The Impact of Antibiotic Therapy on Intestinal Microbiota: Dysbiosis, Antibiotic Resistance, and Restoration Strategies

Abstract

The human gut microbiota-an intricate and dynamic ecosystem-plays a pivotal role in metabolic regulation, immune modulation, and the maintenance of intestinal barrier integrity. Although antibiotic therapy is indispensable for managing bacterial infections, it profoundly disrupts gut microbial communities. Such dysbiosis is typified by diminished diversity and shifts in community structure, especially among beneficial bacterial genera (e.g., Bifidobacterium and Eubacterium), and fosters antibiotic-resistant strains and the horizontal transfer of resistance genes. These alterations compromise colonization resistance, increase intestinal permeability, and amplify susceptibility to opportunistic pathogens like Clostridioides difficile. Beyond gastrointestinal disorders, emerging evidence associates dysbiosis with systemic conditions, including chronic inflammation, metabolic syndrome, and neurodegenerative diseases, underscoring the relevance of the microbiota-gut-brain axis. The recovery of pre-existing gut communities post-antibiotic therapy is highly variable, influenced by drug spectrum, dosage, and treatment duration. Innovative interventions-such as fecal microbiota transplantation (FMT), probiotics, synbiotics, and precision microbiome therapeutics-have shown promise in counteracting dysbiosis and mitigating its adverse effects. These therapies align closely with antibiotic stewardship programs aimed at minimizing unnecessary antibiotic use to preserve microbial diversity and curtail the spread of multidrug-resistant organisms. This review emphasizes the pressing need for microbiota-centered strategies to optimize antibiotic administration, promote long-term health resilience, and alleviate the disease burden associated with antibiotic-induced dysbiosis.

Keywords: antibiotic resistance; dysbiosis; fecal microbiota transplantation; gut microbiota; microbial diversity; prebiotics and synbiotics; probiotics.

Figure 1

Study flowchart following the PRISMA Extension for Scoping Reviews (PRISMA-ScR) guidelines [20]. The diagram illustrates the sequential phases of identification, screening, eligibility assessment, and the final inclusion of studies. It provides a clear overview of the number of records retrieved, excluded, and ultimately included in the review.

Figure 2

This diagram depicts the multifactorial contributors to dysbiosis, a disruption of microbial homeostasis. Key factors include diet, drugs, the intestinal mucosa, and the immune system, which regulate microbial stability. Oxidative stress, bacteriophages, and bacteriocins further modulate microbial composition, while microbial alterations can sustain dysbiosis, compromising gut and systemic homeostasis.