Fig. 3

Characteristics of the gut virus catalog and gut virome. A, Pie plot shows the proportions of complete, high-quality, medium-quality, and low-quality vOTUs in the non-redundance virus catalog. B, Venn plot shows the overlap of the current virus catalog and the other three public gut virus catalogs. C, Pie plot shows the family-level taxonomic annotation of the virus catalog. D, Rarefaction curve analysis of the number of observed vOTUs on each group of samples. The number of species in different groups is calculated based on a randomly selected specific number of samples with 30 replacements, and the median and quartile values are plotted. E, F, Boxplot shows the Shannon diversity index (E) and the Simpson index (F) of gut virome that differ among two groups. Boxes represent the interquartile range between the first and third quartiles and median (internal line); whiskers denote the lowest and highest values within 1.5 times the range of the first and third quartiles, respectively; and nodes represent outliers beyond the whiskers. The significance level is calculated based on the Student’s t-test. G, PCoA analysis of Bray–Curtis distance based on the composition of gut virome, revealing the separations between two groups. The location of samples (represented by nodes) in the first two principal coordinates is shown. Lines connect samples in the same group, and circles cover samples near the center of gravity for each group. H, Volcano plot shows the fold change vs. q-values for all vOTUs. The X-axis shows the ratio of vOTU abundance in GA patients compared with that in healthy controls. The Y-axis shows the q-value (-log10 transformed) of a vOTU. The vOTUs that enriched in GA patients and healthy controls are shown in red and blue points, respectively. I, J, Pie plots show the taxonomic distribution of GA-enriched (J) and control-enriched (K) vOTUs. K, The occurrence rate of the KOs differed in frequency between the GA-enriched and ocntrol-enriched vOTUs