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)

https://ciptaindomedica.files.wordpress.com/2011/01/antimicrobial-herb-and-spice-compounds-in-food.pdf

Antimicrobial herb and spice compounds in food.

Recently, the focus of scientific investigations has moved from the primary role of food as the source of energy and body-forming substances to the more subtle action of biologically active food components on human health. There has been an explosion of consumer interest in the active role of food in the well-being and life prolongation, as well as in the prevention of initiation, promotion, and development of nontransmissible chronic diseases. As a result, a new term—functional food—was proposed. Among these foods, probiotics may exert positive effects on the composition of gut microbiota and overall health, and the market is increasing annually. An increased demand for nondairy probiotic products comes from vegetarianism, milk cholesterol content, and lactose intolerance. Therefore, the development of these products is a key research priority for food design and a challenge for both industry and science sectors. This article presents an overview of functional food development, emphasizing nondairy foods that contain probiotic bacteria strains.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1541-4337.2010.00110.x

Functional Foods and Nondairy Probiotic Food Development: Trends, Concepts, and Products.

Advancement and comparative profiles in the production technologies using solid-state and submerged fermentation for microbial cellulases

Summary Bacterial cellulose, an exopolysaccharide produced by some bacteria, has unique structural and mechanical properties and is highly pure as compared to plant cellulose. This article presents a critical review of the available information on the bacterial cellulose with special emphasis on its fermentative production and applications. Information on the biosynthetic pathway of bacterial cellulose, enzymes and precursors involved in bacterial cellulose synthesis has been specified. Characteristics of bacterial cellulose with respect to its structure and physicochemical properties are discussed. Current and potential applications of bacterial cellulose in food, pharmaceutical and other industries are also presented.

/pdf/microbial-cellulose-fermentative-production-and-applications-bqh4jn98f9.pdf

Microbial Cellulose: Fermentative Production and Applications

Current status and future trends of high-pressure processing in food industry

The rhizomes of the Zingiberaceae family are a vegetable widely used in many Asian countries, and their medicinal functions have been broadly discussed and accepted in many traditional recipes. In this study, 18 species of five genus of Zingiberaceae plants from Taiwan area were collected and analyzed for their functional properties. Methanolic extracts of the plants were analyzed for their total phenol compounds, alpha,alpha-diphenyl-beta-picrylhydrazyl (DPPH) scavenging activity, and reducing power. Antimicrobial activity of these samples was also determined. The results showed that the total phenol compounds of the Alpinia genus averaged 17, 30 mg/g for Curcumas, and the highest, 36.5 mg/g for Vanoverberghia sasakiana. Antioxidant performances were best observed in Vanoverberghia and Hedychium, both 89%, and DPPH scavenging activity followed similar trends. Particularly, Zingiber oligophyllum, considered as a traditional medicinal plant used in Taiwan exhibited low DPPH scavenging activity and reducing power. Most Zingiberaceae plant extracts exhibited antimicrobial activity against all tested food microorganisms. Hedychium and Vanoverberghia, did not show antimicrobial activities on Escherichia coli and Vibrio parahaemolyticus. This study is a positive demonstration of the utility of screening Taiwan's endemic Zingiberaceous plants for their food and medicinal uses.

Yuan-Tay Shyu

Papers

Current status and future trends of high-pressure processing in food industry

Antioxidant and Antimicrobial Activity of Zingiberaceae Plants in Taiwan

Probiotic properties of Lactobacillus strains isolated from the feces of breast-fed infants and Taiwanese pickled cabbage.

Purification and characterization of a novel halostable cellulase from Salinivibrio sp. strain NTU-05

Antioxidant activities of citrus herbal product extracts