title: HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes.
abstract: The Human Pan-Microbe Communities (HPMC) database (http://www.hpmcd.org/) provides a manually curated, searchable, metagenomic resource to facilitate investigation of human gastrointestinal microbiota. Over the past decade, the application of metagenome sequencing to elucidate the microbial composition and functional capacity present in the human microbiome has revolutionized many concepts in our basic biology. When sufficient high quality reference genomes are available, whole genome metagenomic sequencing can provide direct biological insights and high-resolution classification. The HPMC database provides species level, standardized phylogenetic classification of over 1800 human gastrointestinal metagenomic samples. This is achieved by combining a manually curated list of bacterial genomes from human faecal samples with over 21000 additional reference genomes representing bacteria, viruses, archaea and fungi with manually curated species classification and enhanced sample metadata annotation. A user-friendly, web-based interface provides the ability to search for (i) microbial groups associated with health or disease state, (ii) health or disease states and community structure associated with a microbial group, (iii) the enrichment of a microbial gene or sequence and (iv) enrichment of a functional annotation. The HPMC database enables detailed analysis of human microbial communities and supports research from basic microbiology and immunology to therapeutic development in human health and disease.
authors.affiliation: Host Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton 3168, Australia Department of Molecular and Translational Sciences, Monash University, Clayton 3800, Australia sf15@sanger.ac.uk.
authors.forename: Samuel C
authors.identifier: http://orcid.org/0000-0003-4144-2537
authors.initials: SC
authors.lastname: Forster
authors.affiliation: Host Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
authors.forename: Hilary P
authors.initials: HP
authors.lastname: Browne
authors.affiliation: Host Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
authors.forename: Nitin
authors.initials: N
authors.lastname: Kumar
authors.affiliation: Pathogen Informatics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
authors.forename: Martin
authors.initials: M
authors.lastname: Hunt
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK.
authors.forename: Hubert
authors.initials: H
authors.lastname: Denise
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK.
authors.forename: Alex
authors.initials: A
authors.lastname: Mitchell
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK.
authors.forename: Robert D
authors.initials: RD
authors.lastname: Finn
authors.affiliation: Host Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK tl2@sanger.ac.uk.
authors.forename: Trevor D
authors.initials: TD
authors.lastname: Lawley
mesh_terms: D030561:Databases, Nucleic Acid; D004194:Disease; D041981:Gastrointestinal Tract / Q000382:microbiology / Q000821:virology; D064351:Genes, Microbial; D064349:Genome, Microbial; D006801:Humans; D020407:Internet; D056186:Metagenomics / Q000592:standards; D064307:Microbiota; D058977:Molecular Sequence Annotation; D012015:Reference Standards; D017422:Sequence Analysis, DNA