Deep-Ocean Metagenomics: Comparative Investigations of Microbes Inhabiting Hydrothermal Vents and the Cold Deep Ocean

submitted by: dougramsey
The deep-ocean accounts for the majority of the water on our planet. While the cold deep-ocean is the dominant nutrient-challenged ecosystem, hydrothermal vents represent oases along tectonically active areas of the seafloor. Hydrothermal vents and the surrounding cold deep-ocean each support unique communities of microbes and viruses that have become highly adapted to local conditions. Through cycles of infection and host cell lysis, bacteriophages (viruses that specifically infect...

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...