The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Empirical threshold values for quantitative trait mapping.

Bacteriocins of gram-positive bacteria.

Lactic acid bacteria produce a variety of bacteriocins that have recently come under detailed investigation. The biochemical and genetic characteristics of these antimicrobial proteins are reviewed and common elements are discussed between the different classes of bacteriocins produced by these Gram-positive bacteria.

Genetics of bacteriocins produced by lactic acid bacteria

The production of fermented foods is based on the use of starter cultures, for instance lactic acid bacteria that initiate rapid acidification of the raw material. Recently, new starter cultures of lactic acid bacteria with an industrially important functionality are being developed. The latter can contribute to the microbial safety or offer one or more organoleptic, technological, nutritional, or health advantages. Examples are lactic acid bacteria that produce antimicrobial substances, sugar polymers, sweeteners, aromatic compounds, vitamins, or useful enzymes, or that have probiotic properties.

http://mummified.persiangig.com/new_folder/lact1.pdf

Lactic acid bacteria as functional starter cultures for the food fermentation industry

The primary concern in food safety issues focuses on microorganisms and microbial toxins. Effective food preservation requires that the growth and proliferation of hazardous microorganisms be well controlled, and that the presence of significant quantities of microbial toxins in foods be prevented. The traditional effective preservation methodologies, such as canning, are being supplemented by new technologies which are less destructive of the food qualities. New strategies are therefore needed to prevent the transmission of microbial contamination or to prevent the formation of microbial toxins which remain in food. This paper discusses the role of modern processing methodologies in helping protect consumers from hazards of microbial origin.

Microorganisms and Microbial Toxins

U.S. consumer practices of homemade nut-based dairy analogs and soaked nuts.

Author(s): Harris, Linda J | Abstract: This guide includes safety tips for preserving peppers along with recommended methods for storing, freezing, drying, pickling, and canning Also includes seven recipes for pickled peppers, salsa, jellies, and relishes

/pdf/peppers-safe-methods-to-store-preserve-enjoy-1hu95wufge.pdf

Peppers: Safe Methods to Store, Preserve, & Enjoy

Transfer of Enterococcus faecium and Salmonella enterica during simulated postharvest handling of yellow onions (Allium cepa)

Fusarium graminearum is a plant pathogen, attacking a wide range of plant species including corn (ear and stalk rot), barley, and wheat (head blight). Fusarium epidemics result in millions of dollars of losses in crop revenues. Fusarium graminearum infection in the cereals reduces both grain yield and quality. Mycotoxins are produced by many fungal Fusarium species and thus the grain becomes contaminated with these mycotoxins, such as the trichothecenes. The major trichothecene produced by F. graminearum is deoxynivalenol (abbreviated as DON, also known as vomitoxin). Trichothecenes are potent protein synthesis inhibitors and are quite toxic to humans and livestock. A yeast gene has been identified which confers upon yeast tolerant of the trichothecene, trichodermin. A corresponding plant gene has been prepared, which has been used to transform plants. These transformed plants have an increased resistance to Fusarium infestation.

Tolerance of trichothecene mycotoxins in plants through the modification of the ribosomal protein L3 gene

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