Several human intestinal microbiota studies suggest that bacteriophages, viruses infecting bacteria, play a role in gut homeostasis. Currently, bacteriophages are considered a tool to precisely engineer the intestinal microbiota, but they have also attracted considerable attention as a possible solution to fight against bacterial pathogens resistant to antibiotics. These two applications necessitate bacteriophages to reach and kill their bacterial target within the gut environment. Unfortunately, exploitable clinical data in this field are scarce. Here, we review the administration of bacteriophages to target intestinal bacteria in mammalian experimental models. While bacteriophage amplification in the gut was often confirmed, we found that in most studies, it had no significant impact on the load of the targeted bacteria. In particular, we observed that the outcome of bacteriophage treatments is linked to the behavior of the target bacteria toward each animal model. Treatment efficacy ranges from poor in asymptomatic intestinal carriage to high in intestinal disease. This broad range of efficacy underlines the difficulties to reach a consensus on the impact of bacteriophages in the gut and calls for deeper investigations of key parameters that influence the success of such interventions before launching clinical trials.

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Author Bios

Microbiotas Hosts Antibiotics and bacterial Resistances (MiHAR), University of Nantes, Nantes, France
Department of Emergency Medicine, University Hospital of Nantes, Nantes, France
François Javaudin, M.D., M.S., is Assistant Professor of Emergency Medicine at Nantes University Hospital, Nantes, France. He is currently a Ph.D. student at the MiHAR Lab (Microbiotas, Hosts, Antibiotics, and bacterial Resistances, University of Nantes), where the prevention of antibiotic resistance is a key research topic, as well as in the emergency department of the Nantes University Hospital. Experimental research in the MiHAR Lab includes the use of bacteriophages to reduce the intestinal carriage of multiresistant bacteria.
Chloé Latour
Department of Medicine, Hospital of Pontivy, Pontivy, France
Chloé Latour, M.D., is a physician at Pontivy Hospital, Pontivy, France. She received her medical degree at Nantes University Hospital, where she worked for several years in the emergency unit.
Institut Pasteur, Université de Paris, Bacteriophage Bacterium Host Laboratory, Paris, France
Laurent Debarbieux, Ph.D., is leading the Bacteriophage, Bacterium, Host Laboratory of the Institut Pasteur. Following an initial training in the molecular biology of the bacterial cell at the University of Lille, France, and at Harvard Medical School, Boston, MA, he turned his attention to bacteriophages in 2006. Since then, he has used mainly experimental animal models to decipher the mechanisms governing the activity of bacteriophages targeting bacterial pathogens.
Institut Pasteur, Université de Paris, Bacteriophage Bacterium Host Laboratory, Paris, France
Quentin Lamy-Besnier is a Ph.D. student at Institut Pasteur. He graduated from the biology department of the Ecole Normale Supérieure with a M.S.c in ecology and evolution. His research focuses on understanding bacteriophage-bacterium interactions in the mammalian gut across scales from animal studies to molecular mechanisms. He also has bioinformatics skills that he deploys to analyze viromes.

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cover image Clinical Microbiology Reviews
Clinical Microbiology Reviews
Volume 34Number 415 December 2021
eLocator: e00136-21
PubMed: 34668734


Published online: 20 October 2021


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  1. enteric pathogens
  2. gastrointestinal infection
  3. intestinal colonization



Microbiotas Hosts Antibiotics and bacterial Resistances (MiHAR), University of Nantes, Nantes, France
Department of Emergency Medicine, University Hospital of Nantes, Nantes, France
Chloé Latour
Department of Medicine, Hospital of Pontivy, Pontivy, France
Institut Pasteur, Université de Paris, Bacteriophage Bacterium Host Laboratory, Paris, France
Institut Pasteur, Université de Paris, Bacteriophage Bacterium Host Laboratory, Paris, France

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