The Role of the Gut Microbiome in Antibiotic Resistance and Therapy: Mechanisms and Implications
A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Antibiotic Therapy in Infectious Diseases".
Deadline for manuscript submissions: 15 October 2025 | Viewed by 754
Special Issue Editor
Interests: microbiology; antibiotics; microbiome; sequencing; fluoroquinolones; colistin; Klebsiella pneumoniae; animal models
Special Issues, Collections and Topics in MDPI journals
Special Issue Information
Dear Colleagues,
This Special Issue addresses the complex relationship between the gut microbiome, antibiotic resistance and therapy.
Antibiotics, although essential in the treatment of bacterial infections, can significantly disrupt the gut microbiome, reducing microbial diversity by eliminating beneficial bacteria along with harmful pathogens, allowing opportunistic and resistant strains of bacteria to proliferate. The gut microbiome acts as a reservoir of antibiotic resistance genes, facilitating their horizontal transfer between bacterial species, which contributes to the spread of multidrug-resistant pathogens. In contrast, beneficial commensal bacteria can reduce resistance through mechanisms such as competitive exclusion and colonization resistance, where they outcompete pathogens for resources and produce antimicrobial compounds.
The gut microbiome acts as a reservoir of antibiotic resistance genes, facilitating their horizontal transfer between bacterial species, allowing the spread of multidrug-resistant pathogens. Antibiotic therapy disrupts the gut microbiome by killing not only harmful bacteria but also beneficial microbes, leading to a loss of microbial diversity. This disruption weakens the gut’s natural defenses, allowing opportunistic and antibiotic-resistant bacteria to thrive. Resistant strains can multiply, making infections more difficult to treat.
Recent advances in metagenomics and metabolomics offer personalized antibiotic treatment strategies that minimize collateral damage to beneficial bacteria. Adjunctive therapies such as probiotics and prebiotics hold promise in restoring gut balance and alleviating the side effects of antibiotics. Understanding these mechanisms is key to developing new therapeutic approaches to combat antibiotic resistance and preserve the efficacy of existing antibiotics.
Prof. Dr. Dóra Szabó
Guest Editor
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Keywords
- gut microbiome
- antibiotic resistance
- antibiotic therapy
- pre- and probiotics
- horizontal gene transfer
- ESBL-producing enterobacterales
- Carbapenem-resistant enterobacterales
- intestinal colonization
- clostrioides difficile
- fecal microbiota transplantation (FMT)
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