Fig. 3: Depletion of prokaryotic viruses and expansion of eukaryotic viruses in CD. | Nature Communications

Fig. 3: Depletion of prokaryotic viruses and expansion of eukaryotic viruses in CD.

From: The gut ileal mucosal virome is disturbed in patients with Crohn’s disease and exacerbates intestinal inflammation in mice

Fig. 3

a Altered ileal viral species in CD (remission and flare-up) compared to HC in the Guangzhou (left) and Kunming (right) cohorts, identified via MaAsLin2 analysis controlling for medications and dietary habit. Only the top 60 significant associations (BH-FDR q < 0.2 [p < 0.05]) were plotted. The enriched viral species are plotted in red and the decreased viral families are shown in blue. The bubble size denotes the prevalence rate of the viral species across study participants, and bubble shading indicates magnitude of the correlation. Viral taxa colour-coated in black denote prokaryotic viruses/bacteriophages, whilst those colour-coated in red denote eukaryotic viruses. Statistical significance was determined by a two-tailed multivariable association test, adjusted by the BH-FDR adjustment. b Venn diagram of the number of shared viral species between groups. GZ Guangzhou, KM Kunming. c Feature viral species (increased or decreased in relative abundance) in CD compared to HC, plotted with respect to CD remission, flare-up, and cohorts. The host of each feature species were depicted. For the bacterial hosts, probiotic bacteria were colour-coated in green, and pathogenic bacteria were colour-coated in orange. d Taxonomic distribution of the host bacteria for the ileal mucosal bacteriophages, ranked by the relative abundance of their predator bacteriophages. e The relative abundance of bacteriophages categorised by the host bacterial phyla in HC, CD remission and flare-up. Between-group comparison was conducted by t-test. f Differentially enriched bacteriophages, classified according to their host bacteria species, between HC and CD. Enriched species were identified via LEfSe analysis (LDA > 2, KW p value < 0.05), albeit no specific species were identified in CD flare-up. Host bacteria prediction was based on CRISPR-spacer analysis on viral contigs in PHYBOX (CHERRY). The richness of ileal prokaryotic virome/bacteriophages (g) and ileal eukaryotic virome (h) in CD remission and flare-up compared to HC in the Guangzhou (left, n = 102) and Kunming (right, n = 102) cohorts. Between-group comparison was conducted by Mann–Whitney test. For box plots, the boxes extend from the 1st to the 3rd quartile (25th to 75th percentiles), with the median depicted by a horizontal line.

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