skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Databases for Microbiologists

Journal Article · · Journal of Bacteriology
DOI:https://doi.org/10.1128/JB.00330-15· OSTI ID:1327628
ORCiD logo [1]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Computer Science and Mathematics Division; Univ. of Tennessee, Knoxville, TN (United States). Department of Microbiology

Databases play an increasingly important role in biology. They archive, store, maintain, and share information on genes, genomes, expression data, protein sequences and structures, metabolites and reactions, interactions, and pathways. All these data are critically important to microbiologists. Furthermore, microbiology has its own databases that deal with model microorganisms, microbial diversity, physiology, and pathogenesis. Thousands of biological databases are currently available, and it becomes increasingly difficult to keep up with their development. Finally, the purpose of this minireview is to provide a brief survey of current databases that are of interest to microbiologists.

Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); National Institues of Health
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC05-00OR22725
OSTI ID:
1327628
Journal Information:
Journal of Bacteriology, Vol. 197, Issue 15; ISSN 0021-9193
Publisher:
American Society for MicrobiologyCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 17 works
Citation information provided by
Web of Science

References (152)

rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development journal November 2014
IMG/M 4 version of the integrated metagenome comparative analysis system journal October 2013
Submission of Microarray Data to Public Repositories journal August 2004
GenoBase: comprehensive resource database of Escherichia coli K-12 journal November 2014
PlasmoDB: a functional genomic database for malaria parasites journal January 2009
Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction journal June 2012
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy journal November 2011
The sequence read archive: explosive growth of sequencing data journal October 2011
TB database: an integrated platform for tuberculosis research journal January 2009
LPSN—list of prokaryotic names with standing in nomenclature journal November 2013
MetaRef: a pan-genomic database for comparative and community microbial genomics journal November 2013
Data, information, knowledge and principle: back to metabolism in KEGG journal November 2013
Network portal: a database for storage, analysis and visualization of biological networks journal November 2013
Global catalogue of microorganisms (gcm): a comprehensive database and information retrieval, analysis, and visualization system for microbial resources journal January 2013
The BioGRID interaction database: 2015 update journal November 2014
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs journal September 1997
TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels journal January 2007
BIGSdb: Scalable analysis of bacterial genome variation at the population level journal December 2010
MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data journal November 2014
HoPaCI-DB: host- Pseudomonas and Coxiella interaction database journal October 2013
SITVITWEB – A publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology journal June 2012
SporeWeb: an interactive journey through the complete sporulation cycle of Bacillus subtilis journal October 2013
Subti Wiki–a database for the model organism Bacillus subtilis that links pathway, interaction and expression information journal October 2013
CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria journal November 2013
Ribosomal Database Project: data and tools for high throughput rRNA analysis journal November 2013
SCOP2 prototype: a new approach to protein structure mining journal November 2013
P2CS: updates of the prokaryotic two-component systems database journal October 2014
PSORTdb--an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea journal November 2010
DEOP: a database on osmoprotectants and associated pathways journal January 2014
yStreX: yeast stress expression database journal January 2014
RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more journal November 2012
VIRmiRNA: a comprehensive resource for experimentally validated viral miRNAs and their targets journal January 2014
metaMicrobesOnline: phylogenomic analysis of microbial communities journal November 2012
Prokka: rapid prokaryotic genome annotation journal March 2014
FungiDB: an integrated functional genomics database for fungi journal November 2011
The TIGRFAMs database of protein families journal January 2003
The NCBI Taxonomy database journal December 2011
ProGlycProt: a repository of experimentally characterized prokaryotic glycoproteins journal October 2011
TriTrypDB: a functional genomic resource for the Trypanosomatidae journal October 2009
CryptoDB: a Cryptosporidium bioinformatics resource update journal January 2006
MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets journal November 2009
ToxoDB: an integrated Toxoplasma gondii database resource journal December 2007
BacDive—the Bacterial Diversity Metadatabase journal November 2013
The carbohydrate-active enzymes database (CAZy) in 2013 journal November 2013
CyanoLyase: a database of phycobilin lyase sequences, motifs and functions journal November 2012
STRING v9.1: protein-protein interaction networks, with increased coverage and integration journal November 2012
MetaProx: the database of metagenomic proximons journal January 2014
DBSecSys: a database of Burkholderia mallei secretion systems journal January 2014
StreptomeDB: a resource for natural compounds isolated from Streptomyces species journal November 2012
SAMMD: Staphylococcus aureus Microarray Meta-Database journal January 2007
Bacterial Carbohydrate Structure Database 3: Principles and Realization journal December 2010
Proteome-wide Subcellular Topologies of E. coli Polypeptides Database (STEPdb) journal September 2014
Quorumpeps database: chemical space, microbial origin and functionality of quorum sensing peptides journal November 2012
COMBREX: a project to accelerate the functional annotation of prokaryotic genomes journal November 2010
AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics journal January 2014
DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information journal October 2007
RegTransBase – a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes journal January 2013
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) journal November 2013
ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes journal January 2009
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases journal November 2013
Pfam: the protein families database journal November 2013
BuchneraBASE: a post-genomic resource for Buchnera sp. APS journal January 2006
Every Site Counts: Submitting Transcription Factor-Binding Site Information through the CollecTF Portal journal May 2015
HBVdb: a knowledge database for Hepatitis B Virus journal November 2012
SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates journal November 2012
EcoCyc: fusing model organism databases with systems biology journal November 2012
MICdb3.0: a comprehensive resource of microsatellite repeats from prokaryotic genomes journal January 2014
The InterPro protein families database: the classification resource after 15 years journal November 2014
Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology journal January 2014
MicrobesOnline: an integrated portal for comparative and functional genomics journal November 2009
VetBact – culturing bacteriological knowledge for veterinarians journal February 2014
The 2015 Nucleic Acids Research Database Issue and Molecular Biology Database Collection journal January 2015
The comprehensive microbial resource journal November 2009
GeneDB--an annotation database for pathogens journal November 2011
The Papillomavirus Episteme: a central resource for papillomavirus sequence data and analysis journal October 2012
NCBI GEO: archive for functional genomics data sets—update journal November 2012
MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data journal November 2012
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea journal December 2011
GenBank journal November 2012
SecReT6: a web-based resource for type VI secretion systems found in bacteria: Genomics update journal July 2015
PhylOPDb: a 16S rRNA oligonucleotide probe database for prokaryotic identification journal January 2014
EcoGene 3.0 journal November 2012
SecReT4: a web-based bacterial type IV secretion system resource journal November 2012
VibrioBase: A Model for Next-Generation Genome and Annotation Database Development journal January 2014
Sequencing technologies — the next generation journal December 2009
The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks journal November 2013
The European Bioinformatics Institute’s data resources 2014 journal November 2013
WebGeSTer DB—a transcription terminator database journal November 2010
PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools journal November 2013
IMG 4 version of the integrated microbial genomes comparative analysis system journal October 2013
ClusterMine360: a database of microbial PKS/NRPS biosynthesis journal October 2012
EBI metagenomics—a new resource for the analysis and archiving of metagenomic data journal October 2013
ECMDB: The E. coli Metabolome Database journal October 2012
DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes journal October 2012
OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis journal November 2012
RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria journal January 2013
Bacteriome.org an integrated protein interaction database for E. coli journal December 2007
xBASE2: a comprehensive resource for comparative bacterial genomics journal December 2007
CDD: NCBI's conserved domain database journal November 2014
OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software journal November 2014
ABCdb: an online resource for ABC transporter repertories from sequenced archaeal and bacterial genomes: ABCdb: transporter repertoires journal March 2006
Expanded microbial genome coverage and improved protein family annotation in the COG database journal November 2014
HelicoBase: a Helicobacter genomic resource and analysis platform journal January 2014
Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes journal October 2010
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes journal September 2005
GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis journal January 2009
OMPdb: a database of  -barrel outer membrane proteins from Gram-negative bacteria journal October 2010
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification journal October 2014
Genome annotation: from sequence to biology journal July 2001
EcoProDB: the Escherichia coli protein database journal July 2007
PATRIC, the bacterial bioinformatics database and analysis resource journal November 2013
BacMet: antibacterial biocide and metal resistance genes database journal December 2013
tbvar: a comprehensive genome variation resource for Mycobacterium tuberculosis journal January 2014
The Transporter Classification Database journal November 2013
mVOC: a database of microbial volatiles journal December 2013
POGO-DB—a database of pairwise-comparisons of genomes and conserved orthologous genes journal November 2013
AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species journal October 2010
The future of biocuration journal September 2008
WholeCellKB: model organism databases for comprehensive whole-cell models journal November 2012
ProOpDB: Prokaryotic Operon DataBase journal November 2011
ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria journal October 2011
ASAP: a resource for annotating, curating, comparing, and disseminating genomic data journal January 2006
BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species text January 2014
BacMap: an interactive picture atlas of annotated bacterial genomes journal December 2004
EuPathDB: a portal to eukaryotic pathogen databases journal November 2009
ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage journal November 2011
The COG database: an updated version includes eukaryotes journal January 2003
The MiST2 database: a comprehensive genomics resource on microbial signal transduction journal November 2009
VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA journal December 2011
Virus Variation Resource—recent updates and future directions journal December 2013
CyanoBase and RhizoBase: databases of manually curated annotations for cyanobacterial and rhizobial genomes journal November 2013
Saccharomyces Genome Database: the genomics resource of budding yeast journal November 2011
FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus journal September 2014
T3DB: an integrated database for bacterial type III secretion system journal January 2012
CATH: comprehensive structural and functional annotations for genome sequences journal October 2014
SMART: recent updates, new developments and status in 2015 journal October 2014
ViralZone: recent updates to the virus knowledge resource journal November 2012
AtlasT4SS: A curated database for type IV secretion systems journal January 2012
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education journal November 2014
CoryneBase: Corynebacterium Genomic Resources and Analysis Tools at Your Fingertips journal January 2014
Phagocytosis-like cell engulfment by a planctomycete bacterium journal December 2019
Carbohydrate-controlled serine protease inhibitor (serpin) production in Bifidobacterium longum subsp. longum journal March 2021
Environmental dissemination of pathogenic Listeria monocytogenes in flowing surface waters in Switzerland journal April 2021
Database resources of the National Center for Biotechnology Information journal January 2006
Draft Genome Sequence of Comamonas aquatilis Strain LK (= CSUR P6418 = CECT 9772), Isolated from the Planarian Schmidtea mediterranea journal February 2021
BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species journal June 2014
GeneDB--an annotation database for pathogens. text January 2012
Database resources of the National Center for Biotechnology Information journal October 2020
BacMap: An interactive picture atlas of annotated bacterial genomes
  • M. J., Stothard, P. ; Van Domselaar, G. ; Cruz, J. ; Wishart, D. S. ; Shrivistava, S. ; Guo, A. C. ; O'Neill, B. ; Ellison,
  • University of Alberta Libraries https://doi.org/10.7939/r3sz8p
text January 2005
STRING v9.1: protein-protein interaction networks, with increased coverage and integration text January 2013
Database resources of the National Center for Biotechnology Information journal November 2018
SwissRegulon : a database of genome-wide annotations of regulatory sites: recent updates text January 2012

Cited By (3)

The Microbe Directory v2.0: An Expanded Database of Ecological and Phenotypical Features of Microbes posted_content December 2019
Dependency of DNA extraction efficiency on cell concentration confounds molecular quantification of microorganisms in groundwater journal August 2018
Computational profiling of the gut–brain axis: microflora dysbiosis insights to neurological disorders journal November 2017

Similar Records

Colloquium and Report on Systems Microbiology: Beyond Microbial Genomics
Conference · Mon Dec 13 00:00:00 EST 2004 · OSTI ID:1327628

Uncharted Microbial World: Microbes and Their Activities in the Environment
Conference · Mon Dec 31 00:00:00 EST 2007 · OSTI ID:1327628

Microbial Forensics: A Scientific Assessment
Conference · Mon Feb 17 00:00:00 EST 2003 · OSTI ID:1327628