For my analysis, I'd like to know if identified species are aerobic or anaerobic.
I found that I could retrieve this information from BacDive database. However, I can only search by taxonomic information.
Would search by 16S sequence be more reliable?
Are there other tools to do that?
Sorry this has taken us so long to get back to you! You could add a taxonomic annotation to your 16S samples and then query using the annotations. Check out the Parkinson's Mouse tutorial for an example of how to do this.
I think the only advantage to searching only by 16S sequence data is that if you had a sample that was unable to be matched to an annotation and there was a classification of aerobic/anaerobic assigned to that sequence in the database, it would allow you to ascribe this characteristic to that sample without knowing the taxonomic information. I find this to be a pretty unlikely scenario, though I would love to hear from some of our more experienced researchers on here.
It is a few extra steps, but I think this process will get you the results you are seeking.