Genomic and metabolic characterisation of spoilage-associated Pseudomonas species

<p><em>Pseudomonas</em> are common spoilage agents of aerobically stored fresh foods. Their ability to cause spoilage is species- and may be strain-specific. To improve our understanding of the meat and milk spoilage agents <em>Pseudomonas fragi</em> and <em>Pseudomonas lundensis</em>, we sequenced the genomes of 12 <em>P</em>. <em>fragi</em> and seven <em>P</em>. <em>lundensis</em> isolates. These genomes provided a dataset for genomic analyses. Key volatile organic compounds (VOCs) produced or metabolised by the isolates were determined during their growth on a beef paste and where possible, metabolic activity was associated with gene repertoire.</p><p>Genome analyses showed that the isolates included in this work may belong to more than two <em>Pseudomonas</em> species with possible spoilage potential. Pan-genome analyses demonstrated a high degree of diversity among the <em>P</em>. <em>fragi</em> and genetic flexibility and diversity may be traits of both species. Growth of the <em>P</em>. <em>lundensis</em> isolates was characterised by the production of large amounts of 1-undecene, 5-methyl-2-hexanone and methyl-2-butenoic acid. <em>P</em>. <em>fragi</em> isolates produced extensive amounts of methyl and ethyl acetate and the production of methyl esters predominated over ethyl esters. Some of the <em>P</em>. <em>fragi</em> produced extremely low levels of VOCs, highlighting the importance of strain-specific studies in food matrices. Furthermore, although usually not considered to be denitrifiers, all isolates generated molecular nitrogen, indicating that at least some steps of this pathway are intact.</p>