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Comparison of microbial communities in marinated and unmarinated broiler meat by metagenomics

Nieminen, T.T., Koskinen, K., Laine, P., Hultman, J., Säde, E., Paulin, L., Paloranta, A., Johansson, P., Björkroth, J., Auvinen, P.
International journal of food microbiology 2012 v.157 no.2 pp. 142-149
Brochothrix, Carnobacterium, Clostridium, Enterobacteriaceae, Lactobacillus, Leuconostoc gasicomitatum, Leuconostoc gelidum, Vagococcus, Vibrio, acetic acid, bacterial communities, carbohydrate metabolism, fillets, genes, lactic acid, marinating, meat, metagenomics, modified atmosphere packaging, nucleotide sequences, oils, poultry, ribosomal RNA, spices, spoilage, sugars, Finland
Most raw poultry sold in Finland at the retail level is mixed with marinades containing oil, sugar, spices and acetic acid and packaged under modified atmosphere. Premature spoilage of marinated poultry preparations has been observed and associated with high levels of Leuconostoc spp. in meat. In this study we investigated whether marination of broiler fillet strips increased the proportion of Leuconostoc spp. in the microbial communities. To obtain a comprehensive view of the microbiota, we sequenced total DNA and 16S rRNA gene amplicons from the microbial communities. The lactic acid bacterial communities were characterized also by identification of colonies. The results showed that marinade increased the proportions of the spoilage-associated Leuconostoc gasicomitatum in the communities as well as the proportions of Leuconostoc gelidum and Lactobacillus spp. The proportions of Carnobacterium, Vagococcus, Brochothrix thrermosphacta, Clostridium, Enterobacteriaceae and Vibrio were diminished in marinated meat. Analysis of 16S rRNA gene amplicons resulted in 312 and 284 operational taxonomical units (dissimilarity 0.03) in unmarinated and marinated meat, respectively, indicating that the meat communities were more diverse than hitherto shown. Metagenomic analysis revealed a number of bacterial taxa that have not been associated with late shelf-life meat before, including Vagococcus and Vibrio that belonged to the predominating part of the microbial community in unmarinated meat. According to the functional analysis of the metagenomes, the communities in both marinated and unmarinated poultry were characterized by high proportions (15.6% or 17.9%) of genes involved in carbohydrate metabolism.