What set of primers do I have to use for the phylogenetic analysis of actinobacteria from a metagenomic soil sample?

11 November 2014 1 5K Report

for 16s rRNA specific primers.

Back to 2007/2008, I've used the primer set from "Stach JEM, Maldonado LA, Ward AC, Goodfellow M, Bull AT (2003) New primers for the class Actinobacteria: application to marine and terrestrial environments. Environmental Microbiology, 5, 828–841." to explore the actinobacterial diversity in marine sponges and it worked really well.

Thanks to Sebastian we know another recent report on actinobacteria-specific primers. My suggestion is to trace the papers citing the two articles and find out which primers were commonly used in your field and their performances.

Just a reminder, actinobacteria has strong cell-wall which makes it harder to extract DNA. I recommend bead-beating based Kits to extract the environmental DNA.

Good luck.

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