Similarly, pyrosequencing analysis of microbes resident in diabetic selleck compound foot ulcers identified 38 distinct genera and again yielded a subset of sequences unmatched to any recognized microbial sequences (Dowd et al., 2008b). The microbiome of the healthy oral cavity when examined by cloning and sequencing comprises more than 1000 distinct taxa with over half of them yet to be cultured (Dewhirst et al., 2010). This heretofore unappreciated microbial diversity raises significant questions about the relative importance of the component

organisms, individually and in communities, to health and disease. Much progress has also been made in the examination of bacterial gene expression patterns associated with biofilm formation, including whole transcriptomic studies on multiple microbial species. The vast majority of these studies have been on in vitro biofilms and employ a range of technologies. DNA microarray analysis of microbial transcriptomes has now been accomplished for a variety of organisms associated with human disease, including LDK378 supplier Escherichia coli (Reshamwala & Noronha, 2011), Streptococcus mutans (Shemesh et al., 2010), Streptococcus pyogenes (Kreth et al., 2011), and

Candida (Sellam et al., 2009). Direct RNA sequencing (RNA Seq) has also been undertaken to distinguish biofilm-specific patterns of gene expression. Dotsch et al. used RNA Seq to compare planktonic cultures of P. aeruginosa with stationary phase cultures and bacteria grown as a biofilm. They found that although there was substantial similarity in the gene expression profiles of stationary phase and biofilm cells, there were also significant differences, indicating that the physiology of biofilm bacteria was not simply surface-attached stationary phase cells. Some studies have begun to examine the transcriptomes of bacteria in vivo. Bielecki et al. (2011) Bacterial neuraminidase investigated the expression profiles of three distinct clonal isolates of P. aeruginosa from burn wounds in five different conditions: directly from a burn wound sample, in a plant infection, in a murine tumor infection, and as planktonic and biofilm cultures. They found distinct patterns of

gene expression in each condition, indicating distinct adaptive responses of P. aeruginosa to different environments. Immunohistochemical or immunofluorescent techniques represent another targeted approach to identifying pathogens in host tissue. Polyclonal or monoclonal sera specific to pathogens are routinely used to detect encapsulated pathogens in fluids such as S. pneumoniae, Neisseria meningiditis, and Haemophilus influenzae. These antibodies have not been consistently applied for the detection of bacteria in biofilms often because it is thought the matrix may bind antibodies nonspecifically. However, antibodies can be used by performing parallel controls and careful testing of sera, as well as using blocking steps to reduce nonspecific interactions (Fig. 2) (Hall-Stoodley et al., 2006).