RT info:eu-repo/semantics/article
T1 Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments
A1 Barcenilla, Coral
A1 Cobo Díaz, José Francisco
A1 De Filippis, Francesca
A1 Valentino, Vincenzo
A1 Cabrera Rubio, Raúl
A1 O’Neil, Dominic
A1 Mahler de Sanchez, Luisa
A1 Armanini, Federica
A1 Carlino, Nicolo
A1 Blanco-Míguez, Aitor
A1 Pinto, Federica
A1 Calvete Torre, Inés
A1 Sabater, Carlos
A1 Delgado, Susana
A1 Ruas Madiedo, Patricia
A1 Quijada, Narciso M.
A1 Dzieciol, Monika
A1 Skírnisdóttir, 
AD  Sigurlaug
A1 Knobloch, Stephen l
A1 Puente, Alba
A1 López Fernández, María Mercedes
A1 Prieto Maradona, Miguel
A1 Marteinsson, Viggó Thór
A1 Wagner, Martin
A1 Margolles, Abelardo
A1 Segata, Nicola
A1 Cotter, Paul D.
A1 Ercolini, Danilo
A1 Álvarez Ordóñez, Avelino
A2 Microbiologia
K1 Tecnología de los alimentos
K1 DNA extraction
K1 Microbiome
K1 Food processing environments
K1 3309 Tecnología de Los Alimentos
AB [EN] Deep investigation of the microbiome of food-production and foodprocessing environments through whole-metagenome sequencing (WMS) can provide detailed information on the taxonomic composition and functional potential of the microbial communities that inhabit them, with huge potential benefits for environmental monitoring programs. However, certain technical challenges jeopardize the application of WMS technologies with this aim, with the most relevant one being the recovery of a sufficient amount of DNA from the frequently low-biomass samples collected from the equipment, tools and surfaces of food-processing plants. Here, we present the first complete workflow, with optimized DNA-purification methodology, to obtain high-quality WMS sequencing results from samples taken from food-production and food-processing environments and reconstruct metagenome assembled genomes (MAGs). The protocol can yield DNA loads >10 ng in >98% of samples and >500 ng in 57.1% of samples and allows the collection of, on average, 12.2 MAGs per sample (with up to 62 MAGs in a single sample) in ~1 week, including both laboratory and computational work. This markedly improves on results previously obtained in studies performing WMS of processing environments and using other protocols not specifically developed to sequence these types of sample, in which <2 MAGs per sample were obtained. The full protocol has been developed and applied in the framework of the European Union project MASTER (Microbiome applications for sustainable food systems through technologies and enterprise) in 114 food-processing facilities from different production sectors.
PB Nature Publishing Group
SN 1754-2189
LK https://hdl.handle.net/10612/18105
UL https://hdl.handle.net/10612/18105
NO Barcenilla, C., Cobo-Díaz, J.F., De Filippis, F. et al. Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments. Nat Protoc (2024). https://doi.org/10.1038/s41596-023-00949-x
DS BULERIA. Repositorio Institucional de la Universidad de León
RD 12-may-2024