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Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies.
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, Alice 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.
Afiliación
  • Kennedy KM; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
  • de Goffau MC; Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada.
  • Perez-Muñoz ME; Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, Amsterdam, The Netherlands.
  • Arrieta MC; Department of Vascular Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands.
  • Bäckhed F; Wellcome Sanger Institute, Cambridge, UK.
  • Bork P; Department of Agriculture, Food and Nutrition Sciences, University of Alberta, Edmonton, Alberta, Canada.
  • Braun T; International Microbiome Center, University of Calgary, Calgary, Alberta, Canada.
  • Bushman FD; The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
  • Dore J; Department of Clinical Physiology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden.
  • de Vos WM; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
  • Earl AM; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
  • Eisen JA; Max Delbrück Centre for Molecular Medicine, Berlin, Germany.
  • Elovitz MA; Yonsei Frontier Lab (YFL), Yonsei University, Seoul, South Korea.
  • Ganal-Vonarburg SC; Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
  • Gänzle MG; Department of Obstetrics and Experimental Obstetrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
  • Garrett WS; Department of Microbiology Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
  • Hall LJ; Université Paris-Saclay, INRAE, MetaGenoPolis, AgroParisTech, MICALIS, Jouy-en-Josas, France.
  • Hornef MW; Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
  • Huttenhower C; Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
  • Konnikova L; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Boston, MA, USA.
  • Lebeer S; Department of Evolution and Ecology, University of California, Davis, Davis, CA, USA.
  • Macpherson AJ; Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, USA.
  • Massey RC; UC Davis Genome Center, University of California, Davis, Davis, CA, USA.
  • McHardy AC; Maternal and Child Health Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
  • Koren O; Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
  • Lawley TD; Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland.
  • Ley RE; Department of Agriculture, Food and Nutrition Sciences, University of Alberta, Edmonton, Alberta, Canada.
  • O'Mahony L; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
  • O'Toole PW; Harvard T.H. Chan Microbiome in Public Health Center, Boston, MA, USA.
  • Pamer EG; Department of Medicine and Division of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
  • Parkhill J; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Raes J; Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
  • Rattei T; Norwich Medical School, University of East Anglia, Norwich, UK.
  • Salonen A; Chair of Intestinal Microbiome, ZIEL-Institute for Food and Health, School of Life Sciences, Technical University of Munich, Freising, Germany.
  • Segal E; Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany.
  • Segata N; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
  • Shanahan F; Broad Institute of Harvard and MIT, Cambridge, MA, USA.
  • Sloboda DM; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
  • Smith GCS; Departments of Pediatrics and Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA.
  • Sokol H; Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium.
  • Spector TD; Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland.
  • Surette MG; APC Microbiome Ireland, University College Cork, Cork, Ireland.
  • Tannock GW; School of Microbiology, University College Cork, Cork, Ireland.
  • Walker AW; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.
  • Yassour M; German Center for Infection Research (DZIF), Hannover Braunschweig site, Braunschweig, Germany.
  • Walter J; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.
Nature ; 613(7945): 639-649, 2023 01.
Article en En | MEDLINE | ID: mdl-36697862
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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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Biomasa / Contaminación de ADN / Feto / Microbiota Límite: Animals / Female / Humans / Pregnancy Idioma: En Revista: Nature Año: 2023 Tipo del documento: Article País de afiliación: Canadá Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Biomasa / Contaminación de ADN / Feto / Microbiota Límite: Animals / Female / Humans / Pregnancy Idioma: En Revista: Nature Año: 2023 Tipo del documento: Article País de afiliación: Canadá Pais de publicación: Reino Unido