We are planning for the Molecular Identification of Bacterial and Fungal Isolates, identified form various samples/sources. While, for Bacterial 16s rRNA gene, there are universal primers that can be used. But, in the case of a fungus, there is no universal primer, and most papers suggest using ITS regions for a primer for the 18s rRNA gene. I would appreciate it if you could suggest preferred primers for molecular characterization of bacteria and fungi (using 18s and 16s DNA/rRNA sequences).
For fungi: http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2009.02635.x/full They describe and evaluate the benefits of different standard primer targets and make a good case for ITS4 and ITS5 as universal fungal primers.
For bacteria: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049755
The authors prefer chaperonin as a target for bacterial species identification from environmental samples.
I see this question has been asked already a while ago. Any update on this project?
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