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MBGD specifications


Unique identifier OMICS_05348
Alternative name Microbial Genome Database
Restrictions to use None
Database management system Other
Community driven Yes
Data access File download, Browse
User data submission Not allowed
Maintained Yes


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Plants and Fungi
    • Arabidopsis thaliana
  • Primates
    • Homo sapiens


  • MyMBGD


  • person_outline Ikuo Uchiyama

Publications for Microbial Genome Database

MBGD citations


Automatic identification of optimal marker genes for phenotypic and taxonomic groups of microorganisms

PLoS One
PMCID: 5931505
PMID: 29718935
DOI: 10.1371/journal.pone.0195537

[…] Biological Data. Genome and protein data were obtained as outlined in [] from the 2016 version of the orthologous protein cluster table created and maintained by the microbial genome database (MBGD) [] and freely available at http://mbgd.genome.ad.jp/htbin/view_arch.cgi. This table is updated yearly and is arranged so that each row is an orthologous cluster (i.e. […]


Genomics Based Identification of Microorganisms in Human Ocular Body Fluid

Sci Rep
PMCID: 5841358
PMID: 29515160
DOI: 10.1038/s41598-018-22416-4
call_split See protocol

[…] ii) reads that aligned to human sequences in the non-redundant nucleotide collection (nt) database from NCBI. (3) Detection of ambiguous sequences in public reference genomes and creation of curated microbial genome database that was composed of 5751 different genomes: archaea (251), bacteria (5166), fungi (225), protozoa (73), viruses (35) and the human reference GRCh38.p7 (Supplementary Table ) […]


Exploring Viral Diversity in a Unique South African Soil Habitat

Sci Rep
PMCID: 5758573
PMID: 29311639
DOI: 10.1038/s41598-017-18461-0

[…] taviromes may be due to the presence of unknown prophages in bacterial genomes, phages carrying host genes, relatively large size of bacterial genomes compared to viral genomes and larger size of the microbial genome database which is statistically increasing the chance of matching bacterial sequences. The MG-RAST pipeline was used to analyse the reads, not the contigs and shows, therefore a highe […]


Genetic adaptation of microbial populations present in high intensity catfish production systems with therapeutic oxytetracycline treatment

Sci Rep
PMCID: 5727513
PMID: 29235508
DOI: 10.1038/s41598-017-17640-3

[…] eness or over 20% contamination were excluded from phylogenetic analysis.Gene prediction and annotation of metagenomic reconstructions were performed using the DOE Joint Genome Institute’s Integrated Microbial Genome database tool (version 4.15.1). Briefly, open read frames were predicted by Prodigal (version 2.6.3) and Prokaryotic GeneMark.hmm (version 2.8). Conserved protein families and domains […]


Comparative metagenomics of hydrocarbon and methane seeps of the Gulf of Mexico

Sci Rep
PMCID: 5700182
PMID: 29167487
DOI: 10.1038/s41598-017-16375-5

[…] ectivity since the ANME-1 16S rRNA gene sequences recovered from metagenomes had 3 mismatches with the primers used in amplicon-based analyses. Consequently, the relative proportion of members of the MBGD as well as Thermoplasmatales, detected as predominant archaeal members of the archaeal community by 16S rRNA gene amplicon analysis (Fig. ), represented less than 5 and 10% of reads recovered fro […]


Genomic Comparison of Two Family Level Groups of the Uncultivated NAG1 Archaeal Lineage from Chemically and Geographically Disparate Hot Springs

Front Microbiol
PMCID: 5671600
PMID: 29163388
DOI: 10.3389/fmicb.2017.02082

[…] /crispr.i2bc.paris-saclay.fr/Server/ (). Individual SAG data are located at http://microbialdarkmatter.org (Supplementary Table ). The NAG1 metagenome assembled genome was deposited in the Integrated Microbial Genome database (IMG genome ID 2751185538). […]


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MBGD institution(s)
Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan; Data Integration and Analysis Facility, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan; Dynacom Co., Ltd., Kobe, Japan; Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan
MBGD funding source(s)
Supported by National Bioscience Database Center, Japan Science Technology Agency; JSPS KAKENHI [17H03610].

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