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redbiom: a Rapid Sample Discovery and Feature Characterization System

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dc.contributor.authorMcDonald, Daniel
dc.contributor.authorKaehler, Benjamin
dc.contributor.authorGonzalez, Antonio
dc.contributor.authorDeReus, Jeff
dc.contributor.authorAckermann, Gail
dc.contributor.authorMarotz, Clarisse
dc.contributor.authorHuttley, Gavin
dc.contributor.authorKnight, Rob
dc.date.accessioned2020-03-19T22:43:57Z
dc.date.available2020-03-19T22:43:57Z
dc.date.issued2019-06-25
dc.date.updated2019-11-25T07:43:28Z
dc.description.abstractMeta-analyses at the whole-community level have been important in microbiome studies, revealing profound features that structure Earth’s microbial communities, such as the unique differentiation of microbes from the mammalian gut relative to free-living microbial communities, the separation of microbiomes in saline and nonsaline environments, and the role of pH in driving soil microbial compositions. However, our ability to identify the specific features of a microbiome that differentiate these community-level patterns have lagged behind, especially as ever-cheaper DNA sequencing has yielded increasingly large data sets. One critical gap is the ability to search for samples that contain specific features (for example, sub-operational taxonomic units [sOTUs] identified by high-resolution statistical methods for removing amplicon sequencing errors). Here we introduce redbiom, a microbiome caching layer, which allows users to rapidly query samples that contain a given feature, retrieve sample data and metadata, and search for samples that match specified metadata values or ranges (e.g., all samples with a pH of >7), implemented using an in-memory NoSQL database called Redis. By default, redbiom allows public anonymous sample access for over 100,000 publicly available samples in the Qiita database. At over 100,000 samples, the caching server requires only 35 GB of resident memory. We highlight how redbiom enables a new type of characterization of microbiome samples and provide tutorials for using redbiom with QIIME 2. redbiom is open source under the BSD license, hosted on GitHub, and can be deployed independently of Qiita to enable search of proprietary or clinically restricted microbiome databases.en_AU
dc.format.mimetypeapplication/pdfen_AU
dc.identifier.citationMcDonald D, Kaehler B, Gonzalez A, DeReus J, Ackermann G, Marotz C, Huttley G, Knight R. 2019. redbiom: a rapid sample discovery and feature characterization system. mSystems 4:e00215-19. https://doi.org/10 .1128/mSystems.00215-19.en_AU
dc.identifier.issn2379-5077en_AU
dc.identifier.urihttp://hdl.handle.net/1885/202390
dc.language.isoen_AUen_AU
dc.provenanceThis is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International licenseen_AU
dc.publisherAmerican Society for Microbiologyen_AU
dc.rights© 2019 McDonald et al.en_AU
dc.rights.licenseCreative Commons Attribution 4.0 International licenseen_AU
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en_AU
dc.sourcemSystemsen_AU
dc.subjectdatabaseen_AU
dc.subjectmeta-analysisen_AU
dc.subjectmicrobiomeen_AU
dc.titleredbiom: a Rapid Sample Discovery and Feature Characterization Systemen_AU
dc.typeJournal articleen_AU
dcterms.accessRightsOpen Accessen_AU
dcterms.dateAccepted2019-06-07
local.bibliographicCitation.issue4en_AU
local.bibliographicCitation.lastpage5en_AU
local.bibliographicCitation.startpage1en_AU
local.contributor.affiliationMcDonald, Daniel, University of California San Diegoen_AU
local.contributor.affiliationKaehler, Benjamin, University of New South Walesen_AU
local.contributor.affiliationGonzalez, Antonio, University of California San Diegoen_AU
local.contributor.affiliationDeReus, Jeff, University of California San Diegoen_AU
local.contributor.affiliationAckermann, Gail, University of California San Diegoen_AU
local.contributor.affiliationMarotz, Clarisse, University of California San Diegoen_AU
local.contributor.affiliationHuttley, Gavin Austin, College of Science, ANUen_AU
local.contributor.affiliationKnight, Rob, University of California, San Diego Campusen_AU
local.contributor.authoremailu9800703@anu.edu.auen_AU
local.contributor.authoruidHuttley, Gavin Austin, u9800703en_AU
local.description.notesImported from ARIESen_AU
local.identifier.absfor080301 - Bioinformatics Softwareen_AU
local.identifier.absfor010401 - Applied Statisticsen_AU
local.identifier.absfor110899 - Medical Microbiology not elsewhere classifieden_AU
local.identifier.absseo920109 - Infectious Diseasesen_AU
local.identifier.absseo890201 - Application Software Packages (excl. Computer Games)en_AU
local.identifier.absseo890202 - Application Tools and System Utilitiesen_AU
local.identifier.ariespublicationu3102795xPUB4741en_AU
local.identifier.citationvolume4en_AU
local.identifier.doi10.1128/mSystems.00215-19en_AU
local.identifier.thomsonIDWOS:000482629400027
local.identifier.uidSubmittedByu3102795en_AU
local.publisher.urlhttps://msystems.asm.org/en_AU
local.type.statusPublished Versionen_AU

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