Metagenomic analysis of the evolution of microbial communities in foods subjected to refrigeration and in conditions of absence of cold
Abstract
The cold chain is a key element in food safety since most microorganisms stop their growth at low temperatures. Techniques that analyse the bacterial populations of a sample by sequencing a fragment of the 16S ribosomal gene, allowing the microbial characterization of foods have been developed.
The objective of the present study was to identify and quantify bacteria on refrigerated and uncooled foods using massive sequencing of rDNA16S, to describe the role of maintenance of the cold chain on the evolution of microbial communities in food.
Thus, the DNA extracted from the samples was sequenced at 2d and 4d. The OTUs obtained were compared with those of the databases and identified. The culture of microorganisms of the samples was carried out at 0d.
In general, an increase in the amount and diversity of bacteria was observed in the uncooled samples, confirming that the cold chain delays the development of microorganisms in foods, increasing the shelf life of them. In addition, the study demonstrates the efficacy of the massive sequencing of rDNA16S to study the effect of temperature on the development of bacterial communities on food.
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Váquez W. Instrumentación y estandarización del proceso para la elaboración de yogurt mediante el monitoreo de las variables analíticas (pH y temperatura). Tesis doctoral. 2014.
V?trovský T, Baldrian P, Morais D. SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses. Bioinformatics. 2018; 34(13): 2292-2294. - https://doi.org/10.1093/bioinformatics/bty071
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Žif?áková L, V?trovský T, Howe A, Baldrian P. Microbial activity in forest soil reflects the changes in ecosystem poperties between summer and winter. Environ Microbiol. 2016; 18(1): 288-301. - https://doi.org/10.1111/1462-2920.13026
Castro G, Valbuena E, Bríñez W, Sánchez E, Vera H, Tovar A. Comparación del empleo de nisina y cultivos de Lactococcus lactis subsp. Lactis, para la biopreservación de queso blanco. FCV-LUZ. 2009; 19(2): 201-209.
Delgado S, Rachid CT CC, Fernández E, Rychlik T, Alegría A, Peixoto RS, Mayo B. Diversidad de bacterias termófilas en leche cruda pasteurizada y cultivada selectivamente evaluada mediante cultivo de PCR-DGGE y pirosecuenciación. Comida Microbiol. 2013; 36: 103-111. - https://doi.org/10.1016/j.fm.2013.04.015
Ferrocino I., Greppi A., Lastoria A., Rantsiou K., Ercolini D. Impacto de los envases activados con nisina en la microbiota de las hamburguesas de carne durante el almacenamiento. Appl. Reinar. Microbiol. 2016; 82: 1-13.
Filippis F, Storia A, Villani F, Ercolini D. Explorando las fuentes de los spoilers bacterianos en bistecs mediante secuenciación de alto rendimiento independiente del cultivo. Microb. Biotechnol. 2013; 10: 91-102.
Fougy L, Desmonts M, Coeuret G, Fassel C, Hamon E, Hézard B. La reducción de la sal en las salchichas de cerdo crudas aumenta el deterioro y se correlaciona con la diversidad bacteriana reducida. Appl. Reinar. Microbiol. 2016; 82: 3928-3939. - https://doi.org/10.1128/AEM.00323-16
Leff JW, Fierer N. Comunidades bacterianas asociadas con las superficies de frutas y verduras frescas. PLOS ONE. 2013; 8: 59310. - https://doi.org/10.1371/journal.pone.0059310
Lopez-Velasco G, Welbaum GE, Boyer RR, Mane SP, Ponder MA. Cambios en las comunidades de bacterias phylloepiphytic espinacas después de un procesamiento mínimo y almacenamiento refrigerado descrito mediante pyrosequencing de 16S rRNA amplicones. J. Appl. Microbiol. 2011; 110: 1203-1214. - https://doi.org/10.1111/j.1365-2672.2011.04969.x
Mayo B, Rachid CT, Alegría A, Leite AM, Peixoto RS, Delgado S. Impact of next generation sequencing techniques in food microbiology. Curr genomics. 2014; 15(4): 293-309. - https://doi.org/10.2174/1389202915666140616233211
Nieminen TT, Koskinen K, Laine P, Hultman J, Säde E, Paulin L et al. Comparación de comunidades microbianas en carne de pollo marinada y no marinada mediante metagenómica. En t. J. Food Microbiol. 2012; 157: 142-149. - https://doi.org/10.1016/j.ijfoodmicro.2012.04.016
Saati-Santamaría Z, López-Mondéjar R, Jiménez-Gómez A, Díez-Méndez A, V?trovský T, Igual JM, Velázquez E, Kolarik M, Rivas R, García-Fraile P. Discovery of phloeophagus beetles as a source of Pseudomonas strains that produce potentially new bioactive substances and description of Pseudomonas bohemica sp. nov. Frontiers in Microbiology. 2018; 9(913). - https://doi.org/10.3389/fmicb.2018.00913
Vasek OM, Hebert EM, S. de Giori G, Raya R et Fusco AJV. Secuencia parcial del gen 16S rRNA de cepas constituyentes de un fermento para la elaboración de Queso Artesanal de Corrientes. UNNE.
Váquez W. Instrumentación y estandarización del proceso para la elaboración de yogurt mediante el monitoreo de las variables analíticas (pH y temperatura). Tesis doctoral. 2014.
V?trovský T, Baldrian P, Morais D. SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses. Bioinformatics. 2018; 34(13): 2292-2294. - https://doi.org/10.1093/bioinformatics/bty071
Yu C, Séamus F, Sínead P, Kieran J, Shabarinath S. A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food Related Microbiome Studies. Front Microbiol. 2017; 8: 1829. - https://doi.org/10.3389/fmicb.2017.01829
Žif?áková L, V?trovský T, Howe A, Baldrian P. Microbial activity in forest soil reflects the changes in ecosystem poperties between summer and winter. Environ Microbiol. 2016; 18(1): 288-301. - https://doi.org/10.1111/1462-2920.13026
Pires, V., Rivas, R., & García-Fraile, P. (2019). Metagenomic analysis of the evolution of microbial communities in foods subjected to refrigeration and in conditions of absence of cold. FarmaJournal, 4(2), 73–84. https://doi.org/10.14201/fj2019427384
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