Metagenomics 2008

Wellness and Diseases: Implications of Important Microbiota

dougramsey — Fri, 27 Feb 2009 10:53:47 -0800

The microbiota in personalized preventative medicine: how do we get from here to there and what role does metagenomics play?

Metagenomics 2008

Single molecule analyses of DNA in environmental microbes

dougramsey — Mon, 23 Feb 2009 17:17:20 -0800

Comprehensive characterization of genomic composition in environmental microbial samples has been challenging, because the majority of microorganisms are difficult to culture. Additional challenges include a high degree of genetic diversity between and within species, various level of relative abundance and ubiquitous presence of cell-free DNA. Single cells or single molecules genomic assays hold great promise for tackling these challenges.

Metagenomics 2008

The Importance of Marine Picoeukaryotes and the Search for Lost Time

dougramsey — Mon, 23 Feb 2009 17:11:45 -0800

Unicellular eukaryotes are responsible for a massive amount of photosynthetic carbon fixation in marine systems. The smallest among these fall within the “pico” size fraction (<2 micrometers in diameter), are broadly distributed – from coastal to open-ocean environments – and are highly diverse. Picoeukaryotes contribute a significant proportion of the biomass and primary production within this size fraction, often rivaling their cyanobacterial counterparts Prochlorococcus and Synechococcus.

Metagenomics 2008

Setting the Stage: Mobilizing the Metagenomics Community

dougramsey — Mon, 23 Feb 2009 17:03:17 -0800

About 250 leaders in the emerging science of metagenomics converged at the UC San Diego division of the California Institute for Telecommunications and Information Technology (Calit2) earlier this month for the third Annual International Conference on Metagenomics. The conference was a week-long opportunity to share data and discuss the latest research, explore how advances in computing and sequencing technologies might be of benefit, and build or strengthen collaborations in the field.

Metagenomics 2008

Summary of Subgroup Discussions for Metagenomics 2008

dougramsey — Mon, 23 Feb 2009 17:02:46 -0800

John Wooley of UC San Diego makes Closing Remarks for the Metagenomics 2008 Conference

Metagenomics 2008

Structural Genomics (SG) & Beginning a Research Dialogue with the Metagenomics Community

dougramsey — Mon, 23 Feb 2009 17:00:54 -0800

Ian Wilson of The Scripps Research Institute & Stephen Burley, Eli Lilly & Co. Presents "Structural Genomics (SG) & Beginning a Research Dialogue with the Metagenomics Community"

Metagenomics 2008

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

dougramsey — Mon, 23 Feb 2009 16:54:54 -0800

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.

Metagenomics 2008

Rational Approaches of Data Management Across Boodles of Data

dougramsey — Mon, 23 Feb 2009 16:48:28 -0800

Rational Approaches of Data Management Across Boodles of Data

Metagenomics 2008

Towards Transparency of Computational Analyses: A Central SOP Repository

dougramsey — Mon, 23 Feb 2009 16:41:12 -0800

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 samples and clinical samples will be presented.

Metagenomics 2008

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

dougramsey — Mon, 23 Feb 2009 16:37:08 -0800

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 responsible for the bulk of the lignocellulose deconstruction (1).

Metagenomics 2008

International Soil Metagenome - Sequencing Project

dougramsey — Mon, 23 Feb 2009 16:33:54 -0800

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).

Metagenomics 2008

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

dougramsey — Mon, 23 Feb 2009 16:22:04 -0800

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.

Metagenomics 2008

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

dougramsey — Mon, 23 Feb 2009 16:14:37 -0800

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 microbes.

Metagenomics 2008

Genomic and Genetic Insight into Gut Microbiota Function and Manipulation

dougramsey — Mon, 23 Feb 2009 16:09:01 -0800

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 therapeutic target.

Metagenomics 2008

Towards an Open Access Gazetteer

dougramsey — Mon, 23 Feb 2009 16:01:54 -0800

The Gazetteer (Gaz) is a community-based project of the EnvO Consortium for describing instances of organism environments and biological samples supporting consistent annotation of locations and environments. The Gazetteer describes places and place names, and the relations between them. The Gaz, with 130,000 plus terms (over 50 % of terms defined) and relations, is being utilizing in scientific investigations such as applying Gaz terms to organisms based on free-text from the Encyclopedia of Life dataset for the OntoSpecies project.

Metagenomics 2008

Challenges in Ecological Metagenomics

dougramsey — Mon, 23 Feb 2009 16:01:02 -0800

Since the first metagenomics study was published 17 years ago, the ability to make ecological inferences has been limited by sequencing throughput and the ability to analyze the data. Yet, if the potential of metagenomics to help us decipher the structure and function of microbial ecosystems is to be realized, it is essential that our bioinformatics tools motivate our sequencing efforts. This is analogous to the bioinformatics advances that were made to accelerating the sequencing of the human genome, except that metagenomic projects face perhaps even greater obstacles.

Metagenomics 2008

Should Genomics Contextual Data Fly Coach?

dougramsey — Mon, 23 Feb 2009 15:55:16 -0800

Inigo San Gil, University of New Mexico The Long Term Ecological Research Network (LTER) creates long-term ecological data records in twenty six sites across the US. Five years ago the LTER adopted a metadata specification called the Ecological Metadata Language (EML) to facilitate network data integration and synthesis. A growing number of LTER scientists are conducting genomics research, thus the need to adopt an integrated genomics and ecological data management system is urgent.

Metagenomics 2008

The Importance of Context for the Design and Interpretation of Comparative Metagenomics Studies: The MINIMESS Proposal

dougramsey — Mon, 23 Feb 2009 15:52:33 -0800

Jeroen Raes, European Molecular Biology Laboratory Comparative metagenomics is a powerful tool to detect environment-specific adaptation of the communities that inhabit them. However, a wide range of technical and biological interfering factors hamper the correct interpretation of comparative metagenomics results. Here, I will describe some of these factors and pitfalls and propose a minimal metagenome sequence analysis standard (MINIMESS) to cope with these issues.

Metagenomics 2008

Metagenomics 2008 Day 1 Panel Discussion: A Community Vision

dougramsey — Mon, 23 Feb 2009 15:50:01 -0800

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

Metagenomics 2008

Extending MIGS/MIMS to the Description of Ribosomal RNA Sequences

dougramsey — Mon, 23 Feb 2009 15:36:58 -0800

With the MIGS/MIMS specifications the Genomic Standards Consortium has finished the groundwork to enrich our genome and metagenome collections with contextual data. Now, it is time to consider whether these standards could be applied ‘as is’ in the short-term, and ‘with modification/extension’ in the longer-term to any genetic marker sequence retrieved from the environment.

Metagenomics 2008

The Environment Ontology: Linking Environmental Data

dougramsey — Mon, 23 Feb 2009 15:32:04 -0800

Norman Morrison, University of Manchester Every biological specimen that is collected or sampled — whether for a museum collection, for epidemiological studies, for population studies, for ecological research, for research into evolution, biodiversity or sustainability, indeed any biological research — comes from a particular habitat where particular physical conditions prevail. How ever, at present there is no accepted semantic standard for describing the environment from which these biological samples are collected.

Metagenomics 2008

Metadata Capture in the IMG/IMGm: Getting Scientists to Contribute

dougramsey — Mon, 23 Feb 2009 15:29:32 -0800

Metadata Capture in the IMG/IMGm: Getting Scientists to Contribute - Victor Markowitz, Lawrence Berkeley National Lab

Metagenomics 2008

Analyzing the Mobile Metagenome

dougramsey — Mon, 23 Feb 2009 15:25:17 -0800

Metagenomic approaches are being use to investigate many diverse ecosystems and reveal many novel functions therein. However these methods can frequently pass over the DNA which we find in the mobile metagenome or mobilome. Much of this DNA is not easily cloned into fosmids or BACs for functional analysis and DNA based metagenomics projects do not always provide sufficient information to determine from where the sequence arose, genome or mobilome.

Metagenomics 2008

TimeLogic

dougramsey — Mon, 23 Feb 2009 15:21:03 -0800

Delivering the performance equivalent of hundreds to over one thousand CPU cores per accelerated node, the TimeLogic solutions are ideal for data-intensive next-generation genomics. Life science institutions worldwide have chosen the TimeLogic brand as their optimal solution for high-throughput bioinformatics. The DeCypher and CodeQuest biocomputing solutions blend proven bioinformatics algorithms with ultra-fast accelerator hardware to achieve a perfect combination of performance, accuracy, and value for many biological applications.

Metagenomics 2008

New Insights Into Lignocellulose Conversion by Termite Gut Microbes

dougramsey — Mon, 23 Feb 2009 15:18:40 -0800

Termites and their complex hindgut microbiota are able to convert wood lignocellulose into hydrogen and other products used to fuel their metabolisms. Recent gene and genome and metagenome based analyses on the gut community have revealed novel insights into many bacteria-mediated, important symbiotic functions. The system-wide gene analysis of a microbial community specialized towards plant lignocellulose degradation has both basic and applied implications.

Metagenomics 2008

The Genomes Online Database (GOLD): The Value of a Comprehensive Metadata Collection

dougramsey — Mon, 23 Feb 2009 15:13:15 -0800

The Genomes Online Database (GOLD): The Value of a Comprehensive Metadata Collection - Nikos Kyrpides, Joint Genome Institute

Metagenomics 2008

Efficient Metagenomics Data Processing: Pitfalls and Solutions

dougramsey — Mon, 23 Feb 2009 15:10:02 -0800

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.

Metagenomics 2008

Implementing MIGS/MIMS: The Genomic Contextual

dougramsey — Mon, 23 Feb 2009 15:03:04 -0800

The MIGS/MIMS checklist developed by the Genomic Standards Consortium (GSC) aims to enrich our ever growing data collection of genomic and metagenomic sequences. Therefore, the checklist defines what minimal list of contextual data attributes has to be added to the sequences in order to conform to the MIGS/MIMS specification. However, MIGS/MIMS itself does not specify how the contextual data should be documented; thus the GSC is developing the Genomic Contextual Data Markup Language (GCDML), which provides the official implementation of MIGS/MIMS.

Metagenomics 2008

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

dougramsey — Mon, 23 Feb 2009 14:59:21 -0800

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.

Metagenomics 2008

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

dougramsey — Mon, 23 Feb 2009 14:55:27 -0800

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 into the effects of the gut microbiome on human health.

Metagenomics 2008

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

dougramsey — Mon, 23 Feb 2009 14:48:40 -0800

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 from raw sequence reads.

Metagenomics 2008

Exploring Next Generation Sequencing Today

dougramsey — Mon, 23 Feb 2009 14:45:58 -0800

Exploring Next Generation Sequencing Today, Thomas Jarvie, 454 Life Sciences

Metagenomics 2008

Computational Aspects of Metagenome Analysis

dougramsey — Mon, 23 Feb 2009 14:39:42 -0800

Computational Aspects of Metagenome Analysis
Daniel Huson, Tuebingen University

Metagenomics 2008

Towards Computer Assisted Markup of Data: Habitat-Lite

dougramsey — Mon, 23 Feb 2009 14:32:46 -0800

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.

Metagenomics 2008

Molecular characterization of the bacterial flora in the lung of healthy, asthmatic and chronic obstructive pulmonary diseased (COPD) subjects

dougramsey — Mon, 23 Feb 2009 14:29:22 -0800

Molecular characterization of the bacterial flora in the lung of healthy, asthmatic and chronic obstructive pulmonary diseased (COPD) subjects Markus Hilty, Imperial College, London

Metagenomics 2008

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

dougramsey — Mon, 23 Feb 2009 14:26:20 -0800

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

Metagenomics 2008

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

dougramsey — Mon, 23 Feb 2009 14:19:43 -0800

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 electrically conductive appendages known as bacterial nanowires.

Metagenomics 2008

Protein Target Selection Challenges and Charge to Discussion Groups at Metagenomics 2008

dougramsey — Mon, 23 Feb 2009 14:14:08 -0800

Adam Godzik, Burnham Institute of Medical Research and UC San Diego presents "Protein Target Selection Challenges and Charge to Discussion Groups"

Metagenomics 2008

Studying the Metagenomics Protein Universe: Novelty, Diversity and Divergence

dougramsey — Mon, 23 Feb 2009 14:11:13 -0800

Studying the Metagenomics Protein Universe: Novelty, Diversity and Divergence Adam Godzik, Burnham Institute for Medical Research/UC San Diego

Metagenomics 2008

The Evolution of Small Bacterial Genomesin the Ultra-Oligotrophic Ocean

dougramsey — Mon, 23 Feb 2009 14:02:34 -0800

The size and coding capacity of a genome are its most fundamental properties. What selective pressures deter mine the expansion and contraction of genomes, and how is genome size related to adaptive strategies?

Metagenomics 2008

Accessing the Metatranscriptome for Complex Marine Microbial Communities

dougramsey — Mon, 23 Feb 2009 13:58:46 -0800

Sequencing the expressed genetic information of an ecosystem (metatranscriptome) can provide information about the response of organisms to varying environ mental conditions. Until recently, metatranscriptomics has been limited to microarray technology and random cloning methodologies. The application of high-throughput sequencing technology is now enabling access to both known and previously unknown transcripts in natural com munities. We present a study of a complex marine meta transcriptome obtained from random whole-community mRNA using the GS-FLX Pyrosequencing technology.

Metagenomics 2008

Genomic Standards Consortium Report

dougramsey — Mon, 23 Feb 2009 13:52:21 -0800

Genomic Standards Consortium Report Dawn Field, Oxford Centre for Ecology and Hydrology

Metagenomics 2008

Towards a Standards Compliant Literature: The GSC eJournal

dougramsey — Mon, 23 Feb 2009 13:48:16 -0800

George Garrity, Michigan State University Standards in Genomic Sciences (SIGS) is a new Open Access publication that is being created in cooperation with the Genomic Standards Consortium (GSC). It is in tended to fill an unmet need for rapid publication of standards compliant reports on genomes and metagenomes, standard operating procedures relevant to large-scale sequencing initiatives, and various forms of technical reports, policy statements, meeting reports and other con tent that is pertinent to this rapidly evolving field.

Metagenomics 2008

CAMERA Interest in Community Standards for the Capture and Exchange of Metadata

dougramsey — Mon, 23 Feb 2009 13:45:33 -0800

CAMERA Interest in Community Standards for the Capture and Exchange of Metadata - Paul Gilna, CAMERA/UC San Diego

Metagenomics 2008

Jason Flowers Metabolic Characterization of Candidatus Accumulibacter Phosphatis Using Metaproteomic Analysis

dougramsey — Mon, 23 Feb 2009 13:44:11 -0800

In many freshwater bodies, phosphorus is a limiting nutrient for bacterial growth. To prevent eutrophication, enhanced biological phosphorus removal (EBPR) of waste water has been successfully applied at sewage plants for the past thirty years. Previous researchers could only speculate about the biochemical pathways involved in EBPR principally because the organisms responsible for EBPR cannot be isolated in pure culture.

Metagenomics 2008

Overview of the GSC and the Minimum Information About a (Meta) Genome Sequence (MIGS/MIMS) Speci?cation

dougramsey — Mon, 23 Feb 2009 13:40:58 -0800

Overview of the GSC and the Minimum Information About a (Meta) Genome Sequence (MIGS/MIMS) Specification - Dawn Field, Oxford Centre for Ecology and Hydrology

Metagenomics 2008

A Genomic Encyclopedia of Bacteria and Archaea (GEBA) and the Search for the Dark Matter of the Biological Universe

dougramsey — Mon, 23 Feb 2009 13:38:55 -0800

There is a glaring gap in microbial genome sequence availability – the currently available genome sequences show a highly biased phylogenetic distribution compared to the extent of microbial diversity known today. This bias has resulted in major limitations in our knowledge of microbial genome complexity and our understanding of the evolution, physiology and metabolic capacity of microbes. Although there have been small efforts in sequencing genomes from across the tree of life for microbes, there are no systematic efforts.

Metagenomics 2008

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

dougramsey — Mon, 23 Feb 2009 13:28:32 -0800

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

Metagenomics 2008

Integrative Marine Metagenomics

dougramsey — Mon, 23 Feb 2009 13:21:34 -0800

Integrative Marine Metagenomics

Metagenomics 2008

The Human Oral Microbiome by Floyd Dewhirst, Harvard University

dougramsey — Mon, 23 Feb 2009 13:14:47 -0800

The human oral cavity is a diverse habitat that contains approximately bacterial 600 predominant species. The oral microbiome is comprised of 44% named species, 12% isolates representing unnamed species, and 44% phylotypes known only from 16S rRNA based cloning studies. Species from 11 phyla have been identified: Firmicutes (211), Bacteroidetes (106), Proteobacteria (99), Actinobacteria (64), Spirochaetes (49), Fusobacteria (29), TM7 (12), Synergistetes (10), Chlamydiae (1), Chloroflexi (1) and SR1(1).

Metagenomics 2008