FIGURE 2.

Microbial diversity between the four groups. (A) PCoA was done on Bray-Curtis distances displaying β-diversity of the microbiome between the three DOI groups and the control. (B) Among the four groups, the main phylum changed obviously. Because the results of metagenomics included bacteria, fungi, and archaea, the total abundance of bacteria was less than 100%. (C) Phylum distribution of the number of species that were either elevated or depleted in each of the three stages compared with the healthy controls. (D) The ROC curve shows the significance of bacteria in predicting the grouping of the control and DOI-high groups. (E) The PCoA diagrams were done on the Bray-Curtis matrix based on the genes of annotated species which differed significantly between the four groups. The mapping method was to pick out the genes of the corresponding species, and then the vegdist function (method = Bray) in vegan package (version 2.5.5) was used to calculate the distance based on the abundance of the genes. The pcoa function in ape package (version 5.3) was used for calculation, and then the ggplot function (version 3.3.5) of the ggplot2 package was used for PCoA visualization.