A5023696415- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Bacteriophages and microbial interactions
- Legume Nitrogen Fixing Symbiosis
- Gut microbiota and health
- Protist diversity and phylogeny
- RNA and protein synthesis mechanisms
- Probiotics and Fermented Foods
- Anaerobic Digestion and Biogas Production
- Biofuel production and bioconversion
- Plant-Microbe Interactions and Immunity
- Methane Hydrates and Related Phenomena
- Metal Extraction and Bioleaching
- Environmental DNA in Biodiversity Studies
- Plant Virus Research Studies
- Plant Pathogenic Bacteria Studies
- Plant Disease Resistance and Genetics
- Microbial Metabolic Engineering and Bioproduction
- Microbial Natural Products and Biosynthesis
- Plant nutrient uptake and metabolism
- Enzyme Production and Characterization
- Wastewater Treatment and Nitrogen Removal
- Plant Pathogens and Fungal Diseases
- Genetics, Bioinformatics, and Biomedical Research
- Molecular Biology Techniques and Applications
Joint Genome Institute
2016-2025
Lawrence Berkeley National Laboratory
2016-2025
University of California, Berkeley
2002-2023
Pacific Northwest National Laboratory
2022
United States Department of Energy
2008-2022
King Abdulaziz University
2014-2018
Wellcome Centre for Mitochondrial Research
2018
University of Newcastle Australia
2018
Newcastle University
2018
Los Alamos National Laboratory
2009-2017
The Genomes On Line Database (GOLD) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables search page. As September 2009, contains information more than 5800 sequencing which 1100 have been completed sequence data deposited public repository. continues to expand, moving toward the goal providing most repository metadata related...
The application of phylogenetic taxonomic procedures led to improvements in the classification bacteria assigned phylum Actinobacteria but even so there remains a need further clarify relationships within taxon that encompasses organisms agricultural, biotechnological, clinical and ecological importance. Classification morphologically diverse belonging this large based on limited number features has proved be difficult, not least when decisions rested heavily interpretation poorly resolved...
Genome sequencing enhances our understanding of the biological world by providing blueprints for evolutionary and functional diversity that shapes biosphere. However, microbial genomes are currently available limited phylogenetic breadth, owing to historical inability cultivate most microorganisms in laboratory. We apply single-cell genomics target sequence 201 uncultivated archaeal bacterial cells from nine diverse habitats belonging 29 major mostly uncharted branches tree life, so-called...
We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of Minimum Information about Any (x) Sequence (MIxS). The a Single Amplified Genome (MISAG) Metagenome-Assembled (MIMAG), including, but not limited to, assembly quality, estimates completeness contamination. These can be used in combination with other GSC checklists, including (MIGS), Metagenomic (MIMS), Marker Gene (MIMARKS). Community-wide...
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Although considerable progress has been made in recent years regarding the classification of bacteria assigned to phylum Bacteroidetes, there remains a need further clarify taxonomic relationships within diverse assemblage that includes organisms clinical, piscicultural, and ecological importance. Bacteroidetes proved be difficult, not least when decisions rested heavily on interpretation poorly resolved 16S rRNA gene trees limited number phenotypic features. Here, draft genome sequences...
The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in comprehensive integrated context. IMG integrates draft and complete from all three domains life with large number plasmids viruses. provides tools viewers analyzing reviewing the annotations genes IMG's data content analytical capabilities have been continuously extended through regular updates since its first release March 2005. is at http://img.jgi.doe.gov....
The Genomes OnLine Database (GOLD, http://www.genomesonline.org/) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables search page. As September 2011, GOLD, now on version 4.0, contains information 11,472 sequencing which 2907 have been completed sequence data has deposited public repository. Out these 1918 are finished 989...
Abstract Millions of new viral sequences have been identified from metagenomes, but the quality and completeness these vary considerably. Here we present CheckV, an automated pipeline for identifying closed genomes, estimating genome fragments removing flanking host regions integrated proviruses. CheckV estimates by comparing with a large database complete including 76,262 systematic search publicly available metatranscriptomes metaviromes. After validation on mock datasets comparison to...
CRISPR-Cas systems provide microbes with adaptive immunity to infectious nucleic acids and are widely employed as genome editing tools. These tools use RNA-guided Cas proteins whose large size (950 1400 amino acids) has been considered essential their specific DNA- or RNA-targeting activities. Here we present a set of from uncultivated archaea that contain Cas14, family exceptionally compact nucleases (400 700 acids). Despite small size, Cas14 capable targeted single-stranded DNA (ssDNA)...
The bacterial and archaeal genomes that have been sequenced to date were chosen for sequencing based mainly on their physiology, which is fine but has resulted in a distinct phylogenetic bias. An alternative approach taken the Genomic Encyclopedia of Bacteria Archaea (GEBA) project, advocates choosing organism's position, with aim filling gaps along branches tree life. value this demonstrated by pilot study genome sequences 56 culturable species selected maximize coverage. Analysis provides...
Comprehensive, high-quality reference genomes are required for functional characterization and taxonomic assignment of the human gut microbiota. We present Unified Human Gastrointestinal Genome (UHGG) collection, comprising 204,938 nonredundant from 4,644 prokaryotes. These encode >170 million protein sequences, which we collated in Protein (UHGP) catalog. The UHGP more than doubles number proteins comparison to those Integrated Gene Catalog. More 70% UHGG species lack cultured...
Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel type of direct repeat found in wide range bacteria and archaea. CRISPRs beginning to attract attention because their proposed mechanism; that is, defending hosts against invading extrachromosomal elements such as viruses. Existing detection tools do poor job identifying due the presence unique spacer sequences separating repeats. In this study, new tool, CRT, is introduced rapidly accurately identifies large DNA...
A rapidly increasing number of microbial genomes are sequenced by organizations worldwide and eventually included into various public genome data resources. The quality the annotations depends largely on original dataset providers, with erroneous or incomplete often carried over resources difficult to correct.We have developed an Expert Review (ER) version Integrated Microbial Genomes (IMG) system, goal supporting systematic efficient revision annotations. IMG ER provides tools for review...
Bacillus cereus is an opportunistic pathogen causing food poisoning manifested by diarrhoeal or emetic syndromes1. It closely related to the animal and human anthracis insect thuringiensis, former being used as a biological weapon latter pesticide. B. thuringiensis are readily distinguished from presence of plasmid-borne specific toxins (B. thuringiensis) capsule anthracis). But phylogenetic studies based on analysis chromosomal genes bring controversial results, it unclear whether cereus,...
The Critical Assessment of Metagenome Interpretation (CAMI) community initiative presents results from its first challenge, a rigorous benchmarking software for metagenome assembly, binning and taxonomic profiling. Methods profiling are key to interpreting data, but lack consensus about complicates performance assessment. challenge has engaged the global developer benchmark their programs on highly complex realistic data sets, generated ∼700 newly sequenced microorganisms ∼600 novel viruses...
The Integrated Microbial Genomes & Microbiomes system v.5.0 (IMG/M: https://img.jgi.doe.gov/m/) contains annotated datasets categorized into: archaea, bacteria, eukarya, plasmids, viruses, genome fragments, metagenomes, cell enrichments, single particle sorts, and metatranscriptomes. Source include those generated by the DOE's Joint Genome Institute (JGI), submitted external scientists, or collected from public sequence data archives such as NCBI. All submissions are typically processed...
A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded biosynthetic gene clusters. Information about these clusters, is currently dispersed throughout the literature, making it difficult exploit. To facilitate consistent systematic deposition retrieval data on we propose Minimum a Biosynthetic Gene cluster (MIBiG) standard.
Many marine bacteria have evolved to grow optimally at either high (copiotrophic) or low (oligotrophic) nutrient concentrations, enabling different species colonize distinct trophic habitats in the oceans. Here, we compare genome sequences of two bacteria, Photobacterium angustum S14 and Sphingopyxis alaskensis RB2256, that serve as useful model organisms for copiotrophic oligotrophic modes life specifically relate genomic features strategy these define their molecular mechanisms adaptation....