The global analysis of transcription within a bacterial biofilm is an appealing technique to identify genes and specialized gene expression patterns associated with biofilm formation, without the need for extensive and time-consuming studies of individual genes (Beloin & Ghigo, 2005; An & Parsek, 2007). The reduction in the cost of genome sequencing and the availability of custom microarrays has resulted in an increase in studies using microarrays to investigate gene

expression in biofilms of their bacteria of interest. However, INK 128 mw interpretation of results from these studies is problematic because RNA is extracted from cells throughout a biofilm, which are in a wide range of metabolic states. To obtain enough biofilm material for transcriptional profiling, the entire biofilm is normally collected for RNA extraction. This is a major problem, because cells with a range of different physiological and phenotypic states are used for comparison against a homogeneous planktonic culture. Small differences between experimental setups can thus lead to large differences in results. This has been highlighted by the comparison of three independent microarray-based studies of the Pseudomonas aeruginosa quorum-sensing regulon

(An & Parsek, 2007). The independent studies contained as many differences as similarities even when a fivefold change was used as threshold. While reproducibility may have been an early major concern for microarray studies, this issue highlights the importance for researchers to consider what is actually being compared. In microbial fuel cells, there LDK378 are a number of processes that can

occur within the biofilm. Put simply, expression of individual genes may play a role in the process of biofilm formation, in the process of extracellular electron transfer, or in both. To understand these processes in a current-producing Geobacter sulfurreducens biofilm, microarrays have been used to compare gene expression in electrical biofilms, to both planktonic cells and nonelectrical biofilms. These microarrays were designed to examine genes important for biofilm formation and/or genes important for extracellular electron transfer in a biofilm. In these Ribose-5-phosphate isomerase cases, many targets have been identified. However, their importance could only be confirmed through mutational analysis, which identified important features such as nanowire production and extracellular cytochromes for power production, and/or biofilm formation. This highlights an important consideration: how are transcriptome data to be used? Typically, a quantitative reverse transcriptase-PCR reaction is used to corroborate the microarray results. Although useful, this process provides no spatial information about expression within the biofilm. This is a very challenging aspect of biofilm studies.