7, the others <0.3, and JP/others ≥3) are coloured with blue. Three NOGs (ENOG4108MQB, ENOG4108ZIS, and ENOG4105WVE) were depicted in red.

Population-level diversity in human gut microbiomes among the 12 countries. (A) The MDS plot of microbial compositions for all individuals. Each circle represents an individual microbial composition and each colour represents a country of origin. The position based on the average microbial composition for each country is displayed by the abbreviated country name. (B) Comparison of Pearson's correlation coefficients of microbial compositions in individuals within a country and between different countries. Boxes represent the inter-quartile range (IQR), and the lines inside show the median. Whiskers denote the lowest and highest values within 1.5 times the IQR. Asterisk represents P < 0.05. (C) ROC curves and AUC values from the randomForest model. Numbers in parentheses represent the AUC values of the 10 countries.