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Pharmaceuticals
Special Issues
Research on Diagnosis, Treatment and Related Microbiota in Gastrointestinal Diseases
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Research on Diagnosis, Treatment and Related Microbiota in Gastrointestinal Diseases

A special issue of Pharmaceuticals (ISSN 1424-8247). This special issue belongs to the section "Medicinal Chemistry".

Deadline for manuscript submissions: 25 October 2026 | Viewed by 5672

Special Issue Editors

Dr. Edoardo V. Savarino

E-Mail Website
Guest Editor
Department of Surgery, Oncology and Gastroenterology, University of Padua, 35122 Padua, Italy
Interests: irritable bowel syndrome; GERD; inflammatory bowel disease
Special Issues, Collections and Topics in MDPI journals
Dr. Brigida Barberio

E-Mail Website
Guest Editor
Division of Gastroenterology, Department of Surgery, Oncology and Gastroenterology, University of Padua, 35121 Padua, Italy
Interests: inflammatory bowel disease; short bowel syndrome; microbiota; irritable bowel syndrome
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The human gastrointestinal (GI) tract harbors a diverse and complex microbial community that plays a crucial role in health and disease. Advances in microbiome research have deepened our understanding of how gut microbiota influences the onset, progression, and treatment response of various GI disorders. From inflammatory conditions such as inflammatory bowel disease (IBD) and eosinophilic esophagitis (EoE) to liver diseases like primary sclerosing cholangitis (PSC) and metabolic-associated steatotic liver disease (MASLD), gut dysbiosis has emerged as a key factor in pathogenesis and potential therapeutic targeting.

Short-chain fatty acids (SCFAs), gut-derived metabolites with anti-inflammatory and immune-modulating properties, illustrate the microbiota’s role in maintaining intestinal barrier function and systemic homeostasis. Their dysregulation has been implicated in conditions such as IBD, irritable bowel syndrome (IBS), and even extraintestinal diseases, including immune checkpoint inhibitor (ICI)-induced colitis—a growing concern in cancer immunotherapy. Understanding the interplay between gut microbiota, metabolic pathways, and immune responses offers promising avenues for diagnostic advancements and novel treatment strategies.

This Special Issue aims to explore the latest research on microbiota-related mechanisms, diagnostic innovations, and treatment approaches in GI diseases. We welcome original research and review articles addressing microbiota-driven biomarkers, therapeutic modulation (e.g., probiotics, prebiotics, fecal microbiota transplantation), host–microbiome interactions, and precision medicine applications in gastroenterology and hepatology.

We look forward to your valuable contributions to this Special Issue.

P.S. The Editors of this Special Issue extend their sincere gratitude to Dr. Luisa Bertin for her invaluable contributions. Her assistance in meticulous management and dedicated efforts in promoting the Special Issue have significantly enhanced its visibility and impact within the field.

Dr. Edoardo V. Savarino
Dr. Brigida Barberio
Guest Editors

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. Pharmaceuticals 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
  • inflammatory bowel disease
  • eosinophilic esophagitis
  • primary sclerosing cholangitis
  • metabolic-associated steatotic liver disease
  • immune checkpoint inhibitor colitis
  • dysbiosis
  • prebiotics
  • probiotics

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Published Papers (3 papers)

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Research

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23 pages, 6932 KB  
Article
CIGB-258, a Potential Novel Approach to Treat Sepsis-like Hyperinflammation, Reduces Gastrointestinal Hemorrhage in Zebrafish Exposed to Carboxymethyllysine and Ethanol
by Kyung-Hyun Cho, Yunki Lee, Sang Hyuk Lee, Ashutosh Bahuguna, María del Carmen Domínguez-Horta and Gillian Martínez-Donato
Pharmaceuticals 2026, 19(3), 510; https://doi.org/10.3390/ph19030510 - 20 Mar 2026
Viewed by 814
Abstract
Objective: CIGB-258 is a 3 KDa altered peptide ligand recognized for its anti-inflammatory activity. Herein, the effect of CIGB-258 was assessed against carboxymethyllysine (CML) and ethanol (Et-OH)-induced sepsis-like events in zebrafish (Danio rerio). Methodology: Adult zebrafish (n = 30/group) were intraperitoneally [...] Read more.
Objective: CIGB-258 is a 3 KDa altered peptide ligand recognized for its anti-inflammatory activity. Herein, the effect of CIGB-258 was assessed against carboxymethyllysine (CML) and ethanol (Et-OH)-induced sepsis-like events in zebrafish (Danio rerio). Methodology: Adult zebrafish (n = 30/group) were intraperitoneally microinjected (10 μL) with CML (final 3 mM) + Et-OH (final 50%) or CML + Et-OH containing CIGB-258 (final 1 μM) and analyzed for swimming activity, abdominal bleeding and survivability. The zebrafish were sacrificed 180 min after injection, and blood and organs were processed for biochemical and histological evaluation. Results: The CML + Et-OH group showed the lowest survival, compromised swimming ability, and severe abdominal bleeding 60 min post-treatment, which were substantially improved by treatment with CIGB-258. The CML + Et-OH group showed the greatest extent of oxidization and the lowest antioxidant activity in plasma, while co-treatment with CIGB-258 resulted in a remarkable improvement in oxidative extent and antioxidant status. The CML + Et-OH group showed dyslipidemia and an atherogenic lipid profile, which were substantially prevented by the CIGB-258 treatment. The livers and kidneys of the CML + Et-OH group showed the greatest extent of inflammation and senescence, which were substantially ameliorated by treatment with CIGB-258. Similarly, the CML + Et-OH group exhibited severe intestinal bleeding, which decreased 2.2-fold following treatment with CIGB-258. H&E staining and Mason-trichrome staining revealed extreme disruption to intestinal microvillus cell morphology and severe fibrosis in the intestines of the CML + Et-OH group, which effects were mitigated by the treatment with CIGB-258. Conclusions: The CML + Et-OH treatment resulted in acute gastrointestinal bleeding, severe oxidative stress, and hepatic and renal damage, leading to acute septic shock-like death in zebrafish. However, treatment with CIGB-258 reduced these effects through antioxidant and anti-inflammatory actions and by increasing HDL-C levels. Full article
(This article belongs to the Special Issue Research on Diagnosis, Treatment and Related Microbiota in Gastrointestinal Diseases)
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Review

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60 pages, 1795 KB  
Review
Diet and Gut Microbiota in Inflammatory Bowel Disease: A Clinical and Nutritional Perspective
by Luisa Bertin, Sonia Facchin, Brigida Barberio, Daria Maniero, Greta Lorenzon, Francesco Cesaroni, Miriana Zanconato, Giulia Romanelli, Francesco Francini-Pesenti, Luca Busetto, Mara Cananzi, Paola Gaio, Luca Bosa, Fabiana Zingone, Laura Gianolio, Oriana M. Damas and Edoardo Vincenzo Savarino
Pharmaceuticals 2026, 19(2), 318; https://doi.org/10.3390/ph19020318 - 14 Feb 2026
Cited by 3 | Viewed by 3556
Abstract
Inflammatory bowel diseases, comprising Crohn’s disease and ulcerative colitis, represent chronic inflammatory disorders with rising global incidence, underscoring the pivotal role of modifiable environmental factors in disease pathogenesis. Diet and intestinal microbiota have emerged as critical bidirectional therapeutic targets through complex interactions with [...] Read more.
Inflammatory bowel diseases, comprising Crohn’s disease and ulcerative colitis, represent chronic inflammatory disorders with rising global incidence, underscoring the pivotal role of modifiable environmental factors in disease pathogenesis. Diet and intestinal microbiota have emerged as critical bidirectional therapeutic targets through complex interactions with host immune responses. Epidemiological evidence demonstrates that healthy and high fiber diets reduce disease risk, while ultra-processed foods and inflammatory dietary patterns increase susceptibility. Therapeutic nutritional interventions, including exclusive enteral nutrition, the Crohn’s Disease Exclusion Diet combined with partial enteral nutrition, and the Mediterranean diet can induce and maintain clinical remission while promoting favorable microbiome modifications characterized by the enrichment of butyrate-producing taxa such as Faecalibacterium prausnitzii and Roseburia species, alongside a reduction in pathogenic Proteobacteria. Micronutrient deficiencies affect up to 78% of patients through malabsorption, chronic blood losses, dietary restrictions, and drug–nutrient interactions. Nutritional status significantly impacts surgical outcomes, with preoperative malnutrition and sarcopenia associated with increased postoperative complications, and it reciprocally influences biologic therapy response. Integration of personalized, microbiome-informed dietary strategies as complementary components of comprehensive treatment plans represents a promising therapeutic frontier, requiring multidisciplinary collaboration, rigorous clinical trials with standardized microbiome analyses, and precision nutrition algorithms accounting for disease phenotype, baseline microbial composition, and individual patient characteristics to optimize outcomes and improve quality of life. Full article
(This article belongs to the Special Issue Research on Diagnosis, Treatment and Related Microbiota in Gastrointestinal Diseases)
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Other

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13 pages, 234 KB  
Protocol
Fecal Microbiota Transplantation (FMT) as a Prophylaxis of Necrotizing Enterocolitis (NEC)—Protocol for a Safety Study
by Ewa A. Bieganska, Marek Wolski, Magdalena Zarlenga, Jaroslaw Bilinski and Przemyslaw Kosinski
Pharmaceuticals 2026, 19(3), 437; https://doi.org/10.3390/ph19030437 - 9 Mar 2026
Viewed by 521
Abstract
Background/Objectives: Necrotizing enterocolitis (NEC) is an inflammatory disease with an incidence of about one in 1000 live births, much higher in premature and low birth weight newborns. Intestinal dysbiosis is an important element in the pathogenesis of NEC, and for this reason, [...] Read more.
Background/Objectives: Necrotizing enterocolitis (NEC) is an inflammatory disease with an incidence of about one in 1000 live births, much higher in premature and low birth weight newborns. Intestinal dysbiosis is an important element in the pathogenesis of NEC, and for this reason, experimental models have been used to administer fecal microbiota transplants (FMTs) for prophylaxis and treatment of NEC with very satisfactory results. The primary endpoint of the study is safety, defined as the incidence of adverse events (AEs) and serious adverse events (SAEs) occurring from the time of intervention until hospital discharge, classified according to severity and assessed for relatedness to the intervention. Methods: This prospective, single-arm, open-label clinical study will include 20 infants born between 24 0/7 and 36 6/7 weeks of gestation. FMTs will be administered twice as a deep rectal infusion via a Foley catheter. The donors of the material from which the FMT will be prepared will be women in the third trimester of pregnancy. The safety of the therapy will be assessed by comparison with a control group, i.e., 20 patients who will meet the same inclusion criteria and will not meet any of the exclusion criteria, subject to the same hospital observation but without undergoing any medical/therapeutic intervention other than the collection of biological material. Discussion: The study will provide data on the safety and initial efficacy of FMT in this group of patients, which will allow for further research into the use of this method in the prevention of infections and NEC. Ethics: The study protocol was approved by the Bioethics Committee of the Medical University of Warsaw, Warsaw, Poland (KB/52/2025). All procedures will follow the principles of the Declaration of Helsinki. The results of the study will be submitted for knowledge translation in peer-reviewed journals and presented at national and international pediatric society conferences. Clinical Trial Registration: The study is registered at ClinicalTrials.gov: ID: NCT06333405. Full article
(This article belongs to the Special Issue Research on Diagnosis, Treatment and Related Microbiota in Gastrointestinal Diseases)
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