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Intestinal 3D Culture, Organoids and Gut-on-Chip in Intestinal Disorders

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: 20 February 2026 | Viewed by 3406

Special Issue Editors


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Guest Editor
Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
Interests: inflammatory bowel disease; phytochemicals; prebiotics; probiotics; small molecules; gut–brain axis; enteric glial network; pharmacological approaches; obesity; intestinal organoids
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
Interests: inflammatory bowel diseases; inflammation; intestinal functional disorders; animal models; gut–brain axis; obesity; patients
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Three-dimensional (3D) culture systems, including relatively simple cell aggregates (spheroids) and increasingly functional organ-like or organotypic microtissues (organoids and tissue-on-a-chip), have recently garnered significant attention because they often promote levels of cell differentiation and tissue organization not possible in conventional 2D culture systems. Indeed, 3D cultures represent an ideal model for studying the pathophysiological mechanisms underlying the intestinal functional diseases and inflammatory diseases—including inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), obesity, and colorectal cancer—and for testing new drugs. The application of these innovative techniques will provide a great advances in human medicine, contributing to the identification of new molecular targets and personalized medicine.

On these bases, this Special Issue, entitled “Intestinal 3D Culture, Organoids and Gut-on-Chip in Intestinal Disorders”, invites researchers to contribute original research articles, review articles, and short communications related to current knowledge on 3D culture systems used , both technically and scientifically in this research field.

Dr. Vanessa D’Antongiovanni
Dr. Carolina Pellegrini
Guest Editors

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Keywords

  • 3D cultures
  • gut-on-chip
  • intestinal organoids
  • spheroids
  • organotypic cultures
  • morphological studies
  • pharmacological studies
  • intestinal cancer
  • inflammatory bowel disease
  • intestinal functional disorders

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Published Papers (2 papers)

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19 pages, 4142 KB  
Article
Development of Sheep Duodenum Intestinal Organoids and Implementation of High-Throughput Screening Platform for Veterinary Applications
by Giulio Galli, Estela Melcón-Fernández, María Gracia de Garnica García, Beatriz Martínez-Fernández, Mahsa Dehnavi, Sonia Andrés, Yolanda Pérez-Pertejo, Rosa M. Reguera, Carlos García-Estrada, María Martínez-Valladares and Rafael Balaña-Fouce
Int. J. Mol. Sci. 2025, 26(7), 3452; https://doi.org/10.3390/ijms26073452 - 7 Apr 2025
Cited by 4 | Viewed by 2092
Abstract
New therapeutic molecules for farm animals are needed to address worldwide problems in the food industry, like the rise of resistance among ruminant parasites and pathogenic microbes. Since in vivo testing would involve an excessive number of animals, with consequent ethical and economic [...] Read more.
New therapeutic molecules for farm animals are needed to address worldwide problems in the food industry, like the rise of resistance among ruminant parasites and pathogenic microbes. Since in vivo testing would involve an excessive number of animals, with consequent ethical and economic issues, the generation of sheep intestinal organoids represents a promising close-to-reality in vitro model for veterinary drug development; however, the characterization and application of such organoids remain limited. In this study, ovine intestinal organoids were generated from adult LGR5+ stem cells from the intestinal crypts of freshly slaughtered lambs, and developed in an in vitro culture system. Morphological analysis via brightfield microscopy and immunocytochemical staining revealed a pseudostratified epithelium with multiple cell types, and distinct apical–basal polarity, while RNA sequencing validated the preservation of the physiological characteristics of the original organ. The development and characterization of a robust and reproducible protocol for culturing sheep duodenum intestinal organoids in a high-throughput screening (HTS) compatible format demonstrated reliability in HTS applications, with Z’-factor tests indicating robust assay performance. Dose–response studies using pre-identified compounds showed comparable pharmacodynamic profiles between mouse and sheep organoids. These findings establish sheep intestinal organoids as an innovative tool for veterinary pharmacology and toxicology, offering a cost-effective and sustainable platform to address challenges such as drug resistance and improve livestock health. Full article
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13 pages, 2576 KB  
Brief Report
An Ovine Intestinal Organoid–Macrophage Co-Culture Model to Test the Effects of Ovine Colostrum Exosomes on Intestinal Barrier Function and Inflammation
by Mahsa Dehnavi, Giulio Galli, Carlos García-Estrada, Rafael Balaña-Fouce, F. Javier Giráldez, Mercedes Alonso, Nuria Santos, Fernando Rozada and Sonia Andrés
Int. J. Mol. Sci. 2025, 26(23), 11406; https://doi.org/10.3390/ijms262311406 - 25 Nov 2025
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Abstract
Ovine colostrum exosomes obtained from nutritionally programmed dairy ewes (F0) may present modifications in microRNAs, thus having consequences for the intestinal barrier function and immunity parameters of lambs (F1). To test this hypothesis, colostrum exosomes from two ewe groups [F0-MET (nutritionally programmed ewes [...] Read more.
Ovine colostrum exosomes obtained from nutritionally programmed dairy ewes (F0) may present modifications in microRNAs, thus having consequences for the intestinal barrier function and immunity parameters of lambs (F1). To test this hypothesis, colostrum exosomes from two ewe groups [F0-MET (nutritionally programmed ewes being fed methionine during early life) and F0-CTRL (ewes not supplemented with methionine during early life)] were sequenced to compare differences in the miRNAome. In addition, these exosomes were added to an in vitro co-culture in a Transwell chamber system consisting of ovine duodenum intestinal organoids and macrophages to assess the expression of genes encoding tight junction proteins in organoids and immunity parameters in macrophages. Finally, the concentrations of cytokines (e.g., IL-12 and IL-6) were assessed by ELISA kits in the supernatants of the chamber containing macrophages. According to the miRNAome, the expression of two miRNAs (e.g., oar_miR_376c_3p and oar_miR_432) was reduced in the colostrum exosomes obtained from dairy ewes nutritionally programmed with dietary supplementation of methionine during early life (F0-MET ewes). These changes did not seem to modify the expression of intestinal barrier and immune response marker genes when these exosomes were added to a co-culture of ovine intestinal organoids and macrophages. However, the levels of IL-12 produced by macrophages were reduced (p < 0.05), which suggests the inhibition of inflammatory pathways. Further studies using ovine colostrum exosomes obtained from nutritionally programmed ewes will help to clarify their potential to improve the health of suckling lambs. Full article
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