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

Katherine M. Kennedy, Marcus C. de Goffau, Maria Elisa Perez-Muñoz, Marie-Claire Arrieta, Fredrik Bӓckhed, Peer Bork, Thorsten Braun, Frederic D Bushman, Joel Dore, Willem M de Vos, Ashlee M. Earl, Jonathan A. Eisen, Michal A. Elovitz, Stephanie C. Ganal-Vonarburg, Michael G. Gӓnzle, Wendy S Garrett, Lindsay J. Hall, Mathias W. Hornef, Curtis Huttenhower, Liza KonnikovaSarah Lebeer, Andrew J Macpherson, Ruth C. Massey, Alice Carolyn McHardy, Omry Koren, Trevor D. Lawley, Ruth E. Ley, Liam O’Mahony, Paul W. O'Toole, Eric G. Pamer, Julian Parkhill, Jeroen Raes, Thomas Rattei, Anne Salonen, Eran Segal, Nicola Segata, Fergus Shanahan, Deborah M Sloboda, Gordon C.S. Smith, Harry Sokol, Tim D Spector, Michael G. Surette, Gerald W. Tannock, Alan Walker, Moran Yassour, Jens Walter* (Corresponding Author)

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Whether the human fetus and the prenatal intrauterine environment (amniotic fluid, placenta) are stably colonized by microbes in a healthy pregnancy remains the subject of debate. Here, we evaluate recent studies that characterized microbial populations in human fetuses from the perspectives of reproductive biology, microbiology, bioinformatics, immunology, clinical microbiology, and gnotobiology, and assess possible mechanisms by which the fetus might
interact with microbes. Our analysis indicates that the detected microbial signals are likely the result of contamination during the clinical procedures to obtain fetal samples, DNA extraction, and DNA sequencing. Further, 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 also 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, also incorporating biological, ecological, and mechanistic concepts.
Original languageEnglish
Pages (from-to)639–649
Number of pages11
Early online date25 Jan 2023
Publication statusPublished - 26 Jan 2023


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