Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

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dc.contributor.authorKennedy, Katherine M.en
dc.contributor.authorde Goffau, Marcus C.en
dc.contributor.authorPerez-Muñoz, Maria Elisaen
dc.contributor.authorArrieta, Marie-Claireen
dc.contributor.authorBäckhed, Fredriken
dc.contributor.authorBork, Peeren
dc.contributor.authorBraun, Thorstenen
dc.contributor.authorBushman, Frederic D.en
dc.contributor.authorDore, Joelen
dc.contributor.authorde Vos, Willem M.en
dc.contributor.authorEarl, Ashlee M.en
dc.contributor.authorEisen, Jonathan A.en
dc.contributor.authorElovitz, Michal A.en
dc.contributor.authorGanal-Vonarburg, Stephanie C.en
dc.contributor.authorGänzle, Michael G.en
dc.contributor.authorGarrett, Wendy S.en
dc.contributor.authorHall, Lindsay J.en
dc.contributor.authorHornef, Mathias W.en
dc.contributor.authorHuttenhower, Curtisen
dc.contributor.authorKonnikova, Lizaen
dc.contributor.authorLebeer, Sarahen
dc.contributor.authorMacpherson, Andrew J.en
dc.contributor.authorMassey, Ruth C.en
dc.contributor.authorCarolyn McHardy, Aliceen
dc.contributor.authorKoren, Omryen
dc.contributor.authorLawley, Trevor D.en
dc.contributor.authorLey, Ruth E.en
dc.contributor.authorO’Mahony, Liamen
dc.contributor.authorO’Toole, Paul W.en
dc.contributor.authorPamer, Eric G.en
dc.contributor.authorParkhill, Julianen
dc.contributor.authorRaes, Jeroenen
dc.contributor.authorRattei, Thomasen
dc.contributor.authorSalonen, Anneen
dc.contributor.authorSegal, Eranen
dc.contributor.authorSegata, Nicolaen
dc.contributor.authorShanahan, Fergusen
dc.contributor.authorSloboda, Deborah M.en
dc.contributor.authorSmith, Gordon C. S.en
dc.contributor.authorSokol, Harryen
dc.contributor.authorSpector, Tim D.en
dc.contributor.authorSurette, Michael G.en
dc.contributor.authorTannock, Gerald W.en
dc.contributor.authorWalker, Alan W.en
dc.contributor.authorYassour, Moranen
dc.contributor.authorWalter, Jensen
dc.contributor.funderScience Foundation Irelanden
dc.date.accessioned2025-03-12T10:41:57Z
dc.date.available2025-03-12T10:41:57Z
dc.date.issued2023-01-25en
dc.description.abstractWhether the human fetus and the prenatal intrauterine environment (amniotic fluid and placenta) are stably colonized by microbial communities in a healthy pregnancy remains a subject of debate. Here we evaluate recent studies that characterized microbial populations in human fetuses from the perspectives of reproductive biology, microbial ecology, bioinformatics, immunology, clinical microbiology and gnotobiology, and assess possible mechanisms by which the fetus might interact with microorganisms. Our analysis indicates that the detected microbial signals are likely the result of contamination during the clinical procedures to obtain fetal samples or during DNA extraction and DNA sequencing. Furthermore, the existence of live and replicating microbial populations in healthy fetal tissues is not compatible with fundamental concepts of immunology, clinical microbiology and the derivation of germ-free mammals. These conclusions are important to our understanding of human immune development and illustrate common pitfalls in the microbial analyses of many other low-biomass environments. The pursuit of a fetal microbiome serves as a cautionary example of the challenges of sequence-based microbiome studies when biomass is low or absent, and emphasizes the need for a trans-disciplinary approach that goes beyond contamination controls by also incorporating biological, ecological and mechanistic concepts.en
dc.description.statusPeer revieweden
dc.description.versionAccepted Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationKennedy, K. M., de Goffau, M. C., Perez-Muñoz, M. E., Arrieta, M. C., Bäckhed, F., Bork, P., Braun, T., Bushman, F. D., Dore, J., de Vos, W. M., Earl, A. M et al (2023) 'Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies', Nature, 613 (7945), pp. 639-649. https://doi.org/10.1038/s41586-022-05546-8en
dc.identifier.doihttps://doi.org/10.1038/s41586-022-05546-8en
dc.identifier.eissn1476-4687en
dc.identifier.endpage649en
dc.identifier.issn0028-0836en
dc.identifier.issued7945en
dc.identifier.journaltitleNatureen
dc.identifier.startpage639en
dc.identifier.urihttps://hdl.handle.net/10468/17168
dc.identifier.volume613en
dc.language.isoenen
dc.publisherSpringer Nature Ltd.en
dc.relation.ispartofNatureen
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Research Centres Programme::Phase 2/12/RC/2273_P2/IE/APC_Phase 2/en
dc.rights© 2023, Springer Nature. This is a post-peer-review, pre-copyedit version of an article published in Nature on 25 January 2023. The final authenticated version is available online at: https://doi.org/10.1038/s41586-022-05546-8en
dc.subjectHuman fetusen
dc.subjectPrenatal intrauterine environmenten
dc.subjectMicrobial communitiesen
dc.subjectFetal microbiomeen
dc.titleQuestioning the fetal microbiome illustrates pitfalls of low-biomass microbial studiesen
dc.typeArticle (peer-reviewed)en
dc.typejournal-articleen
oaire.citation.issue7945en
oaire.citation.volume613en
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