Caspase deficiency alters the murine gut microbiome

Abstract

Caspases are aspartate-specific cysteine proteases that have an essential role in apoptosis and inflammation, and contribute to the maintenance of homeostasis in the intestine. These facts, together with the knowledge that caspases are implicated in host-microbe crosstalk, prompted us to investigate the effect of caspase (Casp)1, -3 and -7 deficiency on the composition of the murine gut microbiota. We observed significant changes in the abundance of the Firmicutes and Bacteroidetes phyla, in particular the Lachnospiraceae, Porphyromonodaceae and Prevotellacea families, when comparing Casp-1, -7 and -3 knockout mice with wild-type mice. Our data point toward an intricate relationship between these caspases and the composition of the murine gut microflora.

Figure 1

Ecological community analysis of identified 16S rRNA sequences. (a) Rarefaction curves were used to estimate richness of the microbiota belonging to caspase-KO and -WT mice. The vertical axis shows the number of OTUs observed after rarefying samples to a given read depth, as indicated on the horizontal axis. (b) 3D NMDS of Bray–Curtis distance between samples. Dimensions 1 and 3 are shown. Each symbol represents one sample. The variance explained by each dimension is indicated in parentheses on the axes. Dark red, Casp-7 KO; red, Casp-1 KO; orange, Casp-3 KO; blue, WT

Figure 2

Abundance of bacterial phyla in caspase-KO and -WT mice. (a) Abundance plot of the most important phyla. Each horizontal line represents one mouse. (b) Ratio of Firmicutes/Bacteroidetes as determined by sequencing analysis; (c) Ratio of Firmicutes/Bacteroidetes as determined by qPCR. The ratio of a WT mouse was set at 1, and then the relative ratios for all genotypes were calculated. Shown are mean and S.E.M. Number of samples (n) are shown below the figures. Differences between WT and KO samples were tested by t-test. ^*P<0.05, ^**P<0.01, ^***P<0.005 versus WT

Figure 3

Abundance of bacterial families in caspase-KO and -WT mice. (a) Abundance plots of the most abundant families. The designation ‘Other' summarizes low-abundant families that are not explicitly shown in this graph. (b) Families with the most significantly different abundances. Shown are mean and S.E.M. Differential abundance between groups of samples was tested by t-test. ^*P<0.05, ^**P<0.01, ^***P<0.005 versus WT