Antibiotic treatment using amoxicillin-clavulanic acid impairs gut mycobiota development through modification of the bacterial ecosystem

  • Madeleine Spatz (Fédération Hospitalo-Universitaire, Université Paris-Saclay) (Creator)
  • Gregory Da Costa (Fédération Hospitalo-Universitaire, Université Paris-Saclay) (Creator)
  • Rebecka Ventin-Holmberg (University of Helsinki, Folkhälsan Research Center) (Creator)
  • Julien Planchais (Université Paris-Saclay, Fédération Hospitalo-Universitaire) (Creator)
  • Chloé Michaudel (Fédération Hospitalo-Universitaire, Université Paris-Saclay) (Creator)
  • YaZhou Wang (Creator)
  • Camille Danne (Fédération Hospitalo-Universitaire, Université Paris-Saclay) (Creator)
  • Alexia Lapiere (AgroParisTech, Université Paris-Saclay) (Creator)
  • Marie-Laure Michel (AgroParisTech, Université Paris-Saclay) (Creator)
  • Kaija-Leena Kolho (University of Helsinki) (Creator)
  • Philippe Langella (Fédération Hospitalo-Universitaire, Université Paris-Saclay) (Creator)
  • Harry Sokol (Fédération Hospitalo-Universitaire, Université Paris-Saclay, Sorbonne Université) (Creator)
  • Mathias L. Richard (Fédération Hospitalo-Universitaire, Université Paris-Saclay) (Creator)



Abstract Background Effects of antibiotics on gut bacteria have been widely studied, but very little is known about the consequences of such treatments on the fungal microbiota (mycobiota). It is commonly believed that fungal load increases in the gastrointestinal tract following antibiotic treatment, but better characterization is clearly needed of how antibiotics directly or indirectly affect the mycobiota and thus the entire microbiota. Design We used samples from humans (infant cohort) and mice (conventional and human microbiota-associated mice) to study the consequences of antibiotic treatment (amoxicillin-clavulanic acid) on the intestinal microbiota. Bacterial and fungal communities were subjected to qPCR or 16S and ITS2 amplicon-based sequencing for microbiota analysis. In vitro assays further characterized bacterial-fungal interactions, with mixed cultures between specific bacteria and fungi. Results Amoxicillin-clavulanic acid treatment triggered a decrease in the total fungal population in mouse feces, while other antibiotics had opposite effects on the fungal load. This decrease is accompanied by a total remodelling of the fungal population with the enrichment in Aspergillus, Cladosporium, and Valsa genera. In the presence of amoxicillin-clavulanic acid, microbiota analysis showed a remodeling of bacterial microbiota with an increase in specific bacteria belonging to the Enterobacteriaceae. Using in vitro assays, we isolated different Enterobacteriaceae species and explored their effect on different fungal strains. We showed that Enterobacter hormaechei was able to reduce the fungal population in vitro and in vivo through yet unknown mechanisms. Conclusions Bacteria and fungi have strong interactions within the microbiota; hence, the perturbation initiated by an antibiotic treatment targeting the bacterial community can have complex consequences and can induce opposite alterations of the mycobiota. Interestingly, amoxicillin-clavulanic acid treatment has a deleterious effect on the fungal community, which may have been partially due to the overgrowth of specific bacterial strains with inhibiting or competing effects on fungi. This study provides new insights into the interactions between fungi and bacteria of the intestinal microbiota and might offer new strategies to modulate gut microbiota equilibrium. Video Abstract
Date made available13 Apr 2023

Field of science, Statistics Finland

  • 3123 Gynaecology and paediatrics
  • 3121 Internal medicine
  • 3111 Biomedicine

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