Antibiotic treatment using amoxicillin-clavulanic acid impairs gut mycobiota development through modification of the bacterial ecosystem
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Spatz M, Da Costa G, Ventin-Holmberg R, Planchais J, Michaudel C, Wang Y, Danne C, Lapiere A, Michel ML, Kolho KL, Langella P, Sokol H, Richard ML
Journal
Microbiome
Year
2023
Keywords:
Antibiotics, Enterobacteriaceae, Microbiota, Mycobiota
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.
Experiment 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-15
Curated date: 2023/10/10
Curator: Hodan Issah
Revision editor(s): LGeistlinger, Folakunmi, Hodan Issah, MyleeeA
Subjects
- Location of subjects
- France
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Antimicrobial agent , Amoxicillin antibiotic,antibiotics,Antibiotika,Antibiotikum,antibiotique,antimicrobial,antimicrobial agents,microbicide,microbicides,Antimicrobial agent,antimicrobial agent,(2S,5R,6R)-6-,6-(p-hydroxy-alpha-aminophenylacetamido)penicillanic acid,6beta-[(2R)-2-amino-2-(4-hydroxyphenyl)acetamido]-2,2-dimethylpenam-3alpha-carboxylic acid,[H][C@]12SC(C)(C)[C@@H](N1C(=O)[C@H]2NC(=O)[C@H](N)c1ccc(O)cc1)C(O)=O,alpha-amino-p-hydroxybenzylpenicillin,Amolin,Amopenixin,amoxicilina,Amoxicillin anhydrous,amoxicilline,amoxicillinum,amoxycillin,AMPC,AX,C16H19N3O5S,Clamoxyl,InChIKey=LSQZJLSUYDQPKJ-VLWBPTPADT,Moxal,p-hydroxyampicillin,Amoxicillin,amoxicillin
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- mouse before antibiotic treatment
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- mouse after antibiotic treatment
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mouse sample fungal results post-antibiotic treatment using Amoxicillin/clavulanate acid
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- NA
Lab analysis
- Sequencing type
- ITS / ITS2
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-1-15
Source: figure 2D
Description: Amoxicillin/clavulanate acid treatment alters the fungal microbiota
Abundance in Group 1: increased abundance in mouse after antibiotic treatment
NCBI | Quality Control | Links |
---|---|---|
Aspergillus | ||
Cladosporium | ||
Valsa |
Revision editor(s): Hodan Issah
Experiment 2
Reviewed Marked as Reviewed by Folakunmi on 2024-1-15
Curated date: 2023/10/13
Curator: Hodan Issah
Revision editor(s): Hodan Issah, LGeistlinger, Folakunmi
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Mouse before antibiotic treatment
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mouse after antibiotic treatment
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mouse sample bacterial results post-antibiotic treatment using amoxicillin-acid clavulanic
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-1-15
Source: figure 3D
Description: Amoxicillin/clavulanate acid treatment alters the bacterial microbiota
Abundance in Group 1: increased abundance in Mouse after antibiotic treatment
NCBI | Quality Control | Links |
---|---|---|
Enterobacteriaceae | ||
Clostridiales vadin BB60Clostridiales vadin BB60 | ||
Escherichia/Shigella sp. | ||
Enterococcus |
Revision editor(s): Hodan Issah, Folakunmi
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