Overview

Here we present an example analysis report from the OCMS. The data are from a published study that were made publically available. The original article can be found here and the raw data can be downloaded from here. The data are 16S rRNA amplicon sequencing data (V4 region sequenced on the MISeq) from wild-type mice and MMP-9 deficient mice in either untreated or DSS treatemd conditions (i.e. inflammatory bowel disease model. Please see the original article for more details.

Pre-processing

The sequencing have been run through the OCMS Dada2 pipeline (please see the example dada2 report) and the analyses performed here are based on the amplicon sequence variant (ASV) table that is output from that pipeline. It should be noted here that the sequence quality in a lot of the samples was poor. This appeared to cause a problem for Dada2 as we were unable to assign taxononmy even at the phylum level for the majority of sequences from 15 samples. These samples have been removed for the purposes of this analysis i.e. as this is simply an example report.

General features

First we assess the relative abundance of the ASVs along with their taxonomic assignments. We look at the average (across samples) relative abundance distribution of ASVs and the ASV/taxonomic distribution across individual samples. For the purposes of the second plot we are plotting the ASVs that are present at an abundance pf > 5% in at least 5 samples. All of the rest of the ASVs are lumped into the “other” category.

As expected there are many ASVs at low abundance and few that make up the majority of the community. In this dataset it is already fairly clear that there are differences in DSS treated mice in both the mmp-9 KO and WT mice.

Alpha diversity

Here we asses whether there are any differences between the experimental groups in terms of alpha diversity (within-sample diversity) using the Shannon diversity index. The Kruskal-Wallis test is used to determine statistical significance of any difference.