Additional file 1 of Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease
Creators: name: Tian, Xiangge
name: Li, Shenghui
name: Wang, Chao
name: Zhang, Yanyan
name: Feng, Xiaoying
name: Yan, Qiulong
name: Guo, Ruochun
name: Wu, Fan
name: Wu, Chunxue
name: Wang, Yan
name: Huo, Xiaokui
name: Ma, Xiaochi
Publisher: name: figshare
Year: 2024
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Additional File 1: Supplementary Figure 1. Comparison of gut viromes between VLP and bulk datasets. (a) Principal coordinate analysis (PCoA) reveals the difference between the VLP virome and bulk virome at the family level. Samples are shown at the first and second principal coordinates (PCoA1 and PCoA2), and the ratio of variance contributed by these two PCs is shown. (b) Observation of Microviridae vOTUs in the VLP and bulk datasets. Supplementary Figure 2. Correlation analysis (Spearman correlation test) of the gut bacteriome diversity and VLP/bulk virome diversity. For each panel, scatter plot shows the samples and the fitting line are formed based on the diversity indexes in the bacteriome and virome for all samples. Supplementary Figure 3. Comparison of Anelloviridae vOTUs between IBD patients and healthy controls. Barplot showing the number of vOTUs enriched in IBD patients or healthy controls. Dark red or blue indicate vOTUs with a p-value of less than 0.05 from the Wilcoxon rank-sum test comparing the two groups. Supplementary Figure 4. Comparison of gut viral composition between IBD patients and healthy controls at the order level. Wilcoxon rank-sum test: *, p&lt;0.05; **, p&lt;0.01; ***, p&lt;0.001. HC, healthy controls. Supplementary Figure 5. Distribution of prokaryotic hosts of the IBD-associated vOTUs. Supplementary Figure 6. Comparison of functions between IBD-enriched and control-enriched vOTUs. Principal coordinate analysis (PCoA) reveals the differences in functional profiles between IBD-enriched and controls vOTUs. vOTUs are shown at the first and second principal coordinates (PCoA1 and PCoA2), and the ratio of variance contributed by these two PCs is shown. Statistical significance was obtained by PERMANOVA analysis. Supplementary Figure 7. Partial gene structures of several control-enriched vOTUs with the RNA-dependent DNA polymerase (RdDp) gene. The left-hand side text provides the family-level taxonomic annotation and vOTU ID number corresponding to each vOTU, along with the predicted prokaryotic host for each one. Supplementary Figure 8. Viral community variation among 9 public datasets and the VLP and bulk datasets in this study. Principal coordinates analysis (PCoA) based on the Bray-Curtis distance at the vOTU level. Effect size (R2) and statistical significance were obtained by PERMANOVA analysis. Cross-dataset IBD prediction based on 34 IBD-associated vOTUs. Supplementary Figure 9. Heatmap shows the performance assessed as AUC scores of intra-dataset and cross-dataset IBD predictions using random forest models trained based on 34 IBD-associated vOTUs. The models of intra-dataset prediction (diagonal) are validated using five repeats of five-fold cross-validations. The models of cross-dataset prediction (off-diagonal) are built on the dataset corresponding to each row and validated on the dataset corresponding to each column. The LOCO row refers to leave-one-cohort-out analysis in which models are built on ten datasets combined and validated on the remaining one corresponding to each column. Supplementary Figure 10. Bar plot showing the virus-to-bacterium ratio of feces of mouse before and after FVT. Supplementary Figure 11. Colitis scores of HE staining of the colon in Figure 5e. Supplementary Figure 12. Quantitative analysis of the western blot of Figure 5f. Supplementary Figure 13. Venn plot showing the overlap between our gut virus catalog and the existing gut virus catalogs.