In addition, while most studies with C. albicans were carried out with the reference isolate SC5314, a wider variety of isolates have been included in this kind of studies for other organisms. For example, for Escherichia coli strains MG1655 (Schembri et al., 2003; Ito et al., 2009a, b), TG and TG1 (Beloin et al., 2004), JM109 and ATCC 25404 (Ren et al., 2004), BW25113 (Domka Barasertib molecular weight et al., 2007) and PHL628 (Junker et al., 2007) have been used, as well as clinical isolates recovered from asymptomatic bacteriuria (Hancock & Klemm, 2007). Although several of these strains are listed as ‘K12’, subtle differences

between them may confound the comparison of gene expression data. It is important to keep this in mind when looking for genotypic and/or phenotypic adaptation to stress in sessile cells, as the differential expression of particular

genes due to differences in the environmental conditions in the test and control situation may introduce bias and lead to erroneous conclusions. Pseudomonas aeruginosa was one of the first organisms in TSA HDAC chemical structure which gene expression in biofilms was studied, but surprisingly, when Whiteley et al. (2001) compared gene expression levels between cells grown on granite pebbles in a chemostat and cells grown in a liquid culture medium in the same chemostat, very few genes showed differential expression. When gene expression in untreated sessile P. aeruginosa PAO1 cells was compared with the expression in sessile cells treated with high doses of tobramycin [seven times the minimal inhibitory concentration (MIC) for planktonic cells], only 20 genes were differentially expressed (14 were activated and six were repressed). Ten of these genes code for hypothetical proteins with no known function; two additional genes code for hypothetical proteins of a Pf1-like bacteriophage. Upregulated genes include those involved in stress response (dnaK, groES) and efflux systems, while downregulated

genes include both hypothetical phage proteins as well as the β-subunit of urease (Table 2). The tolA gene, whose product affects the lipopolysaccharide structure in such a way that the outer membrane has a decreased affinity for aminoglycoside antibiotics, was overexpressed in untreated sessile cells compared either with planktonic cells, possibly leading to decreased aminoglycoside susceptibility in biofilms. Genes encoding cytochrome c oxidases (subunits I, II and III, encoded by PA0106, PA0105 and PA0108, respectively), on the other hand, were downregulated (2.7–2.9-fold) in untreated sessile cells when compared with planktonic cells. As cytochrome c oxidase is the terminal electron acceptor during aerobic growth and as aminoglycoside transport is coupled with terminal electron transport (Bryan et al., 1980), this downregulation is likely to confer reduced susceptibility as well.