MetaRef: a pan-genomic database for comparative and community microbial genomics
Katherine Huang1, Arthur Brady, Anup Mahurkar
1Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA, Institute for Genome Sciences, University of Maryland School of Medicine, 801 W Baltimore St, Baltimore, MD 21201, USA, Biostatistics Department, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA and Centre for Integrative Biology, University of Trento, via Sommarive 14, 38123 Povo (Trento), Italy.
Nucleic Acids Research
|November 9, 2013
Summary
MetaRef organizes thousands of microbial genomes, providing gene family data for taxonomy and function. This resource aids biological interpretation and metagenomic analysis of the human microbiome.
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- High-throughput sequencing has led to a surge in microbial genome data.
- Existing databases struggle to organize this vast amount of information for gene function, phylogeny, and taxonomy.
- Efficient data organization is crucial for downstream biological interpretation.
Purpose of the Study:
- To introduce MetaRef, a novel online resource for cataloguing microbial pan-genomes.
- To provide a structured approach to organizing bacterial and archaeal genomes.
- To facilitate the analysis of microbial gene function, phylogeny, and taxonomy.
Main Methods:
- Systematically cataloguing a comprehensive pan-genome of all microbial clades with sequenced isolates.
- Organizing draft and finished genomes into quality-controlled clades.
- Reporting core and pan gene families at multiple taxonomic levels, annotating conservation, phylogeny, and function.
- Creating a non-redundant reference gene catalog for metagenomic studies using Human Microbiome Project data.
Main Results:
- MetaRef offers a systematically organized pan-genome for microbial clades.
- It provides detailed annotations on gene family conservation, phylogeny, and function.
- The resource includes a comprehensive reference gene catalog derived from the Human Microbiome Project, detailing gene family abundance and prevalence across body sites.
Conclusions:
- MetaRef serves as a valuable online resource for microbial genomics and bioinformatics.
- It enables systematic mapping of clade-specific microbial functions within the human microbiome.
- The data can be used as a reference for identifying functional biomarkers in disease-associated microbiomes and for offline studies.
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