Additional file 6: of Comparative genomic analysis of Brevibacterium strains: insights into key genetic determinants involved in adaptation to the cheese habitat

Lipid-glycerol. (XLSX 27 kb

Additional file 10: of Comparative genomic analysis of Brevibacterium strains: insights into key genetic determinants involved in adaptation to the cheese habitat

Osmotolerance. (XLSX 24 kb

Number of differentially expressed genes according to ripening time.

<p>Number of differentially expressed genes according to ripening time.</p

Selection of genes showing a differential abundance between Day 1 and Day 14 and/or Day 14 and Day 31.

<p>The log2 fold change and the average number of reads (mean) are indicated only if the gene revealed a significant difference between the two ripening times (adjusted p-value < 0.05).</p><p>Selection of genes showing a differential abundance between Day 1 and Day 14 and/or Day 14 and Day 31.</p

Functional classification of the metatranscriptome during surface-ripened cheese maturation.

<p>Functional classes were determined according to KEGG annotations. Read counts corresponding to all species were cumulated. Read numbers were normalized (according to the library size) to 50,000 reads per sampling day.</p

Reference genomes used for mapping of the sequence reads.

<p>Reference genomes used for mapping of the sequence reads.</p

Lactose metabolism during surface-ripened cheese maturation.

<p>(A) Lactose and lactate concentrations. (B) Expression dynamics of lactose degradation pathways in <i>Lactococcus lactis</i> and <i>Kluyveromyces lactis</i>. Read numbers were normalized (according to the library size) to 50,000 reads per sampling day. For each degradation step, a histogram represents cumulative read numbers when several genes were involved.</p

Changes in the microbial community structure during surface-ripened cheese maturation.

<p>(A) Microbiological counts and pH measurements. (B) Distribution of metagenomic data by species. (C) Distribution of metatranscriptomic data by species (only reads mapping CDS features were taken into account). SE: <i>Staphylococcus equorum</i>. BA: <i>Brevibacterium aurantiacum</i>. AA: <i>Arthrobacter arilaitensis</i>. HA: <i>Hafnia alvei</i>. CC: <i>Corynebacterium casei</i>. DH: <i>Debaryomyces hansenii</i>. GC: <i>Geotrichum candidum</i>. KL: <i>Kluyveromyces lactis</i>. LL: <i>Lactococcus lactis</i>. NA: data not available.</p

Sequencing coverage (C) and percentage of genes (P) with at least an average of five uniquely mapped reads in the DNA-Seq dataset across the three replicates for each microbial genome during ripening.

<p>^aAA = <i>Arthrobacter arilaitensis</i>; BA = <i>Brevibacterium aurantiacum</i>; CC = <i>Corynebacterium casei</i>; DH = <i>Debaryomyces hansenii</i>; GC = <i>Geotrichum candidum</i>; HA = <i>Hafnia alvei</i>; KL = <i>Kluyveromyces lactis</i>; LL = <i>Lactococcus lactis</i>; SE = <i>Staphylococcus equorum</i></p><p>Sequencing coverage (C) and percentage of genes (P) with at least an average of five uniquely mapped reads in the DNA-Seq dataset across the three replicates for each microbial genome during ripening.</p

Protein degradation during surface-ripened cheese maturation.

<p>(A) Proteolysis and free amino acid concentration. Expression data observed for genes encoding proteases (B) and peptidases (C). Read numbers were normalized (according to the library size) to 50,000 reads per sampling day. SE: <i>Staphylococcus equorum</i>. BA: <i>Brevibacterium aurantiacum</i>. AA: <i>Arthrobacter arilaitensis</i>. HA: <i>Hafnia alvei</i>. CC: <i>Corynebacterium casei</i>. LL: <i>Lactococcus lactis</i>. KL: <i>Kluyveromyces lactis</i>. DH: <i>Debaryomyces hansenii</i>. GC: <i>Geotrichum candidum</i>.</p