Regarding the choice of Ref database & a related Question

I created my custom silva.v4.fasta from silva.full_v123.fasta instead of silva.bacteria.fasta mentioned in MiSeq SOP.

I made silva.full_v123.fasta by following instructions provided in:

This is because I wanted to include both Archaea as well as Bacteria.

I just wanted to make sure I am on the right track because we have to analyse some environmental samples – that can include diverse organisms. Is my approach correct?

=== Question 2

By the way, similar to MiSeq SOP (an excellent resource) for mapping taxonomy from 16S data for bacteria and archaea, do we have a similar resource for 18S taxonomy analysis.

This is because in our project we wanted to identify all components of an environmental sample like:
bacteria, fungi, algae, protozoa,…

Please suggest. Thank you in advance.

one of the silva db should contain all domains (can’t remember off the top of my head which one). What primers are you using that hit all 3 domains? Hugenholtz worked on developing some when he was at JGI but they missed big groups of Archaea and were for v9.

Adding to my question above, for example, what could be a comprehensive reference database for eukaryotes (or how to construct one), which can be used in mothur analysis. Thank you.

Primers I use are the following:

All sequences 5’-3’ orientation:


And for the 18S ITS primers:

Thanks for your help.