We evaluated the performance of several DNA extraction kits on urine samples. While we found differences in the quantity of DNA extracted amongst kits, we did NOT find large differences in the microbial composition recovered from individual samples.
Importantly, we found that the kits had a high variability in dilute samples, indicating that kit choice is important for low microbial biomass specimens such as catheter-collected urine.
In our most dilute mock microbial samples, the DNeasy Blood & Tissue kit detected all expected microbes (and others), while the other kits did not. This reminds us that when dealing with low microbial biomass samples, experimental design is key to help identify contaminants.
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