Additional file 7: of Antagonism between Staphylococcus epidermidis and Propionibacterium acnes and its genomic basis

A: Seven genomic islands in strain S. epidermidis AU23. B: Ten genomic islands in strain S. epidermidis FS1. C: Eight genomic islands in strain S. epidermidis 14.1.R1. (XLSX 331 kb

Additional file 3: of Antagonism between Staphylococcus epidermidis and Propionibacterium acnes and its genomic basis

Inhibitory activity of 77 P. acnes strains against 12 S. epidermidis strains. (DOCX 31 kb

How to Kill the Honey Bee Larva: Genomic Potential and Virulence Mechanisms of <i>Paenibacillus larvae</i>

<div><p><i>Paenibacillus larvae</i>, a Gram positive bacterial pathogen, causes American Foulbrood (AFB), which is the most serious infectious disease of honey bees. In order to investigate the genomic potential of <i>P. larvae</i>, two strains belonging to two different genotypes were sequenced and used for comparative genome analysis. The complete genome sequence of <i>P. larvae</i> strain DSM 25430 (genotype ERIC II) consisted of 4,056,006 bp and harbored 3,928 predicted protein-encoding genes. The draft genome sequence of <i>P. larvae</i> strain DSM 25719 (genotype ERIC I) comprised 4,579,589 bp and contained 4,868 protein-encoding genes. Both strains harbored a 9.7 kb plasmid and encoded a large number of virulence-associated proteins such as toxins and collagenases. In addition, genes encoding large multimodular enzymes producing nonribosomally peptides or polyketides were identified. In the genome of strain DSM 25719 seven toxin associated loci were identified and analyzed. Five of them encoded putatively functional toxins. The genome of strain DSM 25430 harbored several toxin loci that showed similarity to corresponding loci in the genome of strain DSM 25719, but were non-functional due to point mutations or disruption by transposases. Although both strains cause AFB, significant differences between the genomes were observed including genome size, number and composition of transposases, insertion elements, predicted phage regions, and strain-specific island-like regions. Transposases, integrases and recombinases are important drivers for genome plasticity. A total of 390 and 273 mobile elements were found in strain DSM 25430 and strain DSM 25719, respectively. Comparative genomics of both strains revealed acquisition of virulence factors by horizontal gene transfer and provided insights into evolution and pathogenicity.</p></div

Maps of the <i>P. larvae</i> DSM 25719 (A) and DSM 25430 (B) chromosome The different circles represent (from inside): (a), GC content; (b), strain-specific regions (orange) and prophages (green); (c), genes present in both analyzed strains (grey) and genes found only in one strain (purple); (d), all ORFs clockwise and anticlockwise or (blue); (e), scale; (g), highlighted genes, gene clusters, including toxins, potential virulence factors mentioned in the manuscript (red).

<p>Maps of the <i>P. larvae</i> DSM 25719 (A) and DSM 25430 (B) chromosome The different circles represent (from inside): (a), GC content; (b), strain-specific regions (orange) and prophages (green); (c), genes present in both analyzed strains (grey) and genes found only in one strain (purple); (d), all ORFs clockwise and anticlockwise or (blue); (e), scale; (g), highlighted genes, gene clusters, including toxins, potential virulence factors mentioned in the manuscript (red).</p

Genetic organization of subtilisin-like serine protease gene locus.

<p>Related ORFs are shown in the same following colors: blue, subtilisin-like serine protease gene; yellow, transposases/integrases; grey, genomic context (A). The similarities between pairs of sequences are depicted. PCR screening of ERIC I and ERIC II strains for functional or disrupted subtilisin-like serine protease genes (B).</p

Comparison of the <i>P. larvae</i> DSM 25719 Tx6 toxin-encoding locus with selected strains.

<p>Related ORFs are shown in the same following colors: yellow, transposases; grey, genomic context; green, botulinum toxin complex components; cyan, binary toxin A domain-containing protein; and red, binary toxin B domain-containing proteins. The arrows indicate the direction of transcription.</p

Genetic organization of toxin complex loci identified in <i>P. larvae</i> DSM 25719 and DSM 25430.

<p>Related ORFs are shown in the same colors. Toxin loci Plx1-7 are encoded within <i>P. larvae</i> DSM 25719 genome (ERIC I) and toxin loci TxI-III within <i>P. larvae</i> DSM 25430 (ERIC II).</p

Genetic organization of lantibiotic biosynthesis clusters from <i>P. larvae</i> DSM 25719 (ERIC I) and DSM 25430 (ERIC II).

<p>Related ORFs are shown in the same following colors: yellow, transposases; grey, genome context; green, type I restriction system; cyan, lantibiotic biosynthesis clusters; and orange, integrase. The arrows indicate the direction of transcription.</p

General genomic features of the <i>P. larvae</i> strains.

<p>General genomic features of the <i>P. larvae</i> strains.</p

<i>P. larvae</i> infection model.

<p><i>P. larvae</i> infection model.</p