Untangling species-level composition of complex bacterial communities through a novel metagenomic approach

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dc.contributor.authorMilani, Christianen
dc.contributor.authorAlessandri, Giuliaen
dc.contributor.authorMangifesta, Martaen
dc.contributor.authorMancabelli, Leonardoen
dc.contributor.authorLugli, Gabriele Andreaen
dc.contributor.authorFontana, Federicoen
dc.contributor.authorLonghi, Giuliaen
dc.contributor.authorAnzalone, Rosariaen
dc.contributor.authorViappiani, Aliceen
dc.contributor.authorDuranti, Sabrinaen
dc.contributor.authorTurroni, Francescaen
dc.contributor.authorCosti, Renatoen
dc.contributor.authorAnnicchiarico, Alfredoen
dc.contributor.authorMorini, Andreaen
dc.contributor.authorSarli, Leopoldoen
dc.contributor.authorOssiprandi, Maria Cristinaen
dc.contributor.authorvan Sinderen, Douween
dc.contributor.authorVentura, Marcoen
dc.contributor.editorJ. Gregory Caporasoen
dc.contributor.funderScience Foundation Irelanden
dc.contributor.funderFondazione Cariparmaen
dc.contributor.funderUniversità degli Studi di Parmaen
dc.date.accessioned2023-11-16T10:55:29Z
dc.date.available2023-11-16T10:55:29Z
dc.date.issued2020-01-01en
dc.description.abstract16S small-subunit (SSU) rRNA gene-based bacterial profiling is the gold standard for cost-effective taxonomic reconstruction of complex bacterial populations down to the genus level. However, it has been proven ineffective in clinical and research settings requiring higher taxonomic resolution. We therefore developed a bacterial profiling method based on the internal transcribed spacer (ITS) region employing optimized primers and a comprehensive ITS database for accurate cataloguing of bacterial communities at (sub)species resolution. Performance of the microbial ITS profiling pipeline was tested through analysis of host-associated, food, and environmental matrices, while its efficacy in clinical settings was assessed through analysis of mucosal biopsy specimens of colorectal cancer, leading to the identification of putative novel biomarkers. The data collected indicate that the proposed pipeline represents a major step forward in cost-effective identification and screening of microbial biomarkers at (sub)species level, with relevant impact in research, industrial, and clinical settings.en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.articleide00404-20en
dc.identifier.citationMilani, C., Alessandri, G., Mangifesta, M., Mancabelli, L., Lugli, G.A., Fontana, F., Longhi, G., Anzalone, R., Viappiani, A., Duranti, S., Turroni, F., Costi, R., Annicchiarico, A., Morini, A., Sarli, L., Ossiprandi, M.C., Van Sinderen, D. and Ventura, M. (2020) ‘Untangling species-level composition of complex bacterial communities through a novel metagenomic approach’, mSystems. 5(4), e00404-20 (12 pp). doi: 10.1128/mSystems.00404-20en
dc.identifier.doi10.1128/msystems.00404-20en
dc.identifier.endpage12en
dc.identifier.issn2379-5077en
dc.identifier.issued4en
dc.identifier.journaltitlemSystemsen
dc.identifier.startpage1en
dc.identifier.urihttps://hdl.handle.net/10468/15235
dc.identifier.volume5en
dc.language.isoenen
dc.publisherAmerican Society for Microbiologyen
dc.relation.ispartofmSystemsen
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/EU Joint Programming Initiative::A Healthy Diet for a Healthy Life JPI (HDHL-JPI)/15/JP-HDHL/3280/IE/Impact of early life on microbiome development and later health (EarlyMicroHealth)/en
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/en
dc.relation.projectFondazione Cariparma (TeachInParma Project)en
dc.rights© 2020 Milani et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectMetagenomicsen
dc.subjectITSen
dc.subjectProfilingen
dc.subject~Microbiology - Journal Articles~en
dc.titleUntangling species-level composition of complex bacterial communities through a novel metagenomic approachen
dc.typeArticle (peer-reviewed)en
dc.typejournal-articleen
oaire.citation.issue4en
oaire.citation.volume5en
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