March 6, 2017 Geographic distribution of biosamples and organisms encompassed by the Genomes OnLine Database. The location where the organism was isolated is marked with pink dots; the location of the biosample is marked with blue dots. Credit: US Department of Energy <\/p>\n
There are more microbes in, on, and around the planet than there are stars in the Milky Way. Microbes affect food production; air quality; natural breakdown of plants, trees and biomass; soil quality for agriculture; and much more. To work with these microbes, scientists need to learn more about how microbes and viruses interact. Viruses influence microbes' abilities to work. Scientists at the U.S. Department of Energy (DOE) Joint Genome Institute built the largest publicly available database for viruses. This single effort increases the number of known viral genes by a factor of 16. Further, in a series of four articles published in Nucleic Acids Research, DOE Joint Genome Institute researchers report on the latest updates to several other publicly accessible databases and computational tools. These databases and tools will benefit the global community of microbial researchers. <\/p>\n
Microbes play key roles in the planet's biogeochemical cycles. Viruses, thought to outnumber microbes by 10 fold, can alter those cycles. Advances in sequencing technologies have generated vast amounts of data about the viruses. Working with the data requires tools to manage and interpret it. The updated database analytical tools offer details on microbes, specifically microbial genomics, and viruses. A new database, available to the public, enables analyses that can help scientists answer questions about the viruses that infect microbes, an interaction that affects countless natural processes and may provide tools for speeding up beneficial (or slowing down harmful) microbial actions. The insights gained from this work are relevant to DOE missions in bioenergy and environment. <\/p>\n
Providing high-quality, publicly accessible sequence data goes hand-in-hand with developing and maintaining the databases and tools that the research community can harness to help answer scientific questions. In a recent series of articles published in Nucleic Acids Research, researchers at DOE's Joint Genome Institute, a national scientific user facility, describe a database called Integrated Microbial Genomes with Virus Samples (IMG\/VR). IMG\/VR is a comprehensive computational platform integrating all the sequences in the database with associated metadata and analytical tools. <\/p>\n
IMG\/VR follows on the heels of a recent DOE Joint Genome Institute viral diversity report in Nature. Additional articles in the same issue describe updates to several publicly accessible, interactive databases since the last set of reports published in 2014. For example, as of July 2016, there were 47,516 archaeal, bacterial, and eukaryotic genomes in the IMG with Microbiome Samples (IMG\/M) system, with researchers noting that number \"represents an over 300% increase since September 2013.\" IMG\/M contains annotated DNA and RNA sequence data of archaeal, bacterial, eukaryotic, and viral genomes from cultured organisms; single cell genomes (SCG) and genomes from metagenomes from uncultured archaea, bacteria, and viruses; and metagenomes from environmental, host-associated, and engineered microbiome samples. <\/p>\n
Another paper concerns the Genomes OnLine Database (GOLD), a manually curated data management system that catalogs sequencing projects with associated metadata from around the world. In the current version of GOLD (v.6), all projects are organized based on a four-level classification system in the form of a study, organism (for isolates) or biosample (for environmental samples), sequencing project, and analysis project. A fourth paper focuses on the IMG Atlas of Biosynthetic gene Clusters (IMG-ABC). Launched in 2015, IMG-ABC enables researchers to search for biosynthetic gene clusters and secondary metabolites. Their latest update now incorporates ClusterScout, a tool for targeted identification of custom biosynthetic gene clusters across several thousand isolate microbial genomes, as well as a new search capability. <\/p>\n
Explore further: Database of DNA viruses and retroviruses debuts on IMG platform <\/p>\n
More information: I-Min A. Chen et al. IMG\/M: integrated genome and metagenome comparative data analysis system, Nucleic Acids Research (2017). DOI: 10.1093\/nar\/gkw929 <\/p>\n
Supratim Mukherjee et al. Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements, Nucleic Acids Research (2017). DOI: 10.1093\/nar\/gkw992 <\/p>\n
David Paez-Espino et al. IMG\/VR: a database of cultured and uncultured DNA Viruses and retroviruses, Nucleic Acids Research (2017). DOI: 10.1093\/nar\/gkw1030<\/p>\n
In a series of four articles published in the Database issue of the Nucleic Acids Research journal, DOE JGI researchers report on the latest updates to several publicly accessible databases and computational tools that benefit ... <\/p>\n
The number of microbes in, on, and around the planet - on the order of a nonillion, or 1030 - is estimated to outnumber the stars in the Milky Way. Microbes are known to play crucial roles in regulating carbon fixation, as ... <\/p>\n
The wealth of genomic and metagenomic datasets for microbes, particularly from previously unstudied environments, within the Integrated Microbial Genomes (IMG) system is being applied in a new public database to the search ... <\/p>\n
Researchers sequenced 230 diverse archaeal and bacterial genomes to learn more about the roles DNA methylation plays in prokaryotes. <\/p>\n
Using a specially designed computational tool as a lure, scientists have netted the genomic sequences of almost 12,500 previously uncharacterized viruses from public databases. <\/p>\n
DOE JGI researchers have developed an automated tool called MetaBAT that automatically groups large genomic fragments assembled from metagenome sequences to reconstruct single microbial genomes. <\/p>\n
A small team of researchers with members from the University of California and the University of Michigan has found that some personality traits unique to a queen wasp are passed down to her offspring, the worker wasps. In ... <\/p>\n
A new computational method can improve the accuracy of gene expression analyses, which are increasingly used to diagnose and monitor cancers and are a major tool for basic biological research. <\/p>\n
Three species and three genera of birdeater spiders are described as new to science in a paper recently published in the open access journal ZooKeys. In their study, the Brazilian spider experts, Drs. Caroline Fukushima and ... <\/p>\n
One of the unique and most iconic features of many modern turtles is that they can withdraw their neck and head to hide and protect them within their shells. The group name of species which do this, Cryptodira, even means ... <\/p>\n
The scientists who uncovered why zebras have black and white stripes (to repel biting flies), took the coloration question to giant pandas in a study published this week in the journal Behavioral Ecology. <\/p>\n
Research by the University of Southampton has found that methods used to predict the effect of species extinction on ecosystems could be producing inaccurate results. This is because current thinking assumes that when a species ... <\/p>\n
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Link: March 6, 2017 Geographic distribution of biosamples and organisms encompassed by the Genomes OnLine Database. The location where the organism was isolated is marked with pink dots; the location of the biosample is marked with blue dots. Continue reading
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