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Antibiotics
Special Issues
After Antibiotics: Dysbiosis and Drug Resistance in Gut Microbiota
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After Antibiotics: Dysbiosis and Drug Resistance in Gut Microbiota

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Antibiotics Use and Antimicrobial Stewardship".

Deadline for manuscript submissions: 31 August 2026 | Viewed by 2097

Special Issue Editor

Prof. Dr. Sercan Karav

E-Mail Website
Guest Editor
Department of Molecular Biology and Genetics, Çanakkale Onsekiz Mart University, Çanakkale 17000, Türkiye
Interests: food-derived bioactives with antimicrobial or microbiome-supporting functions; multidrug-resistant microorganism; enzymatic modulations of microbial ecology; gut microbiota dynamics and post-antibiotic dysbiosis; probiotics, prebiptics and microbiota-targeted interventions
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The growing incidence of antibiotic resistance and an increasing awareness of antibiotic-associated dysbiosis underscore the critical necessity of reevaluating our strategies regarding antimicrobial application and intestinal microbiota well-being. Antibiotic exposure can significantly disrupt the composition and function of the intestinal microbial ecosystem, resulting in enduring metabolic, immunological, and physiological effects. Simultaneously, the rapidly occurring emergence of multidrug-resistant microorganisms continues to pose a significant threat to global public health, highlighting the urgent need for novel therapeutic and preventive approaches.

This Special Issue, “After Antibiotics: Dysbiosis and Drug Resistance in Gut Microbiota”, will provide a comprehensive platform for advanced research examining the mechanisms, effects, and interventions associated with microbiota disturbances and antibiotic resistance. We welcome original research articles, reviews, and perspectives focusing on microbiome restoration strategies, novel antimicrobial alternatives, resistance genetics, host–microbe interactions, and translational approaches to mitigating the adverse effects of antibiotic use.

We look forward to receiving your valuable contributions and working together to advance the scientific understanding of post-antibiotic microbiota resilience and resistance management.

Prof. Dr. Sercan Karav
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Antibiotics is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • gut microbiota
  • dysbiosis
  • antibiotic resistance
  • resistant genes
  • probiotics and prebiotics
  • host–microbe interactions
  • multidrug-resistant bacteria
  • post-antibiotic recovery
  • microbial ecology

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Published Papers (2 papers)

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Research

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18 pages, 558 KB  
Article
Effects of Prebiotic Gum Arabic Under Antibiotic-Containing Conditions in Atopic Dermatitis-Associated Bacteria: In Vitro Evaluation and Development of Semisolid Topical Carriers
by Derya Doğanay, Esra Mertoğlu, Ahmet Arif Kurt, Batuhan Cenk Özkan, Ertuğrul Osman Bursalıoğlu, Mustafa Eray Bozyel, Reyhan Aliusta, Özlem Türkoğlu, Halise Betül Gökçe, Emine Kızılay, Fatih Hacımustafaoğlu, Şaban Kalay, Rana Hamdemir, Ismail Bayır and Ismail Aslan
Antibiotics 2026, 15(4), 378; https://doi.org/10.3390/antibiotics15040378 - 8 Apr 2026
Viewed by 961
Abstract
Background/Objectives: Atopic dermatitis (AD) is associated with gut dysbiosis linked to early-life antibiotic use and Staphylococcus aureus colonization. Gum Arabic (GA), a prebiotic, may modulate this dysbiosis and influence AD-related microbial balance. This study evaluated whether GA could support AD-associated probiotics-Lactobacillus [...] Read more.
Background/Objectives: Atopic dermatitis (AD) is associated with gut dysbiosis linked to early-life antibiotic use and Staphylococcus aureus colonization. Gum Arabic (GA), a prebiotic, may modulate this dysbiosis and influence AD-related microbial balance. This study evaluated whether GA could support AD-associated probiotics-Lactobacillus casei, Bifidobacterium bifidum, and Bifidobacterium infantis-under amoxicillin- or azithromycin-containing conditions, examined the response of S. aureus under the same screening conditions, and developed GA-phospholipid-based semisolid carriers for topical application. Methods: Probiotic strains were cultured with 1–5% GA in the presence and absence of antibiotics, and viable cell counts were assessed. Sixteen topical formulations containing propylene glycol or isopropyl myristate in a hydrogenated phosphatidylcholine base were prepared and screened for rheological properties and galactose release using in vitro release testing (IVRT) and HPLC-UV. Results: GA at 1–2% concentrations promoted probiotic growth in antibiotic-free conditions. GA preserved B. infantis viability under azithromycin exposure in this in vitro screening model. For S. aureus, numerical CFU differences were observed between antibiotic-only and GA-containing conditions; however, the present screening design was not intended to determine antibiotic interaction outcomes. Formulations F14 (2% GA + 7% IPM) and F15 (3% GA + 7% IPM) exhibited optimal spreadability. IVRT showed that 6 h cumulative galactose release varied by formulation (F6 > F10 > F14 > F15). Conclusions: GA demonstrated dose-dependent prebiotic activity and preserved B. infantis viability under azithromycin exposure in this in vitro screening model. For S. aureus, the observed CFU differences between antibiotic-only and GA-containing conditions should be considered exploratory only and do not allow for conclusions regarding interference with antibiotic efficacy. Optimized GA-HPC systems with suitable rheological and release characteristics represent promising candidates for further preclinical investigation. Full article
(This article belongs to the Special Issue After Antibiotics: Dysbiosis and Drug Resistance in Gut Microbiota)
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Review

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17 pages, 1089 KB  
Review
Gut Microbiota and Acute Myeloid Leukemia: State of the Art, Clinical Signals, and Translational Opportunities
by Maria Eugenia Alvaro, Santino Caserta, Enrica Antonia Martino, Mamdouh Skafi, Antonella Bruzzese, Nicola Amodio, Eugenio Lucia, Virginia Olivito, Caterina Labanca, Francesco Mendicino, Ernesto Vigna, Fortunato Morabito and Massimo Gentile
Antibiotics 2026, 15(4), 417; https://doi.org/10.3390/antibiotics15040417 - 20 Apr 2026
Viewed by 730
Abstract
Acute myeloid leukemia (AML) remains a highly morbid malignancy in which outcomes are constrained not only by disease refractoriness and relapse, but also by therapy-related toxicity—particularly infections, mucosal injury, and delayed hematopoietic reconstitution. The gut microbiota has emerged as a potentially modifiable layer [...] Read more.
Acute myeloid leukemia (AML) remains a highly morbid malignancy in which outcomes are constrained not only by disease refractoriness and relapse, but also by therapy-related toxicity—particularly infections, mucosal injury, and delayed hematopoietic reconstitution. The gut microbiota has emerged as a potentially modifiable layer of host vulnerability and resilience during AML treatment. Microbiome disruption is detectable already at diagnosis, even in antibiotic-naïve patients, and is often characterized by reduced community diversity, depletion of anaerobic taxa linked to short-chain fatty acids (SCFAs) production, and enrichment of pathobiont-associated profiles. During induction, cytotoxic therapy and antimicrobials precipitates diversity loss, domination events, and persistent shifts beyond discharge. Clinically, the most consistent translational signal is the association between baseline or early-treatment microbiome features and infectious outcomes, while emerging data suggest that diagnosis-time microbiome structure may also relate to hematologic recovery kinetics. Mechanistic models converge on pathways linking barrier integrity, microbial metabolites (notably butyrate and other SCFAs), immune calibration, and inflammatory translocation of microbial products. These insights support hypotheses: antimicrobial stewardship may preserve microbiome function; ecosystem repair strategies such as autologous fecal microbiota transfer (A-FMT) are feasible and can restore community structure; and metabolite or nutritional interventions merit evaluation in immunocompromised hosts. Regimen-specific microbiome effects and microbiome–drug interactions suggest that treatment choice could have downstream microbiome-mediated consequences. We synthesize evidence, outline interventional concepts, and define methodological priorities for next-generation trials assessing causality and clinical benefit. Progress will require longitudinal sampling, multi-omic integration (metabolomics, resistomics, and barrier/inflammatory biomarkers), and interventional designs linking microbiome dynamics to clinically meaningful outcomes. Full article
(This article belongs to the Special Issue After Antibiotics: Dysbiosis and Drug Resistance in Gut Microbiota)
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