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Article Dans Une Revue Nature Année : 2023

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

Katherine Kennedy (1) , Marcus de Goffau (2, 3, 4) , Maria Elisa Perez-Muñoz (5) , Marie-Claire Arrieta (6) , Fredrik Bäckhed (7, 8, 9) , Peer Bork (10, 11) , Thorsten Braun (12, 13, 14) , Frederic Bushman (15) , Joel Dore (16, 17) , Willem de Vos (18, 19) , Ashlee Earl (20) , Jonathan Eisen (21) , Michal Elovitz (22) , Stephanie Ganal-Vonarburg , Michael Gänzle (23) , Wendy Garrett , Lindsay Hall , Mathias Hornef (24) , Curtis Huttenhower , Liza Konnikova , Sarah Lebeer , Andrew Macpherson , Ruth Massey , Alice Carolyn Mchardy , Omry Koren , Trevor Lawley , Ruth Ley , Liam O’mahony , Paul O’toole , Eric Pamer , Julian Parkhill , Jeroen Raes , Thomas Rattei , Anne Salonen , Eran Segal , Nicola Segata , Fergus Shanahan , Deborah Sloboda , Gordon Smith , Harry Sokol (25, 26, 27, 16) , Tim Spector , Michael Surette , Gerald Tannock , Alan Walker , Moran Yassour , Jens Walter
1 McMaster University [Hamilton, Ontario]
2 Amsterdam UMC - Amsterdam University Medical Centers
3 UvA - University of Amsterdam [Amsterdam] = Universiteit van Amsterdam
4 The Wellcome Trust Sanger Institute [Cambridge]
5 University of Alberta
6 University of Calgary
7 ITU - IT University of Copenhagen
8 Sahlgrenska University Hospital [Gothenburg]
9 Sahlgrenska Academy at University of Gothenburg [Göteborg]
10 EMBL - European Molecular Biology Laboratory [Heidelberg]
11 Universität Heidelberg [Heidelberg] = Heidelberg University
12 Charité - UniversitätsMedizin = Charité - University Hospital [Berlin]
13 HU Berlin - Humboldt-Universität zu Berlin = Humboldt University of Berlin = Université Humboldt de Berlin
14 Freie Universität Berlin
15 University of Pennsylvania School of Veterinary Medicine
16 MICALIS - MICrobiologie de l'ALImentation au Service de la Santé
17 MGP (US 1367) - MetaGenoPolis
18 WUR - Wageningen University and Research [Wageningen]
19 HUS - Helsinki University Hospital [Finland]
20 BROAD INSTITUTE - Broad Institute of MIT and Harvard
21 UC - University of California
22 University of Pennsylvania
23 TUM - Technische Universität Munchen - Technical University Munich - Université Technique de Munich
24 RWTH - Rheinisch-Westfälische Technische Hochschule Aachen University
25 SU - Sorbonne Université
26 CHU Saint-Antoine [AP-HP]
27 CRSA - Centre de Recherche Saint-Antoine
Katherine Kennedy
McMaster University [Hamilton, Ontario]
Marcus de Goffau
Amsterdam University Medical Centers
University of Amsterdam [Amsterdam] = Universiteit van Amsterdam
The Wellcome Trust Sanger Institute [Cambridge]
Maria Elisa Perez-Muñoz
University of Alberta
Marie-Claire Arrieta
University of Calgary
Fredrik Bäckhed
  • Fonction : Auteur
IT University of Copenhagen
Sahlgrenska University Hospital [Gothenburg]
Sahlgrenska Academy at University of Gothenburg [Göteborg]
Peer Bork
European Molecular Biology Laboratory [Heidelberg]
Universität Heidelberg [Heidelberg] = Heidelberg University
Thorsten Braun
Charité - UniversitätsMedizin = Charité - University Hospital [Berlin]
Humboldt-Universität zu Berlin = Humboldt University of Berlin = Université Humboldt de Berlin
Freie Universität Berlin
Frederic Bushman
University of Pennsylvania School of Veterinary Medicine
Joel Dore
MICrobiologie de l'ALImentation au Service de la Santé
MetaGenoPolis
Willem de Vos
  • Fonction : Auteur
Wageningen University and Research [Wageningen]
Helsinki University Hospital [Finland]
Ashlee Earl
Broad Institute of MIT and Harvard
Jonathan Eisen
University of California
Michal Elovitz
University of Pennsylvania
Stephanie Ganal-Vonarburg
Michael Gänzle
Technische Universität Munchen - Technical University Munich - Université Technique de Munich
Wendy Garrett
Lindsay Hall
Mathias Hornef
Rheinisch-Westfälische Technische Hochschule Aachen University
Curtis Huttenhower
Liza Konnikova
Sarah Lebeer
Andrew Macpherson
  • Fonction : Auteur
Ruth Massey
  • Fonction : Auteur
Alice Carolyn Mchardy
Omry Koren
Trevor Lawley
Ruth Ley
Liam O’mahony
Paul O’toole
Eric Pamer
Julian Parkhill
Jeroen Raes
  • Fonction : Auteur
Thomas Rattei
Anne Salonen
Eran Segal
Nicola Segata
Fergus Shanahan
Deborah Sloboda
Gordon Smith
Harry Sokol
Sorbonne Université
CHU Saint-Antoine [AP-HP]
Centre de Recherche Saint-Antoine
MICrobiologie de l'ALImentation au Service de la Santé
CV
Tim Spector
Michael Surette
Gerald Tannock
  • Fonction : Auteur
Alan Walker
Moran Yassour
  • Fonction : Auteur
Jens Walter

Résumé

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.

Domaines

Sciences du Vivant [q-bio]

Romain Briandet  : Connectez-vous pour contacter le contributeur

https://hal.inrae.fr/hal-04565252

Soumis le : mercredi 1 mai 2024-16:00:10

Dernière modification le : mercredi 3 juillet 2024-10:49:35

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hal-04565252 , version 1 (01-05-2024)

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Paternité - Pas de modifications

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Katherine Kennedy, Marcus de Goffau, Maria Elisa Perez-Muñoz, Marie-Claire Arrieta, Fredrik Bäckhed, et al.. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature, 2023, 613 (7945), pp. 639-649. ⟨10.1038/s41586-022-05546-8⟩. ⟨hal-04565252⟩

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