Background: Commensal microbiota help to educate the immune system in the periphery and a number of involved immune cells have recently been characterized. However, specific molecular determinants in these processes are not known and, reciprocally, little information exists about single host determinants that alter the microbiome. Matrix metalloproteinase (MMP)-9 deficiency has previously been linked to alterations in gut microbiota composition in a model of infectious colitis .
Methods: Acute colitis was induced in MMP-9 knockout (KO) mice (n=10) and their wild-type (WT) littermates (n=10) via oral administration of 3% dextran sodium sulphate (DSS) for 7 days followed by 2 days of regular drinking water. Control mice (10 WT and 10 MMP-9 KO) received normal drinking water throughout the experiment. Both genotypes were raised under identical environmental conditions for more than 15 years and were co-housed during the experiment according to phenotype (control vs DSS). Faecal samples were collected at time of sacrifice and immediately frozen at −80°C. Illumina MiSeq sequencer was used for 16S rDNA paired-end sequencing targeting the V4 hypervariable region. Sequencing depth was downsized to 10000 reads/sample. Taxonomic annotation was performed with Ribosomal Database Project. PICRUSt was used for metagenome prediction and analysed with STAMP software (version 2.1.3). R software was used for statistical analysis with multiple testing correction (Bonferroni).
Results: No significant differences in clinical or histopathological parameters were found between both genotypes (WT and MMP-9 KO) after induction of acute colitis. Observed microbial richness (genus level, t-test) and microbiota composition (Bray-Curtis dissimilarities, adonis) were not significantly influenced by genotype. In contrast, weight loss, disease activity index, cage and phenotype (control vs DSS) did significantly influence the intestinal microbiota composition (envfit, r2>0.7, p=0.001). The genera Bacteroides and Alistipes explained most of the variability in microbiota composition between genotype in the control group, whereas this was the case for the genera Bacteroides and Allobaculum in the DSS group (Constrained Principal Coordinate Analyses, capscale). After multivariate analysis (MaAsLin, p<0.05), however, cage was identified as the sole driver of microbiota composition variability. Functional profiling indicated that both genotype and phenotype influenced the metagenome (PICRUSt). However, after multiple testing correction, only phenotype remained significantly associated with changes in metagenomic profile.
Conclusions: Changes in gut microbiota composition were mainly driven by DSS and were not significantly altered by MMP-9 gene knockout.
 Rodrigues DM, (2012), Matrix metalloproteinase 9 contributes to gut microbe homeostasis in a model of infectious colitis, BMC Microbiol, 105, 12