The problem is compounded when the biofilm is associated with tissue, which itself also needs to be digested to release bacteria that may be attached within surface convolutions or have invaded the tissue itself. We have found that the physical disruption of tissue by bead beating, followed by digestion with lysis buffer (Qiagen AL) and proteinase K (Invitrogen), yielded more consistent results than the use of lysozyme alone, which under-represented Gram-positive bacteria relative to Gram-negative bacteria (data not shown). Once nucleic acids are extracted and purified, short nucleic acid primers are used to PCR amplify specific Ku-0059436 chemical structure DNA sequences. Notably, sequences of the 16S ribosomal

DNA that encode the 16S rRNA gene are used because 16S rRNA gene is universal to prokaryotes and is widely used as a phylogenetic ‘fingerprint’

to identify organisms at the species, genus or phylum level. Other genes of interest such as virulence genes Luminespib cell line may be probed to identify antibiotic resistance (i.e. mecA for MRSA) or sets of genes can be probed for multilocus strain typing, although this is usually done on single isolates. After PCR, the resulting amplicon should contain enough material for analysis. The presence and, in some cases the relative abundance, of amplified gene sequences can be measured using a number of techniques including gel electrophoresis and ionizing spray mass spectroscopy. Quantitative real-time PCR can be used to quantify the starting amounts of DNA by monitoring the amplification during Isotretinoin the amplification step. In the case of looking for mRNA to demonstrate not only the presence of a bacterial species but

also activity, the mRNA is converted to cDNA by reverse transcriptase before PCR amplification. It is helpful to visualize a giant forest of mixed bacterial and host DNA that has been extracted from the sample within which small primers seek out corresponding sequences of bases and, when they locate and hybridize with them, produce very large numbers of identical amplicons. The repeated cycling of this process produces very large numbers of identical target sequences termed amplimers or amplicons. The strategies for deciding which genes to amplify, and for selecting methods for the analysis of the amplicons that are produced, have been driven by practical considerations. If one is involved in a leisurely world cruise to study the microbial ecology of the oceans (Ivars-Martinezet al., 2008), speed is not of the essence, and the amplicons can be frozen and analyzed by pyrosequencing over a period of months or years. If one manages a wastewater treatment plant, and is only interested in the detection and identification of a particular invidious bacterium that blocks phosphate removal (Crocettiet al., 2000), a simple and rapid PCR for that particular organism will suffice.