Skip to content
DraconiticResearch
Search Sources API
203,203 studies31 sourcesUpdated 10 min ago
Peer-reviewedCC BY-NC 4.0Nucleic Acids Research

BacMap 3.0: a comprehensive knowledgebase of annotated bacterial genomes

  • Ray Kruger1
  • Megane Kyes1
  • Eponine Oler1
  • Sukanta Saha1
  • Scott Han1
  • Jenna Poelzer1
  • Julia Wakoli1
  • Yamilé López-Hernández1
  • Marcia LeVatte1
  • Mark Berjanskii2
  • Scott MacKay1
  • Prashanthi Kovur1
3 more authors
  • Carolyn J Fitzsimmons3
  • James F Cahill1
  • David S Wishart1,4,5,6,7
7 affiliations
  1. 1Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9 ,
  2. 2Department of Chemistry, University of Alberta , Edmonton, Alberta, T6G 2G2 ,
  3. 3Agriculture and Agri-Food Canada, Lacombe Research Centre , Lacombe, AB, T4L 1W1 ,
  4. 4Department of Computing Science, University of Alberta , Edmonton, AB T6G 2E8 ,
  5. 5Department of Laboratory Medicine and Pathology, University of Alberta , Edmonton, AB T6G 2B7 ,
  6. 6Department of Pharmacy and Pharmaceutical Sciences, University of Alberta , Edmonton, AB T6G 2H7 ,
  7. 7Women and Children’s Health Research Institute, University of Alberta , Edmonton, AB T6G 1C9 ,
Open at sourcePDFDOICite

Abstract

BacMap 3.0 (https://bacmap.ca) is a comprehensive, freely accessible resource integrating 23 524 bacterial and archaeal species, 32 866 genomes, >100 million genes, 1756 primary metabolic pathways, and 45 284 metabolites within one interactive platform. Despite the extraordinary growth of bacterial and archaeal genome sequencing, relevant data remain distributed across numerous specialized databases, impeding comprehensive genome-to-function analysis. While existing microbial resources generally emphasize genome annotation, taxonomy, metabolic pathways, or phenotypes separately, BacMap 3.0 unifies these complementary information layers within an organism-centred framework. It resolves this fragmentation by consolidating genomic, functional, structural, metabolic, phenotypic, ecological, and phylogenetic information into richly detailed, organism-specific “BacCards”. Each BacCard combines an interactive genome map with extensive annotations covering bacterium-specific taxonomy, physiology, morphology, metabolism, protein structures, pathways, and metabolites. To facilitate data exploration, BacMap 3.0 supports taxonomic and phenotype-based browsing, chemical structure searches, interactive genome visualization, as well as gene, genome, 16S RNA, and protein BLAST searches. Building on earlier releases devoted primarily to genome visualization, BacMap 3.0 increases organismal coverage by >13-fold and transforms BacMap into an integrated bacterial knowledgebase for genome-to-function investigation across multiple biological scales. By bringing diverse biological information together in a single searchable environment, BacMap 3.0 offers a powerful platform for comparative genomics, microbiome research, infectious disease investigation, and biotechnology with a goal of accelerating the interpretation of microbial diversity, biology, and function.

Related

  1. Recovering anaerobic bacterial genomes in saliva, tumour and blood whole genome sequencing data from patients with prostate cancer.
    A Gihawi, A Bampalis, S Subramanian +46
    NPJ biofilms and microbiomesPeer-reviewedCC BYFull textMolecular biology & gene regulationEurope PMCDOAJ
  2. A comprehensive assessment of tandem repeat genotyping methods for Nanopore long-read genomes
    Elbay Aliyev, Akshay Avvaru, Wouter De Coster +64
    Genome BiologyPeer-reviewedCC BY-NC-ND 4.0Full text2 citedMolecular biology & gene regulationPMC
  3. SERS-CBP: A Comprehensive SERS Spectral Database of Clinically Important Bacterial Pathogens.
    Liang Wang, Xu-Xia Cui, Jia-Wei Tang +8
    ACS measurement science auPeer-reviewedCC BY-NC-NDFull textBiophysicsEurope PMC
  4. Eight quick tips for using the reactome knowledgebase
    Nancy T. Li, Marija Milacic, Karen Rothfels +1
    PLOS Computational BiologyPeer-reviewedCC BY 4.0Full textEnzymology & metabolismMolecular biology & gene regulationPLOSPMC
  5. LncRNAfunc 2.0: an evidence-integrated knowledgebase for regulatory and functional interpretation of lncRNAs in cancer
    Mengyuan Yang, Jiawei Li, Xingzheng Lu +5
    Nucleic Acids ResearchPeer-reviewedCC BY-NC 4.0Full textMolecular biology & gene regulationCrossref

Cite

BibTeXRIS
BibTeX
@article{kruger2026bacmap,
  title = {{BacMap 3.0: a comprehensive knowledgebase of annotated bacterial genomes}},
  author = {Ray Kruger and Megane Kyes and Eponine Oler and Sukanta Saha and Scott Han and Jenna Poelzer and Julia Wakoli and Yamilé López-Hernández and Marcia LeVatte and Mark Berjanskii and Scott MacKay and Prashanthi Kovur and Carolyn J Fitzsimmons and James F Cahill and David S Wishart},
  journal = {Nucleic Acids Research},
  year = {2026},
  month = oct,
  doi = {10.1093/nar/gkag1049},
  url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1049/9004252},
  note = {CC BY-NC 4.0},
}
RIS
TY  - JOUR
TI  - BacMap 3.0: a comprehensive knowledgebase of annotated bacterial genomes
AU  - Ray Kruger
AU  - Megane Kyes
AU  - Eponine Oler
AU  - Sukanta Saha
AU  - Scott Han
AU  - Jenna Poelzer
AU  - Julia Wakoli
AU  - Yamilé López-Hernández
AU  - Marcia LeVatte
AU  - Mark Berjanskii
AU  - Scott MacKay
AU  - Prashanthi Kovur
AU  - Carolyn J Fitzsimmons
AU  - James F Cahill
AU  - David S Wishart
PY  - 2026
DA  - 2026/10/29
JO  - Nucleic Acids Research
DO  - 10.1093/nar/gkag1049
UR  - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1049/9004252
AB  - BacMap 3.0 (https://bacmap.ca) is a comprehensive, freely accessible resource integrating 23 524 bacterial and archaeal species, 32 866 genomes, >100 million genes, 1756 primary metabolic pathways, and 45 284 metabolites within one interactive platform. Despite the extraordinary growth of bacterial and archaeal genome sequencing, relevant data remain distributed across numerous specialized databases, impeding comprehensive genome-to-function analysis. While existing microbial resources generally emphasize genome annotation, taxonomy, metabolic pathways, or phenotypes separately, BacMap 3.0 unifies these complementary information layers within an organism-centred framework. It resolves this fragmentation by consolidating genomic, functional, structural, metabolic, phenotypic, ecological, and phylogenetic information into richly detailed, organism-specific “BacCards”. Each BacCard combines an interactive genome map with extensive annotations covering bacterium-specific taxonomy, physiology, morphology, metabolism, protein structures, pathways, and metabolites. To facilitate data exploration, BacMap 3.0 supports taxonomic and phenotype-based browsing, chemical structure searches, interactive genome visualization, as well as gene, genome, 16S RNA, and protein BLAST searches. Building on earlier releases devoted primarily to genome visualization, BacMap 3.0 increases organismal coverage by >13-fold and transforms BacMap into an integrated bacterial knowledgebase for genome-to-function investigation across multiple biological scales. By bringing diverse biological information together in a single searchable environment, BacMap 3.0 offers a powerful platform for comparative genomics, microbiome research, infectious disease investigation, and biotechnology with a goal of accelerating the interpretation of microbial diversity, biology, and function.
SN  - 0305-1048
SN  - 1362-4962
ER  -