J Clin Microbiol 2007, 45:2048–2050.CrossRefPubMed Authors’ contributions ZWJ wrote the proposal for the fund, supervised
all the experimental work and wrote the manuscript. QOA participated in the PCR experiments, 16S rDNA sequencing and alignment, and manuscript writing. IMS participated in supervising the work at the laboratory. NAS isolated the Cronobacter spp. isolates from foods. AMR participated in PCR experiments and chromogenic identification of the pathogens. All authors read and C646 in vitro approved the final manuscript.”
“Background We recently described methods aimed at unifying classical and genomic classification of bacteriophages by integration of protein sequence data and physicochemical parameters. We developed two protein sequence similarity-based tools, CoreExtractor and CoreGenes , to parse-out and quantify relationships between pairs of phages resulting in a single URMC-099 correlation score . This analysis is followed by a deconstruction and literature analysis of the known morphological and physicochemical characteristics of these phages. The biological interpretation of molecular correlations between 55 fully sequenced NSC 683864 ic50 Podoviridae show that this approach agrees with the current phage classification of the International Committee on Taxonomy of Viruses (ICTV) and suggests that, generally, horizontal gene transfer
only partially masks evolutionary relationships between phages. Using a cut-off value of 40% homologous proteins, we verified relationships between phages known to be similar and identified several new bacteriophage genera. At the 20-30% homology level, we identified relationships of a higher order
justifying the introduction of the subfamily taxonomical category. The Myoviridae in the VIIIth ICTV Report comprise five genera of bacteriophages (Mu, P1, P2, SPO1, and T4-like viruses) and one genus of archeal viruses, phiH. I3 and phiKZ-like phages have been recently proposed as additional genera http://www.ncbi.nlm.nih.gov/ICTVdb/Ictv/fs_myovi.htm. These genera include only a small fraction of presently known myoviruses with fully Terminal deoxynucleotidyl transferase sequenced genomes . We analyze and interpret here the correlations between 102 Myoviridae genomes found in the National Center for Biotechnology Information (NCBI) and the Tulane University T4 Genome databases. Results and discussion Figure 1 shows the correlation, based on the CoreExtractor distance measure, among all available Myoviridae genomes in the NCBI databases. To verify and more subtly compare individual correlations, the CoreGenes approach was applied to subsets of related phages, including several genomes not currently available in public databases (Table 1). As in previous analyses of the Podoviridae , threshold values of 40% and 20% (and 0.6 and 0.8 relative dissimilarity, respectively) of homologous proteins strongly suggest genus and subfamily boundaries, respectively (Additional file 1).