Hello, have a good time. I have a question. I wanted to know if it was possible to combine different datasets that worked on the same subject, for example, five different datasets in various studies worldwide, all of which examined the salivary microbiome in cancerous and healthy people. Then the output of dada2 (OTU-table)from 5 studies Combine together with QIIME2 and perform downstream analyzes. Is this reportable in the articles, and is it practically correct? How can we combine different datasets that have done the same thing?
Check out Qiita, it was created for the metanalysis of microbial studies specifically.
As long as you operate on public data (i.e. downloaded from EBI or SRA), your approach is right, and using unified preprocessing params would eliminate systemic errors.
If each run was processed identically with the same primers, then you can merge your feature-tables, sequences and taxonomy files. Here is an example from the Fecal microbiota transplant tutorial.
If these data were produced via different primer sets, you can use closed-reference OTU picking. More details are here: