MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice

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• dc.contributor.author Manghi, Paolo
• dc.contributor.author Vallès Colomer, Mireia
• dc.contributor.author Segata, Nicola
• dc.date.accessioned 2025-04-29T09:44:21Z
• dc.date.available 2025-04-29T09:44:21Z
• dc.date.issued 2023
• dc.description.abstract Mouse models are key tools for investigating host-microbiome interactions. However, shotgun metagenomics can only profile a limited fraction of the mouse gut microbiome. Here, we employ a metagenomic profiling method, MetaPhlAn 4, which exploits a large catalog of metagenome-assembled genomes (including 22,718 metagenome-assembled genomes from mice) to improve the profiling of the mouse gut microbiome. We combine 622 samples from eight public datasets and an additional cohort of 97 mouse microbiomes, and we assess the potential of MetaPhlAn 4 to better identify diet-related changes in the host microbiome using a meta-analysis approach. We find multiple, strong, and reproducible diet-related microbial biomarkers, largely increasing those identifiable by other available methods relying only on reference information. The strongest drivers of the diet-induced changes are uncharacterized and previously undetected taxa, confirming the importance of adopting metagenomic methods integrating metagenomic assemblies for comprehensive profiling.en
• dc.description.sponsorship The work was supported by the European Research Council (ERC-STG project MetaPG-716575 and ERC-CoG microTOUCH-101045015) to N.S. and ERC-CoG (project grant agreement no. 101001355) to O.K., by the European H2020 program (ONCOBIOME-825410 project and MASTER-818368 project) to N.S., by the National Cancer Institute of the National Institutes of Health (1U01CA230551) to N.S., by the Premio Internazionale Lombardia e Ricerca 2019 to N.S., by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (ERC-2016-StG-71577) to H.S., by VolkswagenStiftung’s initiative “Niedersächsisches Vorab” (grant no. 76251-99) to T.S, and by the European Research Council (CoG 865466) to T.S.en
• dc.format.mimetype application/pdf
• dc.identifier.citation Manghi P, Blanco-Míguez A, Manara S, NabiNejad A, Cumbo F, Beghini F, et al. MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice. Cell Rep. 2023 May;42(5):112464. DOI: 10.1016/j.celrep.2023.112464
• dc.identifier.doi http://dx.doi.org/10.1016/j.celrep.2023.112464
• dc.identifier.issn 2211-1247
• dc.identifier.uri http://hdl.handle.net/10230/70234
• dc.language.iso eng
• dc.publisher Elsevier
• dc.relation.ispartof Cell Reports. 2023 May;42(5):112464
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/825410
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/818368
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/825410
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/716575
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/101045015
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/101001355
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/865466
• dc.rights © 2023 The Authors. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Mouse microbiomeen
• dc.subject.keyword Metagenomicsen
• dc.subject.keyword Dieten
• dc.subject.keyword Uncharacterized microbial speciesen
• dc.subject.keyword MetaPhlAnen
• dc.title MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in miceen
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion