Psychrophile spoilers dominate the bacterial microbiome in musculature samples of slaughter pigs

The aim of this study was to disentangle the microbial diversity on porcine musculature. The hypervariable V1–V2 region of the 16S rRNA gene was amplified from DNA samples of clinically healthy slaughter pigs (n = 8). Pyrosequencing yielded 37,000 quality-controlled reads and a diverse microbiome with 54–159 OTUs per sample was detected. Interestingly, 6 out of 8 samples were strongly dominated by 1–2 highly abundant OTUs (best hits of highly abundant OTUs: Serratia proteamaculans, Pseudomonas syringae, Aeromonas allosaccharophila, Brochothrix thermosphacta, Acidiphilium cryptum and Escherichia coli). In 1 g musculature scraping, 3.20E + 06 16S rRNA gene copies and 4.45E + 01 Enterobacteriaceae rRNA gene copies were detected with qPCR. We conclude that i.) next-generation sequencing technologies help encompass the full content of complex, bacterial contamination, ii.) psychrophile spoilers dominated the microbiota and iii.) E. coli is an effective marker species for pork contamination, as it was one of very few abundant species being present in all samples.