Taxonomic analysis

Taxonomic bar plots were generally created as follows:

qiime taxa barplot \
--i-table feature_table_samples.qza \
--i-taxonomy classified_rep_seqs.qza \
--m-metadata-file ../metadata_for_qiime2.txt \
--o-visualization sample_barplots.qzv

The 18S rRNA data was filtered to remove bacterial sequences (designated simply “Eukaryota”) and human sequences (Mammalia)

# Remove Eukaryota by exact match
qiime taxa filter-table \
--i-table feature_table_samples.qza \
--i-taxonomy classified_rep_seqs.qza \
--p-mode exact \
--p-exclude "D_0__Eukaryota" \
--o-filtered-table tmp.qza

# Remove anything that contains 'Mammalia'
qiime taxa filter-table \
--i-table tmp.qza \
--i-taxonomy classified_rep_seqs.qza \
--p-exclude "Mammalia" \
--o-filtered-table feature_table_samples_filtered.qza

rm tmp.qza

# Do the barplots again
qiime taxa barplot \
--i-table feature_table_samples_filtered.qza \
--i-taxonomy classified_rep_seqs.qza \
--m-metadata-file ../metadata_for_qiime2.txt \
--o-visualization sample_barplots_filtered.qzv

# Also check remaining read counts
qiime feature-table summarize \
--i-table feature_table_samples_filtered.qza \
--o-visualization feature_table_samples_filtered.qzv \
--m-sample-metadata-file ../metadata_for_qiime2.txt