Comparison of bacterial diversity in wet- and dry-aged beef using traditional microbiology and next generation sequencing

Luiz Gustavo de Matosa, Anderson Clayton da Silva Abreua, Vanessa Pereira Perez Alonsoe, Juliano Leonel Gonçalvesa, Maristela da Silva do Nascimentob, Sérgio Bertelli Pflanzer Jrb, Jonatã Henrique Rezende-de-Souzab, Chiara Ginic, Natália Faraj Muradd, Marcelo Mendes Brandãod, Nathália Cristina Cirone Silvaa

aDepartment of Food Science and Nutrition, School of Food Engineering (FEA), Universidade Estadual de Campinas (UNICAMP), 13083-862, Campinas, Sao Paulo, Brazil
bDepartment of Food Engineering and Technology, School of Food Engineering (FEA), Universidade Estadual de Campinas (UNICAMP), 13083-862, Campinas, Sao Paulo, Brazil
cDepartment of Veterinary Medicine, Università degli Studi di Milano, Lodi, Lombardia, Italy
dLaboratory of Systemic and Integrative Biology, Center of Molecular Biology and Genetic Engineering, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
eIndependent researcher, Prague, Czechia

The science behind dry-aged meat has increased during the last few years. Differently from wet-aging, where meat is vacuum packed, the dry-aging process happens without packaging or protection, which may change the bacterial diversity of the meat, and this change can alter the sensory characteristics of the meat. Different methods are used to identify the microbial of meat. The most used ones are traditional techniques and the Next Generation Sequencing (NGS), widely used to identify bacteria present in diverse types of food. The aim of this study was to evaluate the bacterial diversity of dry-aged and wet-aged beef by traditional microbiological tests and NGS to compare the bacterial diversity given by those different methodologies, as well as compare their specificity. Beef strip loins (n = 6) were collected directly from the slaughterhouse and transported to the laboratory. Samples were dry or wet-aged for 20 and 34 days. Before and after aging, samples were analyzed by Traditional microbiological analysis and NGS. It was observed, with traditional microbiology tests, a greater increase of total bacterial count in the wet-aged samples from 0 to 20 and 34 days, with psychotropic bacteria having the greatest increase. In the dry-aged samples there was a decrease in the total bacterial count, with only molds and yeast significant growth during aging. No E. coli growth was observed for any treatment. From metagenomics analysis, eleven main bacterial genera were detected in the meat microbiota, with a relative abundance higher than 2%, and the seven most abundant ones were Carnobacterium (47.9%), Pseudomonas (22.2%), Lactobacillus (5.4%), Romboutsia (2.8%), Leuconostoc (2.5%), Candidatus Nitrosotalea (2.4%) and Akkermansia (2.3%). Alpha diversity showed a higher richness on the non-aged samples, whereas wet-aged samples showed the smallest richness, the same for the samples aged for 34 days. In addition, beta diversity showed that the microorganisms are highly related when considering time, but different clustering when comparing aging types. Further, dry-aged beef showed a higher presence of Pseudomonas sp., which is a group of microorganisms with a large range of ideal bacterial growth conditions, whereas the wet-aged samples, due to their controlled anaerobic environment, a higher presence of Carnobacterium was observed. It was possible to observe that traditional microbiology is still an important tool in food safety, once it could clearly identify the main important groups of bacteria, once the microorganisms present in food are already very well described, allowing researchers and producers, depending on the methodology used, to check for them, while NGS show more groups, however, it is still an expensive tool, when considering the number of samples. Even showing different data between them, they were both efficient to differentiate the microbiota of the beef samples in their own specificity.