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MBGD: Microbial Genome Database for Comparative Analysis Featuring Enhanced Functionality to Characterize Gene and
Ikuo Uchiyama1, Motohiro Mihara2, Hiroyo Nishide1
1National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan.
Journal of Molecular Biology
|January 18, 2025
Summary
The Microbial Genome Database for Comparative Analysis (MBGD) provides ortholog data for microbial genomes. It enhances comparative genomics with new MyMBGD features for analyzing newly sequenced genomes and their functions.
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- The Microbial Genome Database for Comparative Analysis (MBGD) is a key resource for ortholog data from published microbial genomes.
- Ortholog tables in MBGD are structured hierarchically, currently encompassing 1,812 genus-level pan-genomes, 6,268 species-level pan-genomes, and a total of 34,079 genomes.
Purpose of the Study:
- To enhance comparative genomic analyses of microbial genomes.
- To provide updated tools for analyzing newly sequenced microbial genomes.
- To improve the utility of MBGD for functional and phylogenetic profiling.
Main Methods:
- MBGD utilizes hierarchical ortholog tables and offers two MyMBGD analysis modes: assignment mode for classifying genes into existing ortholog groups and clustering mode for de novo clustering using DomClust.
- Genomaple software is used in assignment mode to evaluate genomic functions against KEGG Modules and compare results across genomes.
- A method was developed to subdivide MBGD ortholog groups for improved cross-referencing with KEGG Orthology groups.
- A phylogenetic profile search interface allows users to find ortholog groups based on the presence or absence of orthologs in specified organisms, searchable by phenotype, environment, taxonomy, or ortholog group.
Main Results:
- MBGD now contains extensive ortholog data from over 34,000 microbial genomes, organized hierarchically.
- MyMBGD functionality has been updated with assignment and clustering modes to support the analysis of new genomes.
- Enhanced cross-referencing with KEGG Orthology and a versatile phylogenetic profile search interface improve analytical capabilities.
Conclusions:
- MBGD is a valuable and updated resource for comparative microbial genomics.
- The enhanced MyMBGD features facilitate the analysis of newly sequenced genomes and their functional roles.
- The database supports sophisticated analyses, including functional profiling and phylogenetic comparisons, aiding microbial research.
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