Gut Microbes

Antibiotic-Induced Dysbiosis: Mechanisms and Recovery Strategies

The human gut microbiota is composed of trillions of microorganisms, including bacteria, archaea, viruses, and fungi, that reside in a dynamic symbiotic relationship with the host. These communities play essential roles in digestion, nutrient absorption, immune modulation, maintenance of physiological homeostasis, and protection against pathogens. This ecosystem is highly susceptible to external perturbations, and its disruption, termed dysbiosis, can be caused by factors such as diet, stress, infections, environmental exposures, and especially antibiotic use. While antibiotics are indispensable for treating bacterial infections, broad-spectrum agents can reduce microbial diversity, deplete beneficial taxa, and promote the expansion of opportunistic pathogens. Antibiotic-induced dysbiosis compromises intestinal homeostasis and disrupts key metabolic and immune pathways, with effects that may persist long after treatment cessation. Increasing evidence suggests that these alterations extend beyond the gastrointestinal tract, affecting systemic physiology and increasing susceptibility to metabolic, inflammatory, neurological, and oncological diseases.

The high prevalence of antibiotic exposure in clinical and agricultural settings underscores the importance of studying antibiotic-induced gut dysbiosis. Dysbiosis not only increases susceptibility to recurrent infections and antibiotic-resistant pathogens but also has long-term effects on host physiology. Perturbations of the gut microbiota can alter metabolic signalling, modulate immune responses, and disrupt the gut–brain axis, contributing to metabolic, inflammatory, allergic, and neurodevelopmental or neurodegenerative disorders. These findings emphasize the need for responsible antibiotic use and for strategies to maintain or restore gut microbial balance. Understanding the mechanisms underlying antibiotic-induced dysbiosis will inform targeted interventions, including microbiota-based therapeutics, prebiotics, probiotics, and postbiotics, with broad implications for clinical practice and public health.

This Article Collection on antibiotic-induced gut dysbiosis aims to advance understanding of the complex interactions among antibiotics, microbial communities, and host physiology. Key topics include the mechanistic basis of microbial disruption, resilience and recovery dynamics of the gut microbiota after antibiotic exposure, host immune and metabolic consequences, and links to systemic disorders. The influence of age, diet, lifestyle, and genetic factors on dysbiosis severity is also of interest. The journal welcomes a range of article types, including Research Papers/Reports, Reviews, Brief Reports, Research Letters, Commentaries and Views, Creative Commentaries, Meeting Reports, and Data Notes that provide mechanistic, longitudinal, or systems‑level insights. By focusing on pathways, determinants, and predictive frameworks rather than specific therapeutic modalities, this Collection seeks to establish a mechanistic foundation to inform future precision strategies for mitigating antibiotic‑induced dysbiosis and its systemic consequences.

Keywords

• Gut Microbiota
• Antibiotic-induced dysbiosis
• Microbiota-targeted interventions
• Probiotics and Prebiotics
• Immune modulation and metabolic regulation

­­All manuscripts submitted to this Article Collection will undergo a full peer-review; the Guest Advisor for this Collection will not be handling the manuscripts (unless they are an Editorial Board member).

Please review the journal scope and author submission instructions prior to submitting a manuscript.

The deadline for submitting manuscripts is 28 February 2027.

Please contact Zhiyuan Zhang at [email protected] with any queries and discount codes regarding this Article Collection.

Please be sure to select the appropriate Article Collection from the drop-down menu in the submission system.

Guest Advisor

Dr. am Rodriguez Fernandes is a medical writer and scientist with a background in microbiology, specializing in infectious diseases, antimicrobial resistance, and the gut microbiome. She previously completed postdoctoral training at the NCI/NIH, where she investigated the role of the gut microbiota in human health and cancer. Transitioning from research to medical communications, she develops peer-reviewed publications and scientific content that translate complex biomedical findings into clear, impactful narratives, particularly in oncology.