Meta-Analysis of Fecal Microbiota and Metabolites in Experimental Colitic Mice during the Inflammatory and Healing Phases

Abstract

The imbalance of gut microbiota is known to be associated with inflammatory bowel disease, but it remains unknown whether dysbiosis is a cause or consequence of chronic gut inflammation. In order to investigate the effects of gut inflammation on microbiota and metabolome, the sequential changes in gut microbiota and metabolites from the onset of colitis to the recovery in dextran sulfate sodium-induced colitic mice were characterized by using meta 16S rRNA sequencing and proton nuclear magnetic resonance (¹H-NMR) analysis. Mice in the colitis progression phase showed the transient expansions of two bacterial families including Bacteroidaceae and Enterobacteriaceae and the depletion of major gut commensal bacteria belonging to the uncultured Bacteroidales family S24-7, Rikenellaceae, Lachnospiraceae, and Ruminococcaceae. After the initiation of the recovery, commensal Lactobacillus members promptly predominated in gut while other normally abundant bacteria excluding the Erysipelotrichaceae remained diminished. Furthermore, ¹H-NMR analysis revealed characteristic fluctuations in fecal levels of organic acids (lactate and succinate) associated with the disease states. In conclusion, acute intestinal inflammation is a perturbation factor of gut microbiota but alters the intestinal environments suitable for Lactobacillus members.

Keywords: 1H-NMR analysis; Lactobacillus; dysbiosis; experimental colitic mice; gut microbiota; inflammatory bowel disease; meta 16S rRNA analysis; metabolome.

Figure 1

Monitoring of body weight changes and bleeding score of dextran sulfate sodium (DSS)-treated mice. Body weight changes (solid lines) are expressed as the percent of initial body weight. Bleeding (dashed lines) in mice was scored according to the following criteria: no bleeding, 0; bleeding, 1; gross bleeding, 2. The disease phases were categorized according to body weight changes during the experimental period: before DSS administration (phase 1, white), progressive phase (phase 2, red), a peak of weight loss (phase 3, yellow), recovery phase (phase 4, blue). One of the mice (No. 3) died on day 5 (†).

Figure 2

Fecal microbiome profiles during the experimental periods. (A) Changes in the relative abundance at the family level in each DSS-treated mouse; (B) Multidimensional scaling (MDS) plot of fecal microbiome (at the family level) at each time point.

Figure 3

Characteristics of changes in relative abundances of major commensal bacterial groups. (A) Changes in the abundances of eleven bacterial families in four pathological phases; (B) Changes of the top five most abundant operational taxonomic units (OTUs) in each phase. Different letters indicate significant differences between bars.

Figure 4

Characteristics of changes in fecal metabolites of DSS-treated mice. (A) Principal component analysis (PCA) score plots of fecal metabolites at each time point; (B) Changes in relative peak intensities of amino acids; (C) Changes in relative peak intensities of short chain fatty acids and organic acids. Different letters indicate significant differences between bars.

Figure 5

Monitoring of fecal lactate and succinate levels in DSS-treated mice. The solid lines show the average body weight change of five mice during the experimental period. Data of fecal lactate and succinate levels are mean ± standard error of the mean (SEM) (n = 5).