Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies
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Author(s)
Kennedy, Katherine M.
de Goffau, Marcus C.
Perez-Muñoz, Maria Elisa
Arrieta, Marie-Claire
Bäckhed, Fredrik
Bork, Peer
Braun, Thorsten
Bushman, Frederic D.
Dore, Joel
de Vos, Willem M.
Earl, Ashlee M.
Eisen, Jonathan A.
Elovitz, Michal A.
Ganal-Vonarburg, Stephanie C.
Gänzle, Michael G.
Garrett, Wendy S.
Hall, Lindsay J.
Hornef, Mathias W.
Huttenhower, Curtis
Konnikova, Liza
Lebeer, Sarah
Macpherson, Andrew J.
Massey, Ruth C.
McHardy, Carolyn
Koren, Omry
Lawley, Trevor D.
Ley, Ruth E.
O'Mahony, Liam
O'Toole, Paul W.
Pamer Eric G.
Parkhill, Julian
Raes, Jeroen
Rattei, Thomas
Salonen, Anne
Segal, Eran
Segata, Nicola
Shanahan, Fergus
Sloboda, Deborah M.
Smith, Gordon C. S.
Sokol, Harry
Spector, Tim D.
Surette, Michael G.
Tannock, Gerald W.
Walker, Alan W.
Yassour, Moran
Walter, Jens
de Goffau, Marcus C.
Perez-Muñoz, Maria Elisa
Arrieta, Marie-Claire
Bäckhed, Fredrik
Bork, Peer
Braun, Thorsten
Bushman, Frederic D.
Dore, Joel
de Vos, Willem M.
Earl, Ashlee M.
Eisen, Jonathan A.
Elovitz, Michal A.
Ganal-Vonarburg, Stephanie C.
Gänzle, Michael G.
Garrett, Wendy S.
Hall, Lindsay J.
Hornef, Mathias W.
Huttenhower, Curtis
Konnikova, Liza
Lebeer, Sarah
Macpherson, Andrew J.
Massey, Ruth C.
McHardy, Carolyn
Koren, Omry
Lawley, Trevor D.
Ley, Ruth E.
O'Mahony, Liam
O'Toole, Paul W.
Pamer Eric G.
Parkhill, Julian
Raes, Jeroen
Rattei, Thomas
Salonen, Anne
Segal, Eran
Segata, Nicola
Shanahan, Fergus
Sloboda, Deborah M.
Smith, Gordon C. S.
Sokol, Harry
Spector, Tim D.
Surette, Michael G.
Tannock, Gerald W.
Walker, Alan W.
Yassour, Moran
Walter, Jens
Citation for Previous Publication
Kennedy, K.M., de Goffau, M.C., Perez-Muñoz, M.E. et al. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 613, 639–649 (2023). https://doi-org.login.ezproxy.library.ualberta.ca/10.1038/s41586-022-05546-8
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Abstract
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Whether 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.
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http://purl.org/coar/resource_type/c_6501 http://purl.org/coar/version/c_b1a7d7d4d402bcce http://purl.org/coar/version/c_71e4c1898caa6e32
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© Springer Nature Limited 2023 This version of the article has been accepted for publication, after peer review (when applicable) and is subject to Springer Nature’s AM terms of use, but is not the Version of Record and does not reflect post-acceptance improvements, or any corrections. The Version of Record is available online at: https://doi.org/10.1038/s41586-022-05546-8
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en