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

Item Type:	Review
Title:	Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies
Creators Name:	Kennedy, K.M. and de Goffau, M.C. and Perez-Muñoz, M.E. and Arrieta, M.C. and Bäckhed, F. and Bork, P. and Braun, T. and Bushman, F.D. and Dore, J. and de Vos, W.M. and Earl, A.M. and Eisen, J.A. and Elovitz, M.A. and Ganal-Vonarburg, S.C. and Gänzle, M.G. and Garrett, W.S. and Hall, L.J. and Hornef, M.W. and Huttenhower, C. and Konnikova, L. and Lebeer, S. and Macpherson, A.J. and Massey, R.C. and McHardy, A.C. and Koren, O. and Lawley, T.D. and Ley, R.E. and O'Mahony, L. and O'Toole, P.W. and Pamer, E.G. and Parkhill, J. and Raes, J. and Rattei, T. and Salonen, A. and Segal, E. and Segata, N. and Shanahan, F. and Sloboda, D.M. and Smith, G.C.S. and Sokol, H. and Spector, T.D. and Surette, M.G. and Tannock, G.W. and Walker, A.W. and Yassour, M. and Walter, J.
Abstract:	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.
Keywords:	Amniotic Fluid, Biomass, Microbiota, Placenta, Pregnancy, Prenatal Care, Animals, Mammals
Source:	Nature
ISSN:	0028-0836
Publisher:	Nature Publishing Group
Volume:	613
Number:	7945
Page Range:	639-649
Date:	26 January 2023
Official Publication:	https://doi.org/10.1038/s41586-022-05546-8
PubMed:	View item in PubMed

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