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...

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...

Metabonomic profiling of the gut microbiome: Implications for human health James Kinross, Imperial College, London

submitted by: dougramsey
Microbial-mammalian metabolic cooperation is defined as the human ‘metabonome’. Transgenomic co-metabolic interactions within the metabonome greatly increase system complexity and this presents a significant challenge for elucidating the mechanisms by which the intestinal micro biome influences the host phenotype. By measuring and mathematically modelling changes in the levels of products of metabolism found in mammalian biological fluids and tissues, metabonomics offers fresh insight...

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...

Diversity Profile of the Human Skin Microbiome in Health and Disease Elizabeth A. Grice, National Institutes of Health

submitted by: dougramsey

Elizabeth A. Grice of National Institutes of Health discusses "Diversity Profile of the Human Skin Microbiome in Health and Disease"