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)

Nutrient requirements of poultry

Food intake is regulated by the hypothalamus, including the melanocortin and neuropeptide Y (NPY) systems in the arcuate nucleus. The NPY Y2 receptor (Y2R), a putative inhibitory presynaptic receptor, is highly expressed on NPY neurons in the arcuate nucleus, which is accessible to peripheral hormones. Peptide YY3-36 (PYY3-36), a Y2R agonist, is released from the gastrointestinal tract postprandially in proportion to the calorie content of a meal. Here we show that peripheral injection of PYY3-36 in rats inhibits food intake and reduces weight gain. PYY3-36 also inhibits food intake in mice but not in Y2r-null mice, which suggests that the anorectic effect requires the Y2R. Peripheral administration of PYY3-36 increases c-Fos immunoreactivity in the arcuate nucleus and decreases hypothalamic Npy messenger RNA. Intra-arcuate injection of PYY3-36 inhibits food intake. PYY3-36 also inhibits electrical activity of NPY nerve terminals, thus activating adjacent pro-opiomelanocortin (POMC) neurons. In humans, infusion of normal postprandial concentrations of PYY3-36 significantly decreases appetite and reduces food intake by 33% over 24 h. Thus, postprandial elevation of PYY3-36 may act through the arcuate nucleus Y2R to inhibit feeding in a gut–hypothalamic pathway.

BRIEF COMMUNICATION ARISING: Gut hormone PYY3-36 physiologically inhibits food intake

Continued growth and intensi¢cation of aquaculture production depends upon the development of sustainable protein sources to replace ¢sh meal in aquafeeds. This document reviews various plant feedstuis, which currently are or potentially may be incorporated into aquafeeds to support the sustainable production of various ¢sh species in aquaculture. The plant feedstuis considered include oilseeds, legumes and cereal grains, which traditionally have been used as protein or energy concentrates as well as novel products developed through various processing technologies. The nutritional composition of these various feedstuis are considered along with the presence of any bioactive compounds that may positively or negatively aiect the target organism. Lipid composition of these feedstuis is not speci¢cally considered although it is recognized that incorporating lipid supplements in aquafeeds to achieve proper fatty acid pro¢les to meet the metabolic requirements of ¢sh and maximize human health bene¢ts are important aspects. Speci¢c strategies and techniques to optimize the nutritional composition of plant feedstuis and limit potentially adverse eiects of bioactive compounds are also described. Such information will provide a foundation for developing strategic research plans for increasing the use of plant feedstuis in aquaculture to reduce dependence of animal feedstuis and thereby enhance the sustainability of aquaculture.

/pdf/expanding-the-utilization-of-sustainable-plant-products-in-4l188wibvf.pdf

Expanding the utilization of sustainable plant products in aquafeeds: a review

https://www.ars.usda.gov/alternativestoantibiotics/PDF/publications/11CastanonJIR.pdf

History of the Use of Antibiotic as Growth Promoters in European Poultry Feeds

Exogenous enzymes in monogastric nutrition - their current value and future benefits.

1. The mechanism of the anti-nutritive activities of soluble non-starch polysaccharides (NSPs) in broiler diets was investigated with emphasis on the inter-relationship between viscosity and fermentation along the gut. Isolated soluble NSP were added to a control diet to effect high gut viscosity, and in vivo depolymerisation of the NSP was achieved using a commercial glycanase. 2. Addition of soluble NSPs significantly (P < 0.01) increased gut viscosity, reduced the AME of the diet and depressed the growth and FCE of the birds. Enzyme supplementation of the NSP-enriched diet reversed the adverse effects, increasing (P < 0.01) weight gain, FCE and AME. Comparisons of the viscosities (mPa) in birds fed on the NSP-enriched diet and the same diet supplemented with enzyme were respectively: 11.9 v. 2.3 in the duodenum; 78.3 v. 4.4 in the jejunum and 409.3 v. 10.8 in the ileum. 3. Caecal volatile fatty acid concentration was markedly (P < 0.01) elevated by enzyme supplementation, whereas ileal fermentation was inhibited. 4. Microscopic examination revealed that, among birds fed on the NSP-enriched diet, there had been extensive small intestinal fermentation, which was eliminated by the enzyme supplementation. 5. Addition of a synthetic antibiotic (Amoxil) had no beneficial effects. 6. The current study demonstrated that increased fermentation occurs in the small intestine when a large amount of viscous NSPs is present in the diet and this is detrimental to the performance and well-being of poultry.

Increased small intestinal fermentation is partly responsible for the anti‐nutritive activity of non‐starch polysaccharides in chickens

Many feed ingredients in use in monogastric diets contain significant quantities of antinutritional factors (ANF) which limit both their feed value and their use. Almost all enzymes currently being used address such factors to varying degrees, allowing for more economic utilization of raw materials. However, animal response to xylanase, beta-glucanase and even phytase utilization reported in the literature tends to vary. Factors such as enzyme source, ingredient variety and environment under which the ingredient was grown, stored and processed into animal feed, age of animal, interaction with other dietary ingredients, and health status are shown to affect significantly the response obtained. As a result, the mode of action of xylanases and beta-glucanases is still debated due to too much emphasis being placed on interpretation of individual trial results without regard to the interactive factors or the literature dataset as a whole. Better understanding of such factors will improve data interpretation. While results with phytase are not subject to such extreme variation, they are nevertheless inconsistent in the degree to which inorganic phosphorus can be replaced by this enzyme. Greater understanding of the ANF and factors which interact to govern the response to added exogenous enzymes will undoubtedly improve the economic return and confidence in their use. Improved knowledge of ANF structure will result in development of enzymes directed towards far more specific targets, which enhances the likelihood of success and should reduce the overall enzyme usage.

/pdf/exogenous-enzymes-for-pigs-and-poultry-zcp3rs706e.pdf

Exogenous enzymes for pigs and poultry

The effect of dietary rye (0, 200, 400 and 600 g/kg substituting for wheat) and pentosanase concentration (0, 1, 2, 4, 8, 16 g/kg) on weight gain, molecular weight distribution of soluble carbohydrates in the intestinal lumen and lumenal viscosity in broiler chicks was investigated. A 4 x 6 factorial design was used with four replicates per treatment and six birds per replicate pen. Diets were fed from 1 to 19 d of age, at which time body weight, food intake and intestinal viscosity and molecular weight distribution of carbohydrate complexes in proximal and distal gut sections were determined. Weight gain and food conversion efficiency (FCE) improved with increasing pentosanase and decreasing rye concentration. Intestinal viscosity, which rose as digesta passed from the proximal to distal small intestine, fell with pentosanase addition and decreasing rye concentration. Intestinal viscosity, which correlated positively with reduced weight gain and FCE, was in turn correlated with the lumenal concentration of soluble high-molecular-weight carbohydrates (HMC, greater than 500 kDa), which constituted less than 15% of the total lumenal carbohydrate concentration. The arabinose and xylose content of the HMC increased with increasing rye concentration, suggesting that HMC composition in addition to concentration may determine intestinal viscosity. The results indicate that pentosanase isolated from rye by extraction methods may not be representative of those released by digestion.

Reduction of intestinal viscosity through manipulation of dietary rye and pentosanase concentration is effected through changes in the carbohydrate composition of the intestinal aqueous phase and results in improved growth rate and food conversion efficiency of broiler chicks.

Studies with germ-free chicks and antimicrobial compounds have indicated the significance of the interaction between host nutrition and the intestinal microflora. This interaction has suddenly leap...

Michael R. Bedford

Papers

Exogenous enzymes in monogastric nutrition - their current value and future benefits.

Increased small intestinal fermentation is partly responsible for the anti‐nutritive activity of non‐starch polysaccharides in chickens

Exogenous enzymes for pigs and poultry

Reduction of intestinal viscosity through manipulation of dietary rye and pentosanase concentration is effected through changes in the carbohydrate composition of the intestinal aqueous phase and results in improved growth rate and food conversion efficiency of broiler chicks.

Removal of antibiotic growth promoters from poultry diets: implications and strategies to minimise subsequent problems.