A study published in Science by Baker et al (1) sheds light on how some limitations ofusing PCR to collect genomic data from bacterial communities. The authors describe how "PCR-based methods have limited ability to detect organisms whose genes are significantly divergent relative to gene sequences in databases" (1). Additionally, they describe how "most cultivation-independent genomic sequencing approaches are relatively insensitive to organisms that occur in low abundances" (1). In this case the authors were able to concentrate specific acidophilic archaea using a filtration based method to concentrate cells from biofilms growing within the Richmond Mine, California at pH of 0.5 -1.5. Fluorescently labeled oligos specific for 16S rRNA for all previously known Archaeal Richmond Mine Acidophilic Nanorganisms (ARMAN) aided in microscopic analysis of samples.
This really drives home the point of no matter how much data our new tools, like PCR, generate if we are not careful we may be just missing an important piece of the puzzle.
1. Baker, BJ, Tyson GW, Webb RI, et al. Lineages of Acidophilus Archaea Revealed by Community Genomic Analysis. Science, Dec 22, 2006. Vol 314, p 1933-1935.