Microbiome Analysis in Murine Colitis

Feces were collected on the first day of the first and on the last day of the third DSS cycle. Samples were snap frozen in liquid nitrogen and stored at −20 °C. DNA was isolated using the QIAamp Fast DNA stool Mini kit (Qiagen) according to the manufacturer’s instructions, with bead beating using Lysing Matrix E tubes (MP Biomedicals) before extraction. 16S rRNA gene amplicon sequencing and library preparation was performed using a standard Illumina protocol [36 ]. Reads were processed using the software packages DADA2 [37 (link)] and SINA [38 (link)]. For the analysis of sample similarity modified Rhea scripts were used [39 (link)]. Generalized UniFrac distances were visualized using multi-dimensional scaling [40 (link)]. We assessed cluster significance using permutational multivariate analysis of variance. Testing for significant differences in diversity and bacterial abundances was performed using Kruskal-Wallis Rank Sum Test with Benjamin-Hochberg method for correction for multiple comparisons. We used the Mann-Whitney U test to compare phylogenetic distances.