Metabolic pathways that lead to the degradation of all the carbon sources that are discussed in this study were determined with KEGG. Metabolic intermediates that were common between different pathways were used to construct metabolic maps. Pathways for both strains were combined in Figures 5 and 6.

2. Results

2.1 Strain selection using electron micrographs

To determine the ability to form biofilm, electron microscopy was performed with the five strains that were listed in Materials and Methods. Figure 3 depicts one representative illustration of the 10 to 15 images that were obtained per bacterial strain. Most of these strains formed biofilm despite mutations affecting cell surface organelles of either reversible (flagella) or irreversible (type I fimbriae) attachment. The sole exception was the fimH mutant which only showed a small number of scattered bacteria attached across the slide. The fimA mutant exhibited a large number of filamentous appendages. We are currently unable to explain these appendages.

We wanted a strain for the phenotype microarray experiment that was able to form biofilm on complex media, while lacking one of the cell surface organelles. Since the amount of biofilm formed by the flhD mutant was similar to that of the parental strain in the electron micrographs, the flhD mutant was selected for further testing using the PM1 plates. The flhD mutant has as an additional advantage that much of the regulation by FlhD/FlhC has been previously described. This vast amount of information will help us to analyze the complex metabolic data.