Nutrition & Food Science

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    Critical Assessment of Short-Read Assemblers for the Metagenomic Identification of Foodborne and Waterborne Pathogens Using Simulated Bacterial Communities
    (MDPI, 2022-12-06) Chen, Zhao; Meng, Jianghong
    Metagenomics offers the highest level of strain discrimination of bacterial pathogens from complex food and water microbiota. With the rapid evolvement of assembly algorithms, defining an optimal assembler based on the performance in the metagenomic identification of foodborne and waterborne pathogens is warranted. We aimed to benchmark short-read assemblers for the metagenomic identification of foodborne and waterborne pathogens using simulated bacterial communities. Bacterial communities on fresh spinach and in surface water were simulated by generating paired-end short reads of Illumina HiSeq, MiSeq, and NovaSeq at different sequencing depths. Multidrug-resistant Salmonella Indiana SI43 and Pseudomonas aeruginosa PAO1 were included in the simulated communities on fresh spinach and in surface water, respectively. ABySS, IDBA-UD, MaSuRCA, MEGAHIT, metaSPAdes, and Ray Meta were benchmarked in terms of assembly quality, identifications of plasmids, virulence genes, Salmonella pathogenicity island, antimicrobial resistance genes, chromosomal point mutations, serotyping, multilocus sequence typing, and whole-genome phylogeny. Overall, MEGHIT, metaSPAdes, and Ray Meta were more effective for metagenomic identification. We did not obtain an optimal assembler when using the extracted reads classified as Salmonella or P. aeruginosa for downstream genomic analyses, but the extracted reads showed consistent phylogenetic topology with the reference genome when they were aligned with Salmonella or P. aeruginosa strains. In most cases, HiSeq, MiSeq, and NovaSeq were comparable at the same sequencing depth, while higher sequencing depths generally led to more accurate results. As assembly algorithms advance and mature, the evaluation of assemblers should be a continuous process.
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    Enhancement of Thermal Inactivation of Foodborne Pathogenic Bacteria at Mild Heating Temperatures with Inclusion of Butyl Paraben and the Application on Foods
    (2019) Gao, Zhujun; Buchanan, Robert L.; Food Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Thermal processing is widely used in food industry to ensure the microbial safety, however, there is increasing demand on reducing the processing temperature and duration. This study specifically focused on mild heating temperatures (<60 °C) with inclusion of low level (≤ 125 ppm) of the approved preservative butyl-parahydroxy-benzoate (BPB). In a BHI model matrix, four pathogens were studied with submerged coil apparatus: Cronobacter sakazakii 607, Salmonella enterica serotype Typhimurium, attenuated Escherichia coli O157:H7 and Listeria monocytogenes. The results indicated that low concentrations of BPB combined with temperatures < 60 °C achieved 5 – 6 log reductions in less than 15 minutes with tested gram-negative microorganisms, whereas reductions without BPB were only 1 – 2 logs. We further extended the study to food applications: powdered infant formula, non-fat dry milk, and apple juice. The results indicate BPB will be inhibited by proteins, but apple juice is a suitable application.