How to identify Methanobrevibacter smithii and other archeae bacteria via qiime2 ?


THe question is which hypervariable region of bacterial 16S rRNA gene could be target to identify archeae particularly Methanobrevibacter smithii using qiime2 ?


Hi @M_F ,
Your question was moved to "general discussion" because it sounds like it is more about primer selection than it is about QIIME 2.

I recommend referring to the literature to find the best primers for this. E.g., this looks like a good place to start:

As you are interested in a specific species, you could just BLAST those primers against the species to see that it hits... otherwise you could check coverage against a database of full-length 16S rRNA genes from multiple species of interest. (e.g., an easy way with QIIME 2 would be to use qiime feature-classifier extract-reads and see how many sequences you have before/after for each primer set).

That will get you coverage, but if you want to know which region gives you the most taxonomic resolution, RESCRIPt has some methods for taxonomic evaluation, e.g., via cross-validation with a reference sequence database of interest. You can trim a full database (e.g., all SILVA archaea sequences) with your primers of interest, and then use RESCRIPt to evaluate and compare accuracy scores for each region.

Or if you are interested only in M. smithii, extract reads using each primer set as described above, train a classifier, and classify M. smithii reads (from the same region) using each classifier to see the taxonomic depth achieved.

Good luck!


Thanks @Nicholas_Bokulich . Could you tell me which hypervariable region of 16S rRNA gene could be investigated to decipher the gut archeome profile ?