Improved gut microbiome recovery following drug therapy is linked to abundance and replication of probiotic strains

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dc.contributor.authorFitzGerald, Jamie A.
dc.contributor.authorPatel, Shriram
dc.contributor.authorEckenberger, Julia
dc.contributor.authorGuillemard, Eric
dc.contributor.authorVeiga, Patrick
dc.contributor.authorSchäfer, Florent
dc.contributor.authorWalter, Jens
dc.contributor.authorClaesson, Marcus J.
dc.contributor.authorDerrien, Muriel
dc.contributor.funderDanone Nutricia Researchen
dc.contributor.funderScience Foundation Irelanden
dc.contributor.funderHorizon 2020en
dc.date.accessioned2022-11-07T12:19:08Z
dc.date.available2022-11-07T12:19:08Z
dc.date.issued2022
dc.date.updated2022-11-07T12:00:48Z
dc.description.abstractProbiotics have been used for decades to alleviate the negative side-effects of oral antibiotics, but our mechanistic understanding on how they work is so far incomplete. Here, we performed a metagenomic analysis of the fecal microbiota in participants who underwent a 14-d Helicobacter pylori eradication therapy with or without consumption of a multi-strain probiotic intervention (L. paracasei CNCM I-1518, L. paracasei CNCM I-3689, L. rhamnosus CNCM I-3690, and four yogurt strains) in a randomized, double-blinded, controlled clinical trial. Using a strain-level analysis for detection and metagenomic determination of replication rate, ingested strains were detected and replicated transiently in fecal samples and in the gut during and following antibiotic administration. Consumption of the fermented milk product led to a significant, although modest, improvement in the recovery of microbiota composition. Stratification of participants into two groups based on the degree to which their microbiome recovered showed i) a higher fecal abundance of the probiotic L. paracasei and L. rhamnosus strains and ii) an elevated replication rate of one strain (L. paracasei CNCMI-1518) in the recovery group. Collectively, our findings show a small but measurable benefit of a fermented milk product on microbiome recovery after antibiotics, which was linked to the detection and replication of specific probiotic strains. Such functional insight can form the basis for the development of probiotic-based intervention aimed to protect gut microbiome from drug treatments.en
dc.description.sponsorshipScience Foundation Ireland (Grant number 17/CDA/4765)en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationFitzGerald, J. A., Patel, S., Eckenberger, J., Guillemard, E., Veiga, P., Schäfer, F., Walter, J., Claesson, M. J. and Derrien, M. (2022) 'Improved gut microbiome recovery following drug therapy is linked to abundance and replication of probiotic strains', Gut microbes, 14 (1), (20 pp). doi: 10.1080/19490976.2022.2094664en
dc.identifier.doi10.1080/19490976.2022.2094664en
dc.identifier.endpage20en
dc.identifier.issn1949-0984
dc.identifier.issued1en
dc.identifier.journaltitleGut microbesen
dc.identifier.startpage1en
dc.identifier.urihttps://hdl.handle.net/10468/13822
dc.identifier.volume14en
dc.language.isoenen
dc.publisherTaylor & Francisen
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/en
dc.relation.projectinfo:eu-repo/grantAgreement/EC/H2020::MSCA-COFUND-FP/754535/EU/APC Postdoctoral EXcellence Programme/APEXen
dc.rights© 2022 The Author(s). Published with license by Taylor & Francis Group, LLC. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectAntibioticsen
dc.subjectGut microbiome recoveryen
dc.subjectFermented milk producten
dc.subjectProbioticsen
dc.subjectReplicationen
dc.subjectL. paracaseien
dc.subjectCNCM I-1518en
dc.titleImproved gut microbiome recovery following drug therapy is linked to abundance and replication of probiotic strainsen
dc.typeArticle (peer-reviewed)en
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