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An Experimental Metagenome Data Management and AnalysisSystem

Description: The application of shotgun sequencing to environmental samples has revealed a new universe of microbial community genomes (metagenomes) involving previously uncultured organisms. Metagenome analysis, which is expected to provide a comprehensive picture of the gene functions and metabolic capacity of microbial community, needs to be conducted in the context of a comprehensive data management and analysis system. We present in this paper IMG/M, an experimental metagenome data management and analysis system that is based on the Integrated Microbial Genomes (IMG) system. IMG/M provides tools and viewers for analyzing both metagenomes and isolate genomes individually or in a comparative context.
Date: March 1, 2006
Creator: Markowitz, Victor M.; Korzeniewski, Frank; Palaniappan, Krishna; Szeto, Ernest; Ivanova, Natalia N.; Kyrpides, Nikos C. et al.
Partner: UNT Libraries Government Documents Department

Bringing large-scale multiple genome analysis one step closer: ScalaBLAST and beyond

Description: Genome sequence comparisons of exponentially growing data sets form the foundation for the comparative analysis tools provided by community biological data resources such as the Integrated Microbial Genome (IMG) system at the Joint Genome Institute (JGI). We present an example of how ScalaBLAST, a high-throughput sequence analysis program harnesses increasingly critical high-performance computing to perform sequence analysis which is a critical component of maintaining a state-of-the-art sequence data repository. The Integrated Microbial Genomes (IMG) system1 is a data management and analysis platform for microbial genomes hosted at the JGI. IMG contains both draft and complete JGI genomes integrated with other publicly available microbial genomes of all three domains of life. IMG provides tools and viewers for interactive analysis of genomes, genes and functions, individually or in a comparative context. Most of these tools are based on pre-computed pairwise sequence similarities involving millions of genes. These computations are becoming prohibitively time consuming with the rapid increase in the number of newly sequenced genomes incorporated into IMG and the need to refresh regularly the content of IMG in order to reflect changes in the annotations of existing genomes. Thus, building IMG 2.0 (released on December 1st 2006) entailed reloading from NCBI's RefSeq all the genomes in the previous version of IMG (IMG 1.6, as of September 1st, 2006) together with 1,541 new public microbial,viral and eukaryal genomes, bringing the total of IMG genomes to 2,301. A critical part of building IMG 2.0 involved using PNNL ScalaBLAST software for computing pairwise similarities for over 2.2 million genes in under 26 hours on 1,000 processors, thus illustrating the impact that new generation bioinformatics tools are poised to make in biology. The BLAST algorithm2, 3 is a familiar bioinformatics application for computing sequence similarity, and has become a workhorse in large-scale genomics projects. The rapid ...
Date: June 1, 2007
Creator: Oehmen, Christopher S.; Sofia, Heidi J.; Baxter, Douglas; Szeto, Ernest; Hugenholtz, Philip; Kyrpides, Nikos et al.
Partner: UNT Libraries Government Documents Department

The integrated microbial genomes (IMG) system in 2007: datacontent and analysis tool extensions

Description: The Integrated Microbial Genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and annotating genomes, genes and functions, individually or in a comparative context. Since its first release in 2005, IMG's data content and analytical capabilities have been constantly expanded through quarterly releases. IMG is provided by the DOE-Joint Genome Institute (JGI) and is available from http://img.jgi.doe.gov.
Date: August 1, 2007
Creator: Markowitz, Victor M.; Szeto, Ernest; Palaniappan, Krishna; Grechkin, Yuri; Chu, Ken; Chen, I-Min A. et al.
Partner: UNT Libraries Government Documents Department

Metagenomic Analysis of Microbial Symbionts in a Gutless Worm

Description: Symbioses between bacteria and eukaryotes are ubiquitous, yet our understanding of the interactions driving these associations is hampered by our inability to cultivate most host-associated microbes. Here we use a metagenomic approach to describe four co-occurring symbionts from the marine oligochaete Olavius algarvensis, a worm lacking a mouth, gut and nephridia. Shotgun sequencing and metabolic pathway reconstruction revealed that the symbionts are sulphur-oxidizing and sulphate-reducing bacteria, all of which are capable of carbon fixation, thus providing the host with multiple sources of nutrition. Molecular evidence for the uptake and recycling of worm waste products by the symbionts suggests how the worm could eliminate its excretory system, an adaptation unique among annelid worms. We propose a model that describes how the versatile metabolism within this symbiotic consortium provides the host with an optimal energy supply as it shuttles between the upper oxic and lower anoxic coastal sediments that it inhabits.
Date: May 1, 2006
Creator: Woyke, Tanja; Teeling, Hanno; Ivanova, Natalia N.; Hunteman, Marcel; Richter, Michael; Gloeckner, Frank Oliver et al.
Partner: UNT Libraries Government Documents Department

High-resolution metagenomics targets major functional types in complex microbial communities

Description: Most microbes in the biosphere remain uncultured and unknown. Whole genome shotgun (WGS) sequencing of environmental DNA (metagenomics) allows glimpses into genetic and metabolic potentials of natural microbial communities. However, in communities of high complexity metagenomics fail to link specific microbes to specific ecological functions. To overcome this limitation, we selectively targeted populations involved in oxidizing single-carbon (C{sub 1}) compounds in Lake Washington (Seattle, USA) by labeling their DNA via stable isotope probing (SIP), followed by WGS sequencing. Metagenome analysis demonstrated specific sequence enrichments in response to different C{sub 1} substrates, highlighting ecological roles of individual phylotypes. We further demonstrated the utility of our approach by extracting a nearly complete genome of a novel methylotroph Methylotenera mobilis, reconstructing its metabolism and conducting genome-wide analyses. This approach allowing high-resolution genomic analysis of ecologically relevant species has the potential to be applied to a wide variety of ecosystems.
Date: August 1, 2009
Creator: Kalyuzhnaya, Marina G.; Lapidus, Alla; Ivanova, Natalia; Copeland, Alex C.; McHardy, Alice C.; Szeto, Ernest et al.
Partner: UNT Libraries Government Documents Department

IMG/M: A data management and analysis system for metagenomes

Description: IMG/M is a data management and analysis system for microbial community genomes (metagenomes) hosted at the Joint Genome Institute (JGI). IMG/M consists of metagenome data integrated with isolate microbial genomes from the Integrated Microbial Genomes (IMG) system. IMG/M provides IMG's comparative data analysis tools extended to handle metagenome data, together with metagenome-specific analysis tools. IMG/M is available at http://img.jgi.doe.gov/m. Studies of the collective genomes (also known as metagenomes) of environmental microbial communities (also known as microbiomes) are expected to lead to advances in environmental cleanup, agriculture, industrial processes, alternative energy production, and human health (1). Metagenomes of specific microbiome samples are sequenced by organizations worldwide, such as the Department of Energy's (DOE) Joint Genome Institute (JGI), the Venter Institute and the Washington University in St. Louis using different sequencing strategies, technology platforms, and annotation procedures. According to the Genomes OnLine Database, about 28 metagenome studies have been published to date, with over 60 other projects ongoing and more in the process of being launched (2). The Department of Energy's (DOE) Joint Genome Institute (JGI) is one of the major contributors of metagenome sequence data, currently sequencing more than 50% of the reported metagenome projects worldwide. Due to the higher complexity, inherent incompleteness, and lower quality of metagenome sequence data, traditional assembly, gene prediction, and annotation methods do not perform on these datasets as well as they do on isolate microbial genome sequences (3, 4). In spite of these limitations, metagenome data are amenable to a variety of analyses, as illustrated by several recent studies (5-10). Metagenome data analysis is usually set up in the context of reference isolate genomes and considers the questions of composition and functional or metabolic potential of individual microbiomes, as well as differences between microbiome samples. Such analysis relies on efficient management of genome and metagenome ...
Date: August 1, 2007
Creator: Markowitz, Victor M.; Ivanova, Natalia N.; Szeto, Ernest; Palaniappan, Krishna; Chu, Ken; Dalevi, Daniel et al.
Partner: UNT Libraries Government Documents Department

Metagenomic analysis of phosphorus removing sludgecommunities

Description: Enhanced Biological Phosphorus Removal (EBPR) is not wellunderstood at the metabolic level despite being one of the best-studiedmicrobially-mediated industrial processes due to its ecological andeconomic relevance. Here we present a metagenomic analysis of twolab-scale EBPR sludges dominated by the uncultured bacterium, "CandidatusAccumulibacter phosphatis." This analysis resolves several controversiesin EBPR metabolic models and provides hypotheses explaining the dominanceof A. phosphatis in this habitat, its lifestyle outside EBPR and probablecultivation requirements. Comparison of the same species from differentEBPR sludges highlights recent evolutionary dynamics in the A. phosphatisgenome that could be linked to mechanisms for environmental adaptation.In spite of an apparent lack of phylogenetic overlap in the flankingcommunities of the two sludges studied, common functional themes werefound, at least one of them complementary to the inferred metabolism ofthe dominant organism. The present study provides a much-needed blueprintfor a systems-level understanding of EBPR and illustrates thatmetagenomics enables detailed, often novel, insights into evenwell-studied biological systems.
Date: February 1, 2006
Creator: Garcia Martin, Hector; Ivanova, Natalia; Kunin, Victor; Warnecke,Falk; Barry, Kerrie; McHardy, Alice C. et al.
Partner: UNT Libraries Government Documents Department

Symbiosis insights through metagenomic analysis of a microbialconsortium

Description: Symbioses between bacteria and eukaryotes are ubiquitous, yet our understanding of the interactions driving these associations is hampered by our inability to cultivate most host-associated microbes. Here, we used a metagenomic approach to describe four co-occurring symbionts from the marine oligochaete Olavius algarvensis, a worm lacking a mouth, gut, and nephridia. Shotgun sequencing and metabolic pathway reconstruction revealed that the symbionts are sulfur-oxidizing and sulfate-reducing bacteria, all of which are capable of carbon fixation, providing the host with multiple sources of nutrition. Molecular evidence for the uptake and recycling of worm waste products by the symbionts suggests how the worm could eliminate its excretory system, an adaptation unique among annelid worms. We propose a model which describes how the versatile metabolism within this symbiotic consortium provides the host with an optimal energy supply as it shuttles between the upper oxic and lower anoxic coastal sediments which it inhabits.
Date: September 1, 2006
Creator: Woyke, Tanja; Teeling, Hanno; Ivanova, Natalia N.; Hunteman,Marcel; Richter, Michael; Gloeckner, Frank Oliver et al.
Partner: UNT Libraries Government Documents Department

A genomic analysis of the archael system Ignicoccus hospitalis-Nanoarchaeum equitans

Description: BACKGROUND: The relationship between the hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans is the only known example of a specific association between two species of Archaea. Little is known about the mechanisms that enable this relationship. RESULTS: We sequenced the complete genome of I. hospitalis and found it to be the smallest among independent, free-living organisms. A comparative genomic reconstruction suggests that the I. hospitalis lineage has lost most of the genes associated with a heterotrophic metabolism that is characteristic of most of the Crenarchaeota. A streamlined genome is also suggested by a low frequency of paralogs and fragmentation of many operons. However, this process appears to be partially balanced by lateral gene transfer from archaeal and bacterial sources. CONCLUSIONS: A combination of genomic and cellular features suggests highly efficient adaptation to the low energy yield of sulfur-hydrogen respiration and efficient inorganic carbon and nitrogen assimilation. Evidence of lateral gene exchange between N. equitans and I. hospitalis indicates that the relationship has impacted both genomes. This association is the simplest symbiotic system known to date and a unique model for studying mechanisms of interspecific relationships at the genomic and metabolic levels.
Date: September 1, 2008
Creator: Sun, Hui; Anderson, Iain; Makarova, Kira S.; Elkins, James G.; Ivanova, Natalia; Wall, Mark A. et al.
Partner: UNT Libraries Government Documents Department

Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite

Description: From the standpoints of both basic research and biotechnology, there is considerable interest in reaching a clearer understanding of the diversity of biological mechanisms employed during lignocellulose degradation. Globally, termites are an extremely successful group of wood-degrading organisms and are therefore important both for their roles in carbon turnover in the environment and as potential sources of biochemical catalysts for efforts aimed at converting wood into biofuels. Only recently have data supported any direct role for the symbiotic bacteria in the gut of the termite in cellulose and xylan hydrolysis. Here we use a metagenomic analysis of the bacterial community resident in the hindgut paunch of a wood-feeding Nasutitermes species to show the presence of a large, diverse set of bacterial genes for cellulose and xylan hydrolysis. Many of these genes were expressed in vivo or had cellulase activity in vitro, and further analyses implicate spirochete and fibrobacter species in gut lignocellulose degradation. New insights into other important symbiotic functions including H{sub 2} metabolism, CO{sub 2}-reductive acetogenesis and N{sub 2} fixation are also provided by this first system-wide gene analysis of a microbial community specialized towards plant lignocellulose degradation. Our results underscore how complex even a 1-{micro}l environment can be.
Date: October 1, 2007
Creator: Warnecke, Falk; Warnecke, Falk; Luginbuhl, Peter; Ivanova, Natalia; Ghassemian, Majid; Richardson, Toby H. et al.
Partner: UNT Libraries Government Documents Department