Comparative genome analysis of five bacteriophages derived from emetic <i>B</i>. <i>cereus</i> using the Mauve program.

<p>Genomes used for alignment were from phages PfEFR-4, 11143, PfIS075, Tp250, and vB_Bces-IEBH. The putative ORFs are presented as white rectangles and the nine LCBs are indicated as various contiguously colored regions. The genome of PfEFR-4 was used as a reference sequence.</p

Heat-plot analysis of 36 <i>Bacillus</i> phages revealed three clusters and four singletons using Gegenees.

<p>Fragmented alignment based on BLASTN was performed with settings 50/25. The cutoff threshold for non-conserved material was 30%. A dendrogram was produced in SplitsTree 4 (using neighbor joining) made from a Nexus file exported from Gegenees.</p

Transmission electron micrographs of phages isolated in this study.

<p>PfNC7401 (a), PfIS075 (b), PfEFR-4 (c), PfEFR-5 (d), and PfATCC7953 (e) were stained with 2% phosphotungstic acid and visualized. White arrow indicates the putative tail fiber. Scale bars are 50 nm.</p

Lytic activity and antimicrobial spectrum of LysEFR-4.

<p>Lytic activity of LysEFR-4 was measured by (a) turbid reduction assay and (b) plate lysis assay. CK indicates the control with the same volume of dialysis buffer replacing LysEFR-4 in the assay. (c) Antimicrobial spectrum of LysEFR-4. All experiments were carried out in triplicate.</p

Phylogenetic tree based on the tail fiber proteins of 36 <i>Bacillus</i> phages.

<p>Phylogenetic trees were constructed based on the amino acid sequences of the tail fiber proteins of 36 <i>Bacillus</i> phages using neighbor joining with a bootstrap of 1,000. Circles represent the phages derived from emetic isolates. Numbers on the lines indicate branch support. Corresponding clusters (A-C) are also shown on the right.</p

Identification and genomic comparison of temperate bacteriophages derived from emetic <i>Bacillus cereus</i>

<div><p>Cereulide-producing <i>Bacillus cereus</i> isolates can cause serious emetic (vomiting) syndrome and even acute lethality. As mobile genetic elements, the exploration of prophages derived from emetic <i>B</i>. <i>cereus</i> isolates will help in our understanding of the genetic diversity and evolution of these pathogens. In this study, five temperate phages derived from cereulide-producing <i>B</i>. <i>cereus</i> strains were induced, with four of them undergoing genomic sequencing. Sequencing revealed that they all belong to the <i>Siphoviridae</i> family, but presented in different forms in their hosts. PfNC7401 and PfIS075 have typical icosahedral heads, probably existing alone as phagemids in the host with self-replicating capability in the lysogenic state. PfEFR-4, PfEFR-5, and PfATCC7953 have elongated heads, with the genomes of the former two identified as linear dsDNA, which could be integrated into the host genome during the lysogenic state. Genomic comparison of the four phages with others also derived from emetic <i>B</i>. <i>cereus</i> isolates showed similar genome structures and core genes, thus displaying host spectrum specificity. In addition, phylogenic analysis based on the complete genome and conserved tail fiber proteins of 36 <i>Bacillus</i> species-derived phages confirmed that the phages derived from emetic <i>B</i>. <i>cereus</i> strains were highly similar. Furthermore, one endolysin LysPfEFR-4 was cloned and showed lytic activity against all tested emetic <i>B</i>. <i>cereus</i> strains and cross-lytic activity against some other pathogenic bacteria, implying a potential to control bacterial contamination in the food supply.</p></div

The variation of identified root exudates that caused the separation among the different Cd exposed concentrations.

<p>The variation of identified root exudates that caused the separation among the different Cd exposed concentrations.</p

Loadings plot of identified root exudates from <i>S. alfredii</i> for the OPLS-DA model.

<p>Loadings plot of identified root exudates from <i>S. alfredii</i> for the OPLS-DA model.</p

Proteomics analysis of the purified phages.

<p>Structural protein patterns of phages by 15% SDS-PAGE. Lane M: SM0671 protein marker. The PfIS075 and PfEFR-4 proteins identified by LC-MS/MS are shown on the right of the SDS-PAGE gels.</p

Repeatability of the data.

<p>Repeatability of the data.</p