DNA was extracted from the phage resistant subcultured cells derived from the regrowth area within plaques on <i>P</i>. <i>acnes</i> (ATCC 6919).

<p>PCR across the 3’ phage genome overhang displayed a band of approximately 735 bp, potentially indicating the presence of circularised phage episomal DNA. Lanes 1–10 represent DNA extracted from resistant <i>P</i>. <i>acnes</i> (ATCC 6919) strains arising from exposure to PAC1-PAC10. Lane 11 represents control DNA extracted from <i>Propionibacterium freudenreichii</i>.</p

Phylogenetic tree of the 72 known sequenced P. acnes phages.

When bootstrap values <80 were collapsed, 53 distinct strains emerged, with the PAC phage effectively adding another ten strains to the 43 reported previously. Of these, nine highly homologous groups, with members differing by as little as 11–14 base pairs, emerged as distinct clonal strains (strains I-IX), as reported recently (33). Insert shows phylogenetic relationships between PAC1 to PAC10.</p

Enrichment of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in the cecal microbiota of broiler chickens fed a basal diet supplemented with 40 (LYS40), 100 (LYS100), or 200 ppm (LYS200) lysozyme or 400 ppm flavomycin determined by comparison with the KEGG functions observed in the cecal microbiota of broiler chickens fed only the basal diet (control).

Enrichment of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in the cecal microbiota of broiler chickens fed a basal diet supplemented with 40 (LYS40), 100 (LYS100), or 200 ppm (LYS200) lysozyme or 400 ppm flavomycin determined by comparison with the KEGG functions observed in the cecal microbiota of broiler chickens fed only the basal diet (control).</p

PAC1 to PAC10 phage are able to circularise.

<p>PCR was performed across a region incorporating the 11 bp overhang at the 3’ end of the genome. A band of approximately 735 bp was seen in all the phage and was only possible if the genomes were circular. Lanes 1 to 10 represent DNA from PAC phages and lane 11 is <i>Propionibacterium freudenreichii</i> prophage DNA as negative control.</p

Modular structure of PAC1.

<p>The coloured arrows indicate predicted ORFs and direction of translation. Modular structure is indicated in blocks of colour and the putative gene function is noted below.</p

Biodiversity indices of the gut microbiota in broiler chickens fed a basal diet supplemented with 0 (control), 40 (LYS40), 100 (LYS100), or 200 ppm (LYS200) lysozyme or 400 ppm flavomycin.

Biodiversity indices of the gut microbiota in broiler chickens fed a basal diet supplemented with 0 (control), 40 (LYS40), 100 (LYS100), or 200 ppm (LYS200) lysozyme or 400 ppm flavomycin.</p

Effects of dietary supplementation with lysozyme and flavomycin on the composition and distribution of bacterial and fungal OTUs in the cecal microbiota of broiler chickens.

(A&B) Venn diagrams showing the occurrence of bacterial (A) and fungal (B) OTUs identified in 16S rRNA and ITS fragment sequencing of cecal microbiota of chickens fed a basal diet supplemented with or without 40 (LYS40), 100 (LYS100), or 200 ppm (LYS200) lysozyme or 400 ppm flavomycin. (C&D) Grouping of cecal bacterial (C) and fungal (D) communities based on principle component analyses of Illumina sequencing of 16S rRNA amplicons (V3-V4 region) and ITS fragment sequencing, respectively.</p

Phylogenetic classification and differences in the cecal microbiota of broiler chickens fed a basal diet supplemented with or without 40 (LYS40), 100 (LYS100), or 200 ppm (LYS200) lysozyme or 400 ppm flavomycin.

Phylum compositions of the bacterial (A) and fungal (B) communities in the cecal microbiota characterized based on sequencing of 16S rRNA amplicons (V3-V4 region) and ITS fragment sequencing.</p

Enrichment of Gene Ontology (GO) functions in the cecal microbiota of broiler chickens fed a basal diet supplemented with 40 (LYS40), 100 (LYS100), or 200 ppm (LYS200) lysozyme or 400 ppm flavomycin determined by comparison with the GO functions observed in the cecal microbiota of broiler chickens fed only the basal diet (control).

Enrichment of Gene Ontology (GO) functions in the cecal microbiota of broiler chickens fed a basal diet supplemented with 40 (LYS40), 100 (LYS100), or 200 ppm (LYS200) lysozyme or 400 ppm flavomycin determined by comparison with the GO functions observed in the cecal microbiota of broiler chickens fed only the basal diet (control).</p

Effects of dietary supplementation with 0 (control), 40 ppm (LYS40), 100 ppm (LYS100), and 200 ppm (LYS200) lysozyme and 400 ppm flavomycin (FLA) on the growth performance (1–42 d) of broiler chickens.

Effects of dietary supplementation with 0 (control), 40 ppm (LYS40), 100 ppm (LYS100), and 200 ppm (LYS200) lysozyme and 400 ppm flavomycin (FLA) on the growth performance (1–42 d) of broiler chickens.</p