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Beer has been generally recognized as a microbiologically stable beverage. However, deviations in the brewing process may occur due to the activity of lactic acid bacteria (LAB). The growth of LAB during the brewing process implies a competition for nutrients with yeasts, causing decreased ethanol yields. Moreover, quality degradation caused by LAB spoilage can be observed due to the production of off-flavors (high indications of diacetyl and lactic acid), changes in color and excessive turbidity. This study aims at the microbiological investigation of non-pasteurized beer products, before and after filtration, with the main emphasis on the detection and molecular characterization of the biodiversity of LAB. Sampling was performed at selected points in a beer production line on the industrial scale in order to determine the population of Total Viable Counts (TVC), yeasts and LAB. The samples are classified in the “lager” category, fermented using strains of Saccharomyces pastorianus. The sampling points included the pre- and post- filtration step, the buffer line, the filling tank, the packaged but non-pasteurized product and finally, the packaged pasteurized product to confirm the effectiveness of heat treatment. Samples were collected in two different batch productions. The results showed that the population of LAB was relatively low. Specifically, before filtration, levels were 1.52 log CFU/mL and 3.44 log CFU/mL in the first and second batch, respectively. This microbial group was not enumerated (<1.0 log CFU/mL) afterwards in all sampling points. A total of 80 LAB species were initially analyzed by rep-PCR, using the (GTG)5 primer to discriminate the isolates. Representative isolates (20) were selected for further identification using the conserved 16S rRNA region to be sequenced. Three different species were present in both batch productions, namely Lactobacillus brevis, Lactobacillus backii and Lactobacillus harbinensis. Full article