Representative ERIC-PCR fingerprint of different between <i>Salmonella</i> isolates on 2 per cent agarose gel.

<p>M: 1000 bp DNA marker; lane 1 to 13: F34′, F35′, C31′, C32′, C33′, C34′, C36′, L1, L2, L3, L4, L5 and L9.</p

Dendrogram showing the percentage of similarity between typable <i>Salmonella</i> isolates generated from composite fingerprinting.

<p>Genetic similarity between samples in duplicate is 80%.</p

Distribution of <i>Salmonella</i> isolates derived from broilers, clams and cow milk.

<p>Distribution of <i>Salmonella</i> isolates derived from broilers, clams and cow milk.</p

PFGE Dendrogram showing the relationship between <i>Salmonella</i> isolates.

<p>The similarities between strains were evaluated using the Dice coefficient and the UPGMA clustering method. Genetic similarity between samples in duplicate is 80%.</p

Genetic similarities of <i>Salmonella</i> strains isolated from clams, broilers and milk based on ERIC-PCR patterns.

<p>The dendrogram was generated by BioNumerics Software with the bande-matching coefficient of Dice and the UPGMA clustering. Genetic similarity between samples in duplicate is 80%.</p

Time-course comparison of transcriptome and proteome changes in <i>P. freudenreichii</i> CIRM-BIA1^T strain, for genes involved in metabolic categories CD, CE, DNA, E, L, Mi, Nt, and P.

a<p>Spot number (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029083#pone.0029083.s006" target="_blank">Table S4</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029083#pone-0029083-g002" target="_blank">Fig. 2</a>).</p><p>Bold characters indicate genes that are differentially expressed according to microarray experiments (<i>P</i><0.05 and |fold change|>1 for at least one sampling time) and RT-qPCR (<i>P</i><0.05) experiments.</p

Time-course of <i>P. freudenreichii</i> CIRM-BIA1^T metabolic activity over a 40 h-incubation at 30°C followed by a further 9 days at 4°C.

<p>Lactate was added at 64 h (<b>↓</b>) to mimic cheese ripening conditions. <b>A</b>, growth monitored by optical density (650 nm) measurements (black circle), lactate consumption (cross), production of acetate (white triangle) and propionate (black triangle); <b>B</b>, production of pyruvate (white rhombus) and succinate (black rhombus), consumption of aspartate (white triangle) and asparagine (black triangle); <b>C</b>, production of methylbutanoate (sum of 2-methyl- and 3-methylbutanoate acids). ¥: sampling times for microarray experiments.</p

Time-course comparison of transcriptome and proteome changes in <i>P. freudenreichii</i> CIRM-BIA1^T strain, for genes involved in metabolic categories A, AA and C.

a<p>Spot number (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029083#pone.0029083.s006" target="_blank">Table S4</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029083#pone-0029083-g002" target="_blank">Fig. 2</a>).</p><p>Bold characters indicate genes that are differentially expressed according to microarray experiments (<i>P</i><0.05 and |fold change|>1 for at least one sampling time) and RT-qPCR (<i>P</i><0.05) experiments.</p

Time-course comparison of transcriptome and proteome changes in <i>P. freudenreichii</i> CIRM-BIA1^T strain, for genes involved in metabolic category Ph and PM.

a<p>Spot number (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029083#pone.0029083.s006" target="_blank">Table S4</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029083#pone-0029083-g002" target="_blank">Fig. 2</a>).</p><p>Bold characters indicate genes that are differentially expressed according to microarray experiments (<i>P</i><0.05).</p

Figure 2

<p>Two-dimensional analysis of proteins produced during <i>P. freudenreichii</i> CIRM-BIA1^T growth (<b>A</b>) at 30°C (reference time 20 h) and then (<b>B</b>) at 4°C (3 days). Numbers identify spots which volume decreased at 4°C (<b>A</b>), or increased at 4°C (<b>B</b>). The identification by MS/MS of each spot can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029083#pone.0029083.s006" target="_blank">Table S4</a>.</p