The impact of Candida albicans on the transcriptome of Enterococcus faecalis when grown in a biofilm
We sought to identify transcriptomic changes that arise when E. faecalis biofilms are cultivated in the presence of C. albicans. We used RNASeq analaysis to compare the transcriptome of 48 hr biofilm-grown cells of E. faecalis.  We compared the transcriptome of E. faecalis cells grown as a mono-species biofilm to that of E. faecalis cells that were grown in a biofilm that was co-inoculated with the yeast C. albicans. Overall design: Cultures of E. faecalis OG1RF or C. albicans SC5314 were inoculated in BHI broth or Yeast Peptone Dextrose broth, respectively.  The cultures were grown to stationary phase, then cells were harvested by cetnrifugation and washed twice in sterile PBS.  The cell pellets were then suspended in BHI broth supplemented with 20mM glucose (BHIG).  The suspensions were adjusted to OD600 of 0.5 for E. faecalis (~3x10^9 CFU mL-1) or OD600 of 0.3 for C. albicans (~2.5x10^6 CFU mL-1).  Monospecies biofilms were initiated by adding 5mL of the E. faecalis suspension, while dualspecies biofilms were initiated by adding 2.5mL each of the E. faecalis and C. albicans suspensions to the wells of a 6-well plate.  The plates were incubated at 37C for 48hr in a 5% CO2 atmosphere, with fresh medium provided after 24 hrs.  After a total of 48hrs incubation, the media was removed and the cells of each well were suspended in 1mL of RNA Protect Bacterial Reagent (Qiagen).  Total RNA was isolated and prepared for RNA-Seq analysis.