Application of the Differential Display RT-PCR Technique to Examine Conditional Gene Expression in Ruminococcus albus

In vivo expression technologies and differential display RT-PCR provide new approaches to further examine a microbe’s response to experimental conditions which more closely resemble natural microbial associations and habitats. The latter technique also expands the scope of research which can be conducted with bacteria for which there is limited or no genetics protocols. We have used differential display RT-PCR to examine the physiological response of Ruminococcus albus to phenyl-substituted fatty acids. Micromolar concentrations of these acids have previously been shown to dramatically improve the ability of this bacterium to utilize cellulose as a carbon and energy source, thereby improving the environmental fitness of this bacterium in the ruminal environment. Coupled with northern blot analysis, we have been able to identify several transcripts which increase in abundance in response to phenyl-substituted fatty acids. Preliminary cDNA sequence analysis suggest that the transcripts encode enzymes, regulatory and transport proteins which have not been previously identified in this bacterium. It should be possible to further expand the application of differential display RT-PCR to study other aspects of physiological ecology and host-microbe interactions.