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...

Genomic and Genetic Insight into Gut Microbiota Function and Manipulation

submitted by: dougramsey
Trillions of microbes live in our digestive tract and influence our biology in profound and diverse ways. Several diseases, including obesity and inflammatory bowel diseases, have been associated with large-scale shifts in microbiota composition. The ability to address basic questions concerning community function and plasticity are fundamental to understanding the extent of causal relationships between host biology and microbiota perturbations, and whether the microbiota is a viable...

Metagenomics 2008 Day 1 Panel Discussion: A Community Vision

submitted by: dougramsey

The first day at Metagenomics 2008 is discussed in a Q & A panel session at the end of the day.

Efficient Metagenomics Data Processing: Pitfalls and Solutions

submitted by: dougramsey
Nikos Kyrpides, Joint Genome Institute Co-authors: Kostas Mavrommatis, Natalia Ivanova Metagenomics has emerged as a powerful tool for exploration of the functional capabilities of microbial communities regardless of the ability of their members to grow in pure culture. However, little is known for the efficacy of the methods used to process these datasets. Further more, sequencing of environmental genomic DNA usually results in large, highly fragmented datasets representing a significant...

Targeted Gene Identification from Short Gene Fragments in Metagenome and their Use in Biogeochemical Studies

submitted by: dougramsey
Metagenomics allows for a new approach to studying biogeochemical processes in an environment, by giving an approximation of a community’s biogeochemical potential through the genes involved in a given process. Lipid biomarkers are well suited to this kind of approach because they are important for a number of biogeochemical questions and some have well studied biosynthetic pathways. One important class of lipid biomarkers, triterpenoids, were investigated in a new metagenomic sample that...

Integrated Information System for Genomic and Metagenomic Data Analysis at National Center for Biotechnology Information (NCBI)

submitted by: dougramsey
Recent advances in biotechnology and bioinformatics has provided a flood of genomic data and tremendous growth in the number of associated data sets. Sequencing projects now include draft assemblies, complete genomes, comparative genomics, and metagenomics where genetic material is sequenced directly from environmental samples. The NCBI provides integrated systems for data storage, retrieval, and analysis. GenBank, an archival database of DNA sequences, contains consensus sequences assembled...

Towards Computer Assisted Markup of Data: Habitat-Lite

submitted by: dougramsey
Lynette Hirschman, The MITRE Corporation Co-authors: Scott Mardis, Cheryl Clark, Kevin Cohen Habitat-Lite (aka EnvO-Lite) is a set of structured terms designed to facilitate capture of high-level information about habitat and sample source metadata for genomics and metagenomics samples. It is designed to be light-weight and compact. Habitat-Lite terms are drawn from the full EnvO ontology and are made avail able by the EnvO Consortium in the EnvO-Lite-GSC OBO file. Habitat-Lite terms include...

Electromicrobiology: Novel Approaches for Investigating Charge Transfer and Energy Transformation in Microbial Systems

submitted by: dougramsey
Respiratory microorganisms capture energy for growth and maintenance as they transfer electrons from energy sources to appropriate electron acceptors. Controlling the availability of electron donor and acceptor pairs provides opportunities for investigating fundamental aspects of energy transformation and distribution in defined and un defined microbial cultures. For example, we have noted that in all bacteria investigated to date electron acceptor limitation prompts the production of...

How Might S Geno and M Geno Work Together for Getting to Biological Function?

submitted by: dougramsey

Metagenomics 2008 Discussion/Breakouts: Moderator: John Wooley, Chair, Metagenomics 2008, et. al.