Next-generation sequencing to enhance the taxonomic resolution of the microbiological analysis of meat and meat-derived products

Reckem, Emiel Niels Van; Vuyst, Luc De; Weckx, Stefan; Leroy, Frédéric

doi:10.1016/j.cofs.2020.09.004

Cited by 21 publications

(11 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Specifically, synthetization sequencing (also known as the second-generation sequencing technology) is represented by Roche’s 454 technology, Illumina’s Solexa, Hiseq technology, and ABI’s Solid technology ( Lewis et al, 2020 ; Shen et al, 2021b ). Single-molecule sequencing (also known as third-generation sequencing technology) is based on Helicos Bioscience’s HeliScope genetic analysis system, Pacific Biosciences’ PacBio RS single-molecule real-time sequencing system, and Oxfold Nanopore Examples include Technologies’ GridION and MinION ( Yu et al, 2020 ; Gunther et al, 2021 ; Van Reckem et al, 2021 ). Single-cell sequencing technology is to sequence each individual cell through high-throughput sequencing technology to obtain the genetic information of each individual cell ( Davey and Valdivia, 2020 ; Peng et al, 2020a ).…”

Section: Molecular Biology Detection Technologymentioning

confidence: 99%

Research progress on detection techniques for point-of-care testing of foodborne pathogens

Zhao

Huang

et al. 2022

Front. Bioeng. Biotechnol.

View full text Add to dashboard Cite

The global burden of foodborne disease is enormous and foodborne pathogens are the leading cause of human illnesses. The detection of foodborne pathogenic bacteria has become a research hotspot in recent years. Rapid detection methods based on immunoassay, molecular biology, microfluidic chip, metabolism, biosensor, and mass spectrometry have developed rapidly and become the main methods for the detection of foodborne pathogens. This study reviewed a variety of rapid detection methods in recent years. The research advances are introduced based on the above technical methods for the rapid detection of foodborne pathogenic bacteria. The study also discusses the limitations of existing methods and their advantages and future development direction, to form an overall understanding of the detection methods, and for point-of-care testing (POCT) applications to accurately and rapidly diagnose and control diseases.

show abstract

Section: Molecular Biology Detection Technologymentioning

confidence: 99%

Research progress on detection techniques for point-of-care testing of foodborne pathogens

Zhao

Huang

et al. 2022

Front. Bioeng. Biotechnol.

View full text Add to dashboard Cite

show abstract

“…of samples, funding, and computational infrastructure available. When monitoring food safety in terms of screening food for pathogens, a large number of samples may be involved especially at the scale of food industries [ 214 , 215 ]. The rapid analysis timelines offered by HTS compared to culture-based methods promotes the application of metagenomics in food quality control enabling quick and informed decisions on product recall.…”

Section: Applications Of Metagenomics In the Fermented Food Industrymentioning

confidence: 99%

The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods

Srinivas

O’Sullivan

Cotter

et al. 2022

Foods

View full text Add to dashboard Cite

The microbial communities present within fermented foods are diverse and dynamic, producing a variety of metabolites responsible for the fermentation processes, imparting characteristic organoleptic qualities and health-promoting traits, and maintaining microbiological safety of fermented foods. In this context, it is crucial to study these microbial communities to characterise fermented foods and the production processes involved. High Throughput Sequencing (HTS)-based methods such as metagenomics enable microbial community studies through amplicon and shotgun sequencing approaches. As the field constantly develops, sequencing technologies are becoming more accessible, affordable and accurate with a further shift from short read to long read sequencing being observed. Metagenomics is enjoying wide-spread application in fermented food studies and in recent years is also being employed in concert with synthetic biology techniques to help tackle problems with the large amounts of waste generated in the food sector. This review presents an introduction to current sequencing technologies and the benefits of their application in fermented foods.

show abstract

“…Pseudomonas, Serratia, Brochothrix, Psychrobacter, Acinetobacter, Staphylococcus, lactic acid bacteria, and aerobic and anaerobic spore-formers contribute to the resilient microbiota in meat processing plants (Stellato et al, 2016;Fagerlund et al, 2017). Understanding how the individual members of microbial communities influence each other is key in developing foodborne pathogen mitigation strategies (Van Reckem et al, 2020). It is therefore essential to investigate the microbial diversity in food processing plants and the potential relationships between the microbial community compositions with the occurrence of L. monocytogenes (Tan et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

“…It is therefore essential to investigate the microbial diversity in food processing plants and the potential relationships between the microbial community compositions with the occurrence of L. monocytogenes (Tan et al, 2019). The development of high-throughput sequencing technologies made it possible to study microbial populations in their natural environment, enabling researchers to gain snapshots of the world of microorganisms from broader and deeper perspectives (Cao et al, 2017;Van Reckem et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Co-Occurrence of Listeria spp. and Spoilage Associated Microbiota During Meat Processing Due to Cross-Contamination Events

et al. 2021

View full text Add to dashboard Cite

A large part of foodborne outbreaks related to Listeria monocytogenes are linked to meat and meat products. Especially, recontamination of meat products and deli-meat during slicing, packaging, and repackaging is in the focus of food authorities. In that regard, L. monocytogenes persistence in multi-species biofilms is one major issue, since they survive elaborate cleaning and disinfection measures. Here, we analyzed the microbial community structure throughout a meat processing facility using a combination of high-throughput full-length 16S ribosomal RNA (rRNA) gene sequencing and traditional microbiological methods. Samples were taken at different stages during meat cutting as well as from multiple sites throughout the facility environment to capture the product and the environmental associated microbiota co-occurring with Listeria spp. and L. monocytogenes. The listeria testing revealed a widely disseminated contamination (50%; 88 of 176 samples were positive for Listeria spp. and 13.6%; 24 of 176 samples were positive for L. monocytogenes). The pulsed-field gel electrophoresis (PFGE) typing evidenced 14 heterogeneous L. monocytogenes profiles with PCR-serogroup 1/2a, 3a as most dominant. PFGE type MA3-17 contributed to the resilient microbiota of the facility environment and was related to environmental persistence. The core in-house microbiota consisted mainly of the genera Acinetobacter, Pseudomonas, Psychrobacter (Proteobacteria), Anaerobacillus, Bacillus (Firmicutes), and Chryseobacterium (Bacteroidota). While the overall microbial community structure clearly differed between product and environmental samples, we were able to discern correlation patterns regarding the presence/absence of Listeria spp. in both sample groups. Specifically, our longitudinal analysis revealed association of Listeria spp. with known biofilm-producing Pseudomonas, Acinetobacter, and Janthinobacterium species on the meat samples. Similar patterns were also observed on the surface, indicating dispersal of microorganisms from this multispecies biofilm. Our data provided a better understanding of the built environment microbiome in the meat processing context and promoted more effective options for targeted disinfection in the analyzed facility.

show abstract

Next-generation sequencing to enhance the taxonomic resolution of the microbiological analysis of meat and meat-derived products

Cited by 21 publications

References 57 publications

Research progress on detection techniques for point-of-care testing of foodborne pathogens

Research progress on detection techniques for point-of-care testing of foodborne pathogens

The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods

Co-Occurrence of Listeria spp. and Spoilage Associated Microbiota During Meat Processing Due to Cross-Contamination Events

Contact Info

Product

Resources

About