Antibiotic Effects on Gut Microbiota Dynamics

Antibiotics exert profound and multifaceted effects on the gut microbiota, disrupting established microbial communities and altering ecological dynamics. Treatment courses, particularly broad-spectrum regimens, typically precipitate a rapid decline in species richness and evenness, accompanied by a shift towards opportunistic taxa and increased colonisation by pathobionts. Functional repertoires are reshaped through modulation of metabolic pathways—including short-chain fatty acid biosynthesis—and by selection for antibiotic-resistance determinants. While the microbiota often exhibits resilience, returning towards a pretreatment composition over weeks to months, certain taxa may fail to recover fully, leading to long-term dysbiosis. Perturbations can influence host physiology by impairing mucosal integrity, perturbing immune homeostasis and altering nutrient metabolism. Global concerns centre on the contribution of antibiotic-induced dysbiosis to increased susceptibility to infection, metabolic disorders and the dissemination of resistance genes. Mitigation strategies under investigation include dietary modulation, prebiotic supplementation and targeted microbial therapies aimed at preserving or restoring ecological balance during and after antibiotic exposure.

Research from Nature Portfolio

Recent studies have shown that targeted dietary intervention with specific fermentable fibres can attenuate antibiotic-induced dysbiosis by moderating gut redox potential. In murine models, prebiotic supplementation preserved obligate anaerobes by lowering luminal oxidation–reduction potential during antibiotic treatment, thereby preventing overgrowth of aerobes and maintaining key metabolic functions. Chemical measurements corroborated metatranscriptomic evidence of reduced oxidative pathways, indicating that host diet can serve as an adjuvant to protect commensal communities under pharmacological stress.

Antibiotic Effects on Gut Microbiota Dynamics publication trend

The graph below shows the total number of articles in antibiotic effects on gut microbiota dynamics across all publications each year (not limited to Nature Index journals).

Technical terms

Dysbiosis: A state of imbalance in the microbial community structure associated with loss of beneficial functions and overgrowth of opportunistic organisms.

Alpha diversity: A measure of species richness and evenness within a single microbial community sample.

Beta diversity: A comparison of compositional differences between two or more microbial communities.

Redox potential: The chemical measure of oxidation–reduction status in the gut lumen that influences microbial metabolic pathways.

Metaproteomics: The large-scale study of all proteins expressed by microbial and host communities within an environmental sample.

References

1. Fiber supplementation protects from antibiotic-induced gut microbiome dysbiosis by modulating gut redox potential. Nature Communications (2023).
2. Effect of tebipenem pivoxil hydrobromide on the normal gut microbiota of a healthy adult population in Sweden: a randomised controlled trial. The Lancet Microbe (2024).
3. Metaproteomic assessment of gut microbial and host functional perturbations in Helicobacter pylori-infected patients subjected to an antimicrobial protocol. Gut Microbes (2023).
4. The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome Medicine (2016).