g. alginate) and/or other components that can sequester antibiotics (e.g. cyclic glucans) and the differential expression of genes affecting cellular uptake (e.g. tolA). Finally, altering the expression of genes coding for the target of the antimicrobial agent (e.g. ERG genes in C. albicans) and/or activating alternative www.selleckchem.com/products/DAPT-GSI-IX.html pathways can also result in decreased susceptibility. Interestingly, in various organisms, the expression of genes thought to be involved in stress resistance is altered in sessile cells compared with planktonic

cells, even in the absence of the stress, leading to the ‘innate resistance’ of sessile cells. Examples include the upregulation of several genes coding for efflux pumps in C. albicans, the upregulation of tolA in P. aeruginosa, the downregulation of cytochrome c oxidase genes in P. aeruginosa and the upregulation of heat shock proteins in E. coli. Generating diversity by the induction of prophages may also contribute to the intrinsic resistance of biofilm populations. It is a common misconception that all cells in a biofilm are exposed to the same conditions. In contrast, differences in metabolic activities combined with differences in the transport of molecules in a biofilm result in gradients of nutrients, oxygen, signaling molecules and metabolic end products. As a result of

these gradients, considerable structural, chemical and biological heterogeneity can be found within a biofilm (Stewart & Franklin, 2008). For example, tomographic fluorescence imaging using silica nanoparticle sensors showed that within an E. coli biofilm, pH values can vary from Selleckchem EPZ6438 5 to >7, due to the low rates of diffusion of acidic metabolites or accumulation of fermentation products in oxygen-limited

parts of the biofilm (Hidalgo et al., 2009). As a consequence of this diversity, harvesting entire biofilm populations will only allow the identification of genes as being differentially expressed if these genes are uniquely expressed in biofilms and will result in an ‘average’ picture of gene expression (Stewart & Franklin, 2008). Unfortunately, few alternatives are at our disposal. Reporter genes fused to promoter regions PD184352 (CI-1040) of a gene of interest can be used to microscopically monitor the expression of that gene in a biofilm (Stewart & Franklin, 2008). A recent example of such a study is that of Ito et al. (2009a), who used an rpoS-gfp transcriptional fusion mutant to monitor rpoS expression in E. coli biofilms. Their results confirmed the existence of localized expression profiles, with rpoS being expressed in the majority of cells in the early phases of biofilm formation, while in the later stages of biofilm formation, rpoS expression appeared to be limited to cells at the outside of the biofilm. Although useful, this approach requires the use of genetically manipulated microorganisms and is at present not suitable for the simultaneous analysis of a large number of genes. Lenz et al.