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Kennedy KM, de Goffau MC, Perez-Muñoz ME, Arrieta MC, Bäckhed F, Bork P, Braun T, Bushman FD, Dore J, de Vos WM, Earl AM, Eisen JA, Elovitz MA, Ganal-Vonarburg SC, Gänzle MG, Garrett WS, Hall LJ, Hornef MW, Huttenhower C, Konnikova L, Lebeer S, Macpherson AJ, Massey RC, McHardy AC, Koren O, Lawley TD, Ley RE, O'Mahony L, O'Toole PW, Pamer EG, Parkhill J, Raes J, Rattei T, Salonen A, Segal E, Segata N, Shanahan F, Sloboda DM, Smith GCS, Sokol H, Spector TD, Surette MG, Tannock GW, Walker AW, Yassour M, Walter J. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 2023; 613:639-649. [PMID: 36697862 PMCID: PMC11333990 DOI: 10.1038/s41586-022-05546-8] [Citation(s) in RCA: 122] [Impact Index Per Article: 122.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/09/2022] [Indexed: 01/26/2023]
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.
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Affiliation(s)
- Katherine M Kennedy
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Marcus C de Goffau
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Department of Vascular Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
- Wellcome Sanger Institute, Cambridge, UK
| | - Maria Elisa Perez-Muñoz
- Department of Agriculture, Food and Nutrition Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Marie-Claire Arrieta
- International Microbiome Center, University of Calgary, Calgary, Alberta, Canada
| | - Fredrik Bäckhed
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Physiology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany
- Yonsei Frontier Lab (YFL), Yonsei University, Seoul, South Korea
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Thorsten Braun
- Department of Obstetrics and Experimental Obstetrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Frederic D Bushman
- Department of Microbiology Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joel Dore
- Université Paris-Saclay, INRAE, MetaGenoPolis, AgroParisTech, MICALIS, Jouy-en-Josas, France
| | - Willem M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Jonathan A Eisen
- Department of Evolution and Ecology, University of California, Davis, Davis, CA, USA
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, USA
- UC Davis Genome Center, University of California, Davis, Davis, CA, USA
| | - Michal A Elovitz
- Maternal and Child Health Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Stephanie C Ganal-Vonarburg
- Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Michael G Gänzle
- Department of Agriculture, Food and Nutrition Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Wendy S Garrett
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard T.H. Chan Microbiome in Public Health Center, Boston, MA, USA
- Department of Medicine and Division of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lindsay J Hall
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
- Chair of Intestinal Microbiome, ZIEL-Institute for Food and Health, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mathias W Hornef
- Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Curtis Huttenhower
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Liza Konnikova
- Departments of Pediatrics and Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Sarah Lebeer
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Andrew J Macpherson
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Ruth C Massey
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Alice Carolyn McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Center for Infection Research (DZIF), Hannover Braunschweig site, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Trevor D Lawley
- Department of Vascular Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Liam O'Mahony
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- Department of Medicine, University College Cork, Cork, Ireland
| | - Paul W O'Toole
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Jeroen Raes
- VIB Center for Microbiology, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Eran Segal
- Weizmann Institute of Science, Rehovot, Israel
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
- European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Fergus Shanahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Medicine, University College Cork, Cork, Ireland
| | - Deborah M Sloboda
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
- Department of Obstetrics and Gynecology, McMaster University, Hamilton, Ontario, Canada
| | - Gordon C S Smith
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Harry Sokol
- Gastroenterology Department, AP-HP, Saint Antoine Hospital, Centre de Recherche Saint-Antoine, CRSA, INSERM and Sorbonne Université, Paris, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy en Josas, France
| | - Tim D Spector
- Department of Twin Research, King's College London, London, UK
| | - Michael G Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Gerald W Tannock
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alan W Walker
- Gut Health Group, Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Moran Yassour
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jens Walter
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- School of Microbiology, University College Cork, Cork, Ireland.
- Department of Medicine, University College Cork, Cork, Ireland.
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