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Fructose was completely depleted during fermentation with Lc. Citreum TR116 and converted to mannitol with high efficiency (>90%) while overall sugar reduction was >25% in all malt worts. Differences in amino acid composition of malt worts did not significantly affect growth of Lc. Citreum TR116 but did affect the formation of the aroma compounds diacetyl and isoamyl alcohol. Organic acid production and acidification of wort was similar across cereal substrates and acetic acid formation was linked to yield of mannitol. The results suggest that differences in amino acid and fructose content of malt worts considerably change metabolite formation during fermentation with Lc. Citreum TR116, a mannitol hyper-producer. This work gives new insight into the development of consumer acceptable malt based beverages which will provide further options for the health conscious and diabetic consumer, an important step in the age of sugar overconsumption. Torulaspora delbrueckii and Saccharomyces cerevisiae are yeast species found concurrently in wine. In order to commence fermentation, they adapt to the initial harsh environment, maintaining cellular homeostasis and promoting metabolism. These actions involve an intricate regulation of stress tolerance, growth and metabolic genes. Their phenotypes are influenced by the fermentation environment and physiological state of the cell, but such gene-environment interactions are poorly understood. This study aimed to compare the cell physiology of the two species, through genome-wide analysis of gene expression, coupling Oxford Nanopore MinION and Illumina Hiseq sequencing platforms. The early transcriptional responses to stress, nutrients and cell-to-cell communication were analysed. Particular attention was given to the fundamental gene modulations, leading to an understanding of the physiological changes needed to maintain cellular homeostasis, exit the quiescent state and establish dominance in the fermentation. Our findings suggest the existence of species-specific adaptation strategies in response to growth in a high sugar synthetic grape juice medium. The correlation between microbiota succession and flavor development in Chinese traditional fermented fish (Suanyu) inoculated with mixed starter cultures was studied. The results showed that 17 free amino acids, 22 free fatty acids and 9 organic acids were present. A total of 81 aroma compounds were detected during Suanyu fermentation. Aldehydes were the most abundant aroma compounds in the early stage of fermentation and esters contributed most to the aroma in the later stage of fermentation. The correlation analysis of microbial succession and flavor dynamics based on bidirectional orthogonal partial least squares (O2PLS) suggested that in addition to starter cultures, other microorganisms including 2 bacteria genera and 11 fungi genera were also responsible for the formation of flavor compounds. These results may help focus further research to improve the flavor quality of traditional fermented fish. The Lactobacillus casei group, which includes the closely related species L. casei, L. paracasei, L. rhamnosus, and L. chiayiensis, has been under debate regarding its taxonomy because of the difficulty in distinguishing the species from each other. In the present study, we developed a novel real-time PCR assay for distinguishing the L. casei group species. The pan-genome, as determined by the genomes of 44 strains, comprised 6789 genes, comparative genomic analysis showed that L. casei group strains were classified by species. Based on these results, species-specific genes were identified, and primers were designed from those genes. Real-time PCR clearly distinguished each species of the L. casei group and specifically amplified only to the target species. The method was applied to 29 probiotic products, and the detected results and label claims were compared. Total 23 products were in accordance with the label claims, and the remaining products contained species different from those stated in the label claims. Our method can rapidly and accurately distinguish the L. casei group species in a single reaction. Hence, our assay can be applied to identify L. casei group species from food or environmental samples and to accurately determine the nomenclature of the species. Particulates of harvest debris are common in tomato packinghouse dump tanks, but their role in food safety is unclear. In this study we investigated the survival of Salmonella enterica and the shifts in relative abundance of culturable mesophilic aerobic bacteria (cMAB) as impacted by particulate size and interaction with chlorine treatment. Particulates suspended in grape tomato wash water spanned a wide size range, but the largest contribution came from particles of 3-20 μm. Filtration of wash water through 330 μm, applied after 100 mg/L free chlorine (FC) wash, reduced surviving cMAB by 98%. The combination of filtration (at 330 μm or smaller pore sizes) and chlorinated wash also altered the cMAB community, with the survivors shifting toward Gram-positive and spore producers (in both lab-simulated and industrial conditions). When tomatoes and harvest debris inoculated with differentially tagged Salmonella were washed in 100 mg/L FC for 1 min followed by filtration, only cells originating from harvest debris survived, with 85 and 93% of the surviving cells associated with particulates larger than 330 and 63 μm, respectively. This suggests that particulates suspended in wash water can protect Salmonella cells from chlorine action, and serve as a vector for cross-contamination. Shiga toxin producing E. coli are a problem for food producers. STEC's require a combination of virulence factors to cause disease, so ideally detection techniques should detect the presence of multiple virulence factors in a single cell directly from food. Droplet Digital PCR (ddPCR) is commonly used to quantify the number of copies of a gene in a sample, moreover it is able to link two genes to the same piece of DNA. Here stx and an O-antigen specific gene are detected simultaneously with taqman probes confirming that the cells are intact as well as distinguishing between strains based on their genotype. Eganelisib Using ddPCR E. coli O157H7 and O104H4 are quantified from apple juice, milk and spinach washings without an enrichment step, the detection limit of ddPCR in apple juice was 2 cfu/mL. Also, ddPCR was used to detect pathogenic bacterial cells in the presence of background strains which shared one or none of the target genes, including avirulent strains. Whole cell ddPCR is compared to several DNA extraction techniques demonstrating that whole cell ddPCR is more reliable for linking genes within an organism.
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