Practice Lesson 6

This practice lesson is associated with Lesson 6 of the Microbiome Analysis with QIIME 2. In this practice lesson, we will view beta diversity results and determine whether our two conditions (old vs young) demonstrate significant differences in microbial community structure. We will continue working with the data from Zhang et al. 2022.

1. Examine the weighted and unweighted unifrac PCoAs. Do samples demonstrate group clustering?

   Solution

   Yes, more so with unweighted UniFrac distances.

2. Is there a significant difference between microbial communities from old vs young individuals?

   Solution

   qiime diversity beta-group-significance \
   --i-distance-matrix 07_analysis/diversity-core-metrics-phylogenetic/unweighted_unifrac_distance_matrix.qza \
   --m-metadata-file /data/practice/metadata.txt \
   --m-metadata-column 'DataType' \
   --p-method 'permanova' \
   --o-visualization 07_analysis/permanova_results.qzv  
   

3. Is there a significant difference in group dispersion?

   Solution

   qiime diversity beta-group-significance \
   --i-distance-matrix 07_analysis/diversity-core-metrics-phylogenetic/unweighted_unifrac_distance_matrix.qza \
   --m-metadata-file /data/practice/metadata.txt \
   --m-metadata-column 'DataType' \
   --p-method 'permdisp' \
   --o-visualization 07_analysis/permdisp_results.qzv