Rational Approaches of Data Management Across Boodles of Data

submitted by: dougramsey

Rational Approaches of Data Management Across Boodles of Data

Towards Transparency of Computational Analyses: A Central SOP Repository

submitted by: dougramsey
The methodologies used to generate genome and metagenome annotations are diverse and vary between groups and laboratories. Descriptions of the annotation process are helpful in interpreting genome annotation data. Some groups have produced Standard Operating Procedures (SOPs) that describe the annotation process, but standards are lacking for structure and content of these descriptions. A general structure for SOP documents that are relevant to genome annotation, metagenomics, environmental...

Metagenomic Comparison of the Microbial Hindgut Communities in Drywood- and Grass-Feeding Termites

submitted by: dougramsey
Falk Warnecke, Microbial Ecology Program, Joint Genome Institute, DOE Co-authors: Natalia Ivanova, Martin Allgaier, Nikos Kyrpides, Rudolf Scheffrahn, and Phil Hugenholtz Termites are highly efficient in degrading lignocellulosic biomass. In a recent metagenomic study we showed for the first time that microbes inhabiting the termite hindgut encode hundreds of carbohydrate-active enzymes, e.g. glycosyl hydrolases (GHs) and tens of carbohydrate binding modules (CBMs) and by implication are...

International Soil Metagenome - Sequencing Project

submitted by: dougramsey
Soil is often considered to be one of the main reservoirs of microbial diversity on the planet. This diversity could provide a range of information about the origins of microbial functional diversity as well as novel genetic resources. However, our historical inability to cultivate the majority of soil bacteria has hampered our understanding and exploitation of this large diverse community (more than 95% are often considered inaccessible through traditional culture techniques). Over the last...

Metaproteomics as a key technology for characterizing the human microbiome Nathan C. VerBerkmoes, Oak Ridge National Labs

submitted by: dougramsey
The human microbiome is a complex system of many microbial communities inhabiting a diversity of environmental niches throughout the human body. With at least an order of magnitude more cells and even greater diversity of genetic potential these microbial communities continually interact with the human host cells in complex but controlled manner that lead to normal human health. Our knowledge of the structure and function of these communities and the interactions with the human host is...

Metagenomic Analysis of Deep Subsurface Environments Hideto Takami, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)

submitted by: dougramsey
As a deep subsurface biosphere is thought to be the biggest biosphere in the earth, it is very interesting to know the phylogenetic and functional diversity in such environments. However, there is a little biological information for them because it is very hard to recover whole microbial community by only culture-base methods. In that sense, metagenomics is one of major useful methods to elucidate the microbial flora in unknown biosphere, which seems to be constructed by mainly unculturable...