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. 2017 Jan;11(1):15-30.
doi: 10.1038/ismej.2016.114. Epub 2016 Sep 20.

Interleukin-15 Promotes Intestinal Dysbiosis With Butyrate Deficiency Associated With Increased Susceptibility to Colitis

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Free PMC article

Interleukin-15 Promotes Intestinal Dysbiosis With Butyrate Deficiency Associated With Increased Susceptibility to Colitis

Marlies Meisel et al. ISME J. .
Free PMC article

Abstract

Dysbiosis resulting in gut-microbiome alterations with reduced butyrate production are thought to disrupt intestinal immune homeostasis and promote complex immune disorders. However, whether and how dysbiosis develops before the onset of overt pathology remains poorly defined. Interleukin-15 (IL-15) is upregulated in distressed tissue and its overexpression is thought to predispose susceptible individuals to and have a role in the pathogenesis of celiac disease and inflammatory bowel disease (IBD). Although the immunological roles of IL-15 have been largely studied, its potential impact on the microbiota remains unexplored. Analysis of 16S ribosomal RNA-based inventories of bacterial communities in mice overexpressing IL-15 in the intestinal epithelium (villin-IL-15 transgenic (v-IL-15tg) mice) shows distinct changes in the composition of the intestinal bacteria. Although some alterations are specific to individual intestinal compartments, others are found across the ileum, cecum and feces. In particular, IL-15 overexpression restructures the composition of the microbiota with a decrease in butyrate-producing bacteria that is associated with a reduction in luminal butyrate levels across all intestinal compartments. Fecal microbiota transplant experiments of wild-type and v-IL-15tg microbiota into germ-free mice further indicate that diminishing butyrate concentration observed in the intestinal lumen of v-IL-15tg mice is the result of intrinsic alterations in the microbiota induced by IL-15. This reconfiguration of the microbiota is associated with increased susceptibility to dextran sodium sulfate-induced colitis. Altogether, this study reveals that IL-15 impacts butyrate-producing bacteria and lowers butyrate levels in the absence of overt pathology, which represent events that precede and promote intestinal inflammatory diseases.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Overexpression of IL-15 in the intestinal epithelium promotes colitis. WT littermate control and v-IL-15tg mice were either control treated or received 2% DSS into drinking water for 7 days and were then switched to water until mice were killed at day 8. (a) Time course of percent body weight changes. (b) Analysis of colon length at day 8 (left panel) and representative picture of colon (right panel) from DSS-treated WT littermate control and v-IL-15tg mice. (c) Histology (hematoxylin and eosin-stained (H&E), upper panel; periodic acid–Schiff (PAS) staining lower panel) of colon from control and DSS-treated mice. (d) Areas of erosion were quantified by a gastrointestinal pathologist and displayed as percentage of erosion relative to the total mucosal surface area. Data are from two independent experiments (WT (n=5), v-IL-15tg (n=7)). (e) Levels of butyrate were measured by GC-MS in cecal contents of DSS-treated v-IL-15tg mice or WT littermate controls and are displayed as μM per g luminal contents. (ac) (WT water (n=4), v-IL-15tg water (n=2), WT DSS (n=8), v-IL-15tg DSS (n=10). (a–d) Data are from two independent experiments. Error bars, mean±s.e.m.; *P<0.05; **P<0.01; ***P<0.001.
Figure 2
Figure 2
Dysregulated expression of IL-15 in the epithelium induces dysbiosis across intestinal compartments. (a) Bacterial community composition is organized by site (feces, cecum and ileum) and mouse genotype (side-by-side columns). The phyla identified in the samples are according to the GreenGenes taxonomy. The number of samples (n) per intestinal compartment-genotype is noted at the top. Percent composition is the average according to n (see main text and Supplementary Table S1 for statistical support). (b) Principal coordinates analysis (PCoA) based on the weighted UniFrac distance between the bacterial communities from samples according to host genotype (WT (gray squares) and v-IL-15tg mice (open circles)) by site (feces, cecum or ileum). Distinctions between genotype were considered significant by statistical analyses of the underlying UniFrac distances using PERMANOVA at P⩽0.05 based on 999 permutations. (a, b) Data are from two independent experiments; WT: feces (n=9); cecum (n=10), ileum (n=7); v-IL-15tg: feces (n=7), cecum (n=6), ileum (n=6).
Figure 3
Figure 3
Overexpression of IL-15 in the epithelium mediates compartment-specific changes in bacterial community diversity. (a) Principal coordinates analysis (PCoA) based on the weighted UniFrac distance between the bacterial communities from each site (feces (blue circles), cecum (red squares) and ileum (orange triangles)) within each host genotype (WT littermate and v-IL-15tg mice). (b) Boxplots of measure of alpha diversity (Shannon) of bacterial community diversity within each site (feces, cecum, and ileum) according to mouse genotype (WT littermate or v-IL-15tg). (a, b) Data are from two independent experiments; WT: feces (n=9); cecum (n=10), ileum (n=7); v-IL-15tg: feces (n=7), cecum (n=6), ileum (n=6). Significant differences between genotype are noted based on Mann–Whitney U-test at *P<0.05; *P<0.01. The color reproduction of this figure is available at the The ISME Journal online.
Figure 4
Figure 4
Analysis of OTUs reveals that IL-15 overexpression influences the presence and abundance of butyrate-producing bacteria. The figure depicts significant log2-fold changes (based on a FDR (Benjamini–Hochberg) significance threshold of 0.05; Benjamini and Hochberg, 1995) in the relative abundance of specific OTUs between host genotype (WT and v-IL-15tg) in feces, cecum and ileum as heatmaps. On the left are the phylum and family classifications of the OTUs and on the right are the putative genus/species designation based on best similarity matches from the RDP using SeqMatch (numbers in parentheses indicate SeqMatch score (Sab)). OTUs and SeqMatch genus/species assignments in bold italics indicate that the OTU had an increased log2-fold change in the v-IL-15tg mice. The panel to the right of the heatmaps indicate whether butyrate kinase (buk) or butyryl-CoA:acetate CoA-transferase (but) encoding genes have been detected in the genomes of the SeqMatch genus/species assignments based on the buk and but entries in the RDP FunGene Functional Gene Pipeline and Repository. A closed black circle indicates presence of a buk or but gene in that genome, whereas a closed gray circle indicates an alternate annotation (defined at the bottom of the panel). An open circle indicates that no match was found in the RDP FunGene. Data are from two independent experiments; WT: feces (n=9); cecum (n=10), ileum (n=7); v-IL-15tg: feces (n=7), cecum (n=6), ileum (n=6).
Figure 5
Figure 5
IL-15-induced microbial alterations are associated with a significant reduction in luminal (ileum and cecum) and fecal butyrate concentration across intestinal compartments and a reduction of butyrate-producing bacteria. (a) Levels of butyrate were measured by GC-MS in feces or luminal contents (cecum and ileum) of v-IL-15tg mice or WT littermate controls and are displayed as μM g–1 luminal content. Data are from three independent experiments (n=7–14). (b) GF v-IL-15tg mice received fecal microbiota of either SPF WT littermate or v-IL-15tg mice. Panel depicts experimental design for FMT experiment. (c) Graph shows measured concentrations of butyrate in feces or luminal contents (cecum or ileum) from recipient mice by GC-MS at day 7 post-FMT (GF v-IL-15tg mice transplanted with WT littermate feces, n=5; GF v-IL-15tg mice transplanted with v-IL-15tg feces, n=8). (d) qPCR targeting the 16S rRNA-encoding gene was used to measure bacterial load in the feces of mice receiving FMT. No statistical difference was found between both groups. (e) The heatmap depicts significant log2-fold changes in the relative abundance of specific OTUs between recipients based on donor host genotype (WT or v-IL-15tg) in feces (for detailed description of statistics see Figure 4). As in Figure 4, phylum and family classifications of the OTUs are on the left and on the right are the putative genus/species designation based on best similarity matches from the RDP using SeqMatch. OTUs and SeqMatch genus/species assignments in bold italics indicate that the OTU had an increased log2-fold change in the recipient mice transplanted with feces from v-IL-15tg mice; GF v-IL-15tg mice transplanted with WT littermate feces, n=3; GF v-IL-15tg mice transplanted with v-IL-15tg feces, n=5. One representative analysis out of two independent experiments is shown. (a, c) Error bars, mean±s.e.m.; *P<0.05; **P<0.01.

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