title: Characterization of specific spoilage organisms (SSOs) in vacuum-packed ham by culture-plating techniques and MiSeq next-generation sequencing technologies.
abstract: BACKGROUND
  Knowledge regarding microaerophilic and anaerobic specific spoilage organisms (SSOs) is crucial for an appropriate evaluation of vacuum-packed ham. The objective of this study was to characterize the SSO community in vacuum-packed ham by a culture-dependent technique and MiSeq next-generation sequencing (NGS) platform. The relation between changes among the SSO group in the ham and changes in sensory characteristics of the product was also assessed.
  
  
  RESULTS
  In the study, conventional microbiological analyses were employed in order to establish the participation of several groups of microorganisms in the deterioration of vacuum-packed ham. The diversity of the SSO group in the product was further assessed with the use of MiSeq NGS technology. The bacteria identified in sliced cooked ham belonged mostly to four phyla, namely Actinobacteria, Proteobacteria, Firmicutes and Bacteroidetes. A temperature of 4 °C favoured the development of mesophilic and psychrophilic/psychrotrophic flora, mainly Lactobacillaceae, Enterobacteriaceae and Micrococcaceae families. A high ratio of Brochothrix thermosphacta species and new, cold-tolerant Clostridium spp. was also observed. The growth of these microorganisms facilitated changes in the pH value and organoleptic characteristics of the product.
  
  
  CONCLUSIONS
  This study confirms that the combination of culturing and MiSeq NGS technology improves the microbial evaluation of food. © 2016 Society of Chemical Industry.
authors.affiliation: Institute of Food Technology of Plant Origin, Poznań University of Life Sciences, Wojska Polskiego 31, PL-60-624, Poznań, Poland.
authors.forename: Agnieszka
authors.initials: A
authors.lastname: Piotrowska-Cyplik
authors.affiliation: Department of Biotechnology and Food Microbiology, Poznań University of Life Sciences, Wojska Polskiego 48, PL-60-627, Poznań, Poland.
authors.forename: Kamila
authors.initials: K
authors.lastname: Myszka
authors.affiliation: Institute of Forensic Genetics, Al. Mickiewicza 3/4, PL-85-071, Bydgoszcz, Poland.
authors.forename: Jakub
authors.initials: J
authors.lastname: Czarny
authors.affiliation: Institute of Food Technology of Plant Origin, Poznań University of Life Sciences, Wojska Polskiego 31, PL-60-624, Poznań, Poland.
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Ratajczak
authors.affiliation: Institute of Meat Technology, Wojska Polskiego 31, PL-60-624, Poznań, Poland.
authors.forename: Ryszard
authors.initials: R
authors.lastname: Kowalski
authors.affiliation: Institute of Food Technology of Plant Origin, Poznań University of Life Sciences, Wojska Polskiego 31, PL-60-624, Poznań, Poland.
authors.forename: Róża
authors.initials: R
authors.lastname: Biegańska-Marecik
authors.affiliation: Department of Biotechnology and Food Microbiology, Poznań University of Life Sciences, Wojska Polskiego 48, PL-60-627, Poznań, Poland.
authors.forename: Justyna
authors.initials: J
authors.lastname: Staninska-Pięta
authors.affiliation: Institute of Food Technology of Plant Origin, Poznań University of Life Sciences, Wojska Polskiego 31, PL-60-624, Poznań, Poland.
authors.forename: Jacek
authors.initials: J
authors.lastname: Nowak
authors.affiliation: Department of Biotechnology and Food Microbiology, Poznań University of Life Sciences, Wojska Polskiego 48, PL-60-627, Poznań, Poland.
authors.forename: Paweł
authors.initials: P
authors.lastname: Cyplik
mesh_terms: D000818:Animals; D019295:Computational Biology; D004755:Enterobacteriaceae / Q000145:classification / Q000254:growth & development* / Q000302:isolation & purification; D057140:Fast Foods / Q000032:analysis / Q000382:microbiology; D018857:Food Packaging; D005519:Food Preservation; D063427:Food Quality; D061353:Food Storage; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D006863:Hydrogen-Ion Concentration; D007777:Lactobacillaceae / Q000145:classification / Q000254:growth & development* / Q000302:isolation & purification; D008460:Meat / Q000032:analysis / Q000382:microbiology*; D055595:Mechanical Phenomena; D008835:Micrococcaceae / Q000145:classification / Q000254:growth & development* / Q000302:isolation & purification; D058889:Molecular Typing; D011044:Poland; D025341:Principal Component Analysis; D012034:Refrigeration; D012677:Sensation; D034421:Sus scrofa; D014618:Vacuum
keywords: MiSeq next-generation sequencing (NGS) technology; bacterial microbiome; microbial deterioration of food; microbial evaluation of food; specific spoilage organisms (SSOs)