ArticleMicrobiome2020
Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria.
Article in Microbiome, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 98 papers, 2 of them syntheses that pooled it.
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The trial behind it
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Who cites it
98 citing papers in PubMed, 2 syntheses or guidelines pooled it, 138 citations in OpenAlex.
- Pichia kudriavzevii (Candida krusei): A systematic review to inform the World Health Organisation priority list of fungal pathogens.Medical mycology · 2024Pooled it
- Pooled it
- Effect of intrapartum azithromycin on early childhood gut mycobiota development: post hoc analysis of a double-blind randomized trial.Nature communications · 2025Trial
- From gut dysbiosis to eubiosis: understanding microbiome recovery as an ecological process.Gut microbes · 2026Review
- Gut microbiota-derived short-chain fatty acids (SCFAs): immunomodulatory effects and therapeutic potential in infections.Clinical microbiology reviews · 2026Review
- Gut Hi-C metagenomes of severe COVID-19 patients: bacteria and yeast involved in gut-lung axis.mSphere · 2026Article
- Article
- Fungal-Bacterial Interactions in Polymicrobial Infections: Hidden Threats.MicrobiologyOpen · 2026Review
- Breakdown of microbial networks links nutrient stress and reef coral disease.Nature communications · 2026Article
- The gut mycobiome and inter-kingdom microbial networks are linked to COPD severity in lung cancer patients.Scientific reports · 2026Article
- Mycobiome dysbiosis and genetic predisposition to elevated IL-17A contribute to fibrosis in MASLD.JHEP reports : innovation in hepatology · 2026Article
- Gut fungal landscape in colorectal cancer and its cross-kingdom interplay with gut microbial ecology.iScience · 2026Article
- The Gut as a Source of Infection for Fungal Pathogens: Increased Fecal Candida albicans Precedes Onset of Candida Late-Onset Sepsis in Very Preterm Infants.The Journal of infectious diseases · 2026Article
- Longitudinal analysis of gut bacterial and fungal dynamics after solid organ transplantation.BMC microbiology · 2026Article
- Clinical characteristics of invasive candidiasis in infants born before 30 weeks of gestation: a nested case series from a multicenter cohort study in the Netherlands and Belgium.European journal of pediatrics · 2026Article
- Article
- Associations and interactions between prokaryotes and other gut biota in non-human primates.Primates; journal of primatology · 2026Review
- Optimized Selective Media Enhance the Isolation and Characterization of Gut-Derived Probiotic Yeasts.Journal of fungi (Basel, Switzerland) · 2025Article
- Fruiting body-associated Pseudomonas contact triggers ROS-mediated perylenequinone biosynthesis in Shiraia mycelium culture.Bioresources and bioprocessing · 2025Article
- Candida albicans colonization in the human colon correlates with a reduction in acetate- and butyrate-producing bacteria, as simulated using the M-SHIME® model.NPJ biofilms and microbiomes · 2025Article
38 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
18 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAntibiotic treatment has a well-established detrimental effect on the gut bacterial composition, but effects on the fungal community are less clear. Bacteria in the lumen of the gastrointestinal tract may limit fungal colonization and invasion. Antibiotic drugs targeting bacteria are therefore seen as an important risk factor for fungal infections and induced allergies. However, antibiotic effects on gut bacterial-fungal interactions, including disruption and resilience of fungal community compositions, were not investigated in humans. We analysed stool samples collected from 14 healthy human participants over 3 months following a 6-day antibiotic administration. We integrated data from shotgun metagenomics, metatranscriptomics, metabolomics, and fungal ITS2 sequencing.
resultsWhile the bacterial community recovered mostly over 3 months post treatment, the fungal community was shifted from mutualism at baseline to competition. Half of the bacterial-fungal interactions present before drug intervention had disappeared 3 months later. During treatment, fungal abundances were associated with the expression of bacterial genes with functions for cell growth and repair. By extending the metagenomic species approach, we revealed bacterial strains inhibiting the opportunistic fungal pathogen Candida albicans. We demonstrated in vitro how C. albicans pathogenicity and host cell damage might be controlled naturally in the human gut by bacterial metabolites such as propionate or 5-dodecenoate.
conclusionsWe demonstrated that antibacterial drugs have long-term influence on the human gut mycobiome. While bacterial communities recovered mostly 30-days post antibacterial treatment, the fungal community was shifted from mutualism towards competition. Video abstract.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.