how to do the alpha and beta diversity and microbiota composition analysis ?

Thanks for you explanation :slight_smile:. I edited a new metadata file(groups in the sample ID column). And I used the following commands to generate the taxa plots.

qiime feature-table group
--i-table table-dada2.qza
--p-axis sample
--m-metadata-file sample-metadata.tsv
--m-metadata-column trea-line
--p-mode mean-ceiling
--o-grouped-table grouped-table.qza
--verbose

qiime taxa barplot
--i-table grouped-table.qza
--i-taxonomy taxonomy.qza
--m-metadata-file group-metadata.tsv
--o-visualization taxa-bar-plots-grouped.qzv

The genertated plot is as follows:

Is it right?

The .csv file(level 2) is as follows. But I do not know the meaning of the number in the table, is it the number of bacterial?