J Clin Microbiol 2007, 45:2923–2928.PubMedCrossRef 34. Vergnaud G, Pourcel C: Multiple locus variable number of tandem repeats analysis. Methods Mol Biol 2009, 551:141–158.PubMedCrossRef 35. MLVAbank for Bacterial Genotyping [http://​mlva.​u-psud.​fr/​] Authors’ contributions RDes and ACia did the set up of the Brucella MLVA-16 assay. Rdes, ACia and CMa participated to typing work. FL, EDG and MAn did the error checking

analysis. SFi and GFa did various sequence analysis. FL, BGe and RDes were in charge selleck screening library of the database and clustering analyses. FL, MAn, and RDes conceived the study. FL and RDes wrote the report. All authors read and approved the final manuscript”
“Background Microorganisms in natural environments rarely grow as single species, but grow as mixed species consortia in which a variety of intra- and inter-species interactions take place [1, 2]. VE-821 datasheet Previous studies have shown that species interactions play an important role in the development, composition, structure and function of microbial consortia in biofilms as well as in suspended growth communities [3–5]. Studies of species interactions have promoted the understanding of microbial activities in mixed-species communities [6–8]. Identification of relevant genes is an important step toward the elucidation of the molecular mechanisms of Ulixertinib species communication.

cDNA microarray technology has been widely used for mono-species cultures, but only a few cDNA microarray studies have been performed for mixed-species consortia due to broad cross hybridization among species

[6, 9, 10]. Variable conservation of genes existed across bacterial species [11]. Non-target transcripts have been shown to cross hybridize in oligonucleotide microarray studies [12]. The problem was addressed previously by carefully selecting co-cultures consisting of one gram-negative and one gram-positive strain, so that RNA could be selectively OSBPL9 extracted from one strain [6, 9]. However, for most mixed-species communities, selective RNA extraction is not possible and a method needs to be developed in order to apply cDNA microarray technology to such communities. Separating the target species from other community members before extracting RNA could be an approach in minimizing cross hybridization on microarrays. Immuno-magnetic separation (IMS) using magnetic force to recover target cells with paramagnetic beads and specific antibodies has been widely used [13–15]. The IMS procedure has been standardized [16]. However, isolated cells have not been considered for cDNA microarray analysis. While the purity of recovered cells is important for microarray analysis, it was not always considered in previous studies. In addition, preserving the transcription profile of target cells during IMS is critical for downstream microarray analysis and is the most important concern addressed in this study.