title: MetaRef: a pan-genomic database for comparative and community microbial genomics.
abstract: Microbial genome sequencing is one of the longest-standing areas of biological database development, but high-throughput, low-cost technologies have increased its throughput to an unprecedented number of new genomes per year. Several thousand microbial genomes are now available, necessitating new approaches to organizing information on gene function, phylogeny and microbial taxonomy to facilitate downstream biological interpretation. MetaRef, available at http://metaref.org, is a novel online resource systematically cataloguing a comprehensive pan-genome of all microbial clades with sequenced isolates. It organizes currently available draft and finished bacterial and archaeal genomes into quality-controlled clades, reports all core and pan gene families at multiple levels in the resulting taxonomy, and it annotates families' conservation, phylogeny and consensus functional information. MetaRef also provides a comprehensive non-redundant reference gene catalogue for metagenomic studies, including the abundance and prevalence of all gene families in the >700 shotgun metagenomic samples of the Human Microbiome Project. This constitutes a systematic mapping of clade-specific microbial functions within the healthy human microbiome across multiple body sites and can be used as reference for identifying potential functional biomarkers in disease-associate microbiomes. MetaRef provides all information both as an online browsable resource and as downloadable sequences and tabular data files that can be used for subsequent offline studies.
authors.affiliation: Genome 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.
authors.forename: Katherine
authors.initials: K
authors.lastname: Huang
authors.forename: Arthur
authors.initials: A
authors.lastname: Brady
authors.forename: Anup
authors.initials: A
authors.lastname: Mahurkar
authors.forename: Owen
authors.initials: O
authors.lastname: White
authors.forename: Dirk
authors.initials: D
authors.lastname: Gevers
authors.forename: Curtis
authors.initials: C
authors.lastname: Huttenhower
authors.forename: Nicola
authors.initials: N
authors.lastname: Segata
mesh_terms: D001105:Archaea / Q000145:classification; D001419:Bacteria / Q000145:classification; D030541:Databases, Genetic; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D023281:Genomics; D020407:Internet; D056186:Metagenomics; D064307:Microbiota; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D010802:Phylogeny