title: Psychrophile spoilers dominate the bacterial microbiome in musculature samples of slaughter pigs.
abstract: 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 1g 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.
authors.affiliation: Institute of Milk Hygiene, Milk Technology and Food Science, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinärplatz 1, Vienna, Austria; Research Cluster 'Animal Gut Health', University of Veterinary Medicine, Veterinärplatz 1, Vienna, Austria. Electronic address: Evelyne.Mann@vetmeduni.ac.at.
authors.forename: Evelyne
authors.initials: E
authors.lastname: Mann
authors.affiliation: Research Cluster 'Animal Gut Health', University of Veterinary Medicine, Veterinärplatz 1, Vienna, Austria; Institute of Animal Nutrition and Functional Plant Compounds, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinärplatz 1, Vienna, Austria.
authors.forename: Stefanie U
authors.initials: SU
authors.lastname: Wetzels
authors.affiliation: Institute for Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinärplatz 1, Vienna, Austria.
authors.forename: Beate
authors.initials: B
authors.lastname: Pinior
authors.affiliation: Research Cluster 'Animal Gut Health', University of Veterinary Medicine, Veterinärplatz 1, Vienna, Austria; University Clinic for Swine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinärplatz 1, Vienna, Austria.
authors.forename: Barbara U
authors.initials: BU
authors.lastname: Metzler-Zebeli
authors.affiliation: Institute of Milk Hygiene, Milk Technology and Food Science, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinärplatz 1, Vienna, Austria; Research Cluster 'Animal Gut Health', University of Veterinary Medicine, Veterinärplatz 1, Vienna, Austria.
authors.forename: Martin
authors.initials: M
authors.lastname: Wagner
authors.affiliation: Institute of Milk Hygiene, Milk Technology and Food Science, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinärplatz 1, Vienna, Austria; Research Cluster 'Animal Gut Health', University of Veterinary Medicine, Veterinärplatz 1, Vienna, Austria.
authors.forename: Stephan
authors.initials: S
authors.lastname: Schmitz-Esser
mesh_terms: D000003:Abattoirs; D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D064307:Microbiota; D018482:Muscle, Skeletal / Q000382:microbiology*; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013552:Swine / Q000382:microbiology*
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S
keywords: 16S rRNA pyrosequencing; Bacterial; Contamination; Microbiome; Microbiota; Musculature; Slaughter