I've done a little more work with the GenomiPHI kit. It is not a panacea for all that ails with PCR done directly on environmental DNA. I have had mixed results with different samples. Some samples with weak PCR do not fare well with the kit while others do. I have also determined that halving the recommended volumes does not help - you should use their recommendations.
On the plus side, I performed a denaturing gradient gel electrophoresis (DGGE) analysis of an environmental DNA extract directly and after pre-amplification with the genomi-PHI kit. The bacterial 16S ribosomal RNA gene profiles look identical before and after pre-amplification, suggesting that the pre-amplification is not biased.
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