Cellular landscape of avian intestinal organoids revealed by single cell transcriptomics

Jianxuan Sun; Dominika Borowska; James Furniss; Kate Sutton; Dan Macqueen; Lonneke Vervelde

doi:10.1038/s41598-025-95721-4

Cellular landscape of avian intestinal organoids revealed by single cell transcriptomics

Jianxuan Sun, Dominika Borowska, James Furniss, Kate Sutton, Dan Macqueen, Lonneke Vervelde

Research output: Contribution to journal › Article › peer-review

Abstract

Studies of the avian gastrointestinal tract, where nutrient absorption and key host-pathogen
interactions occur, have been strongly enabled by the development of intestinal organoid models. Here we report a single cell transcriptomic atlas of intestinal organoid cells derived from embryos of broiler and layer chickens, capturing mesenchymal, epithelial, endothelial, immune and neuronal cell lineages. Eight inferred mesenchymal subpopulations reflect anatomically distinct intestinal layers, including fibroblasts, telocytes, myofibroblasts, smooth myocytes, pericytes, and interstitial cells of Cajal. Identified heterogeneity within the epithelial lineage included enterocytes, goblet cells, Paneth cells, tuft cells, and diverse enteroendocrine cell subtypes. Additionally, we identified candidate macrophages, monocytes, γδ T cells, NK cells and granulocytes. Layer and broiler organoids showed significant differences in cell-specific transcriptome, most pronounced in epithelial cells, pointing to divergent selection on intestinal physiology. Our analysis finally provides a catalogue of novel cell marker genes to enable future research of chicken intestinal organoids.

Original language	English
Article number	11362
Pages (from-to)	1-17
Number of pages	17
Journal	Scientific Reports
Volume	15
Issue number	1
Early online date	2 Apr 2025
DOIs	https://doi.org/10.1038/s41598-025-95721-4
Publication status	Published - Dec 2025

Keywords / Materials (for Non-textual outputs)

Animals
Cell Lineage
Chick Embryo
Chickens/genetics
Gene Expression Profiling
Intestinal Mucosa/metabolism
Intestines/cytology
Organoids/cytology
Single-Cell Analysis/methods
Transcriptome

Access to Document

10.1038/s41598-025-95721-4

s41598-025-95721-4Final published version, 8.52 MBLicence: Creative Commons: Attribution (CC-BY)

Defining genome activity
Headon, D. (Principal Investigator)
1/04/23 → 31/03/28
Project: Research
ISP 1 2023/28 Genes & Traits for Healthy Animals
Headon, D. (Principal Investigator)
1/04/23 → 31/03/28
Project: Research
Understanding the origins of animal phenotypes
Headon, D. (Principal Investigator)
1/04/23 → 31/03/28
Project: Research

Genomics Platform
Furniss, J. (Manager)
Royal (Dick) School of Veterinary Studies
Facility/equipment: Facility

Cite this

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title = "Cellular landscape of avian intestinal organoids revealed by single cell transcriptomics",

abstract = "Studies of the avian gastrointestinal tract, where nutrient absorption and key host-pathogen interactions occur, have been strongly enabled by the development of intestinal organoid models. Here we report a single cell transcriptomic atlas of intestinal organoid cells derived from embryos of broiler and layer chickens, capturing mesenchymal, epithelial, endothelial, immune and neuronal cell lineages. Eight inferred mesenchymal subpopulations reflect anatomically distinct intestinal layers, including fibroblasts, telocytes, myofibroblasts, smooth myocytes, pericytes, and interstitial cells of Cajal. Identified heterogeneity within the epithelial lineage included enterocytes, goblet cells, Paneth cells, tuft cells, and diverse enteroendocrine cell subtypes. Additionally, we identified candidate macrophages, monocytes, γδ T cells, NK cells and granulocytes. Layer and broiler organoids showed significant differences in cell-specific transcriptome, most pronounced in epithelial cells, pointing to divergent selection on intestinal physiology. Our analysis finally provides a catalogue of novel cell marker genes to enable future research of chicken intestinal organoids.",

keywords = "Animals, Cell Lineage, Chick Embryo, Chickens/genetics, Gene Expression Profiling, Intestinal Mucosa/metabolism, Intestines/cytology, Organoids/cytology, Single-Cell Analysis/methods, Transcriptome",

author = "Jianxuan Sun and Dominika Borowska and James Furniss and Kate Sutton and Dan Macqueen and Lonneke Vervelde",

year = "2025",

month = dec,

doi = "10.1038/s41598-025-95721-4",

language = "English",

volume = "15",

pages = "1--17",

journal = "Scientific Reports",

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T1 - Cellular landscape of avian intestinal organoids revealed by single cell transcriptomics

AU - Sun, Jianxuan

AU - Borowska, Dominika

AU - Furniss, James

AU - Sutton, Kate

AU - Macqueen, Dan

AU - Vervelde, Lonneke

PY - 2025/12

Y1 - 2025/12

N2 - Studies of the avian gastrointestinal tract, where nutrient absorption and key host-pathogen interactions occur, have been strongly enabled by the development of intestinal organoid models. Here we report a single cell transcriptomic atlas of intestinal organoid cells derived from embryos of broiler and layer chickens, capturing mesenchymal, epithelial, endothelial, immune and neuronal cell lineages. Eight inferred mesenchymal subpopulations reflect anatomically distinct intestinal layers, including fibroblasts, telocytes, myofibroblasts, smooth myocytes, pericytes, and interstitial cells of Cajal. Identified heterogeneity within the epithelial lineage included enterocytes, goblet cells, Paneth cells, tuft cells, and diverse enteroendocrine cell subtypes. Additionally, we identified candidate macrophages, monocytes, γδ T cells, NK cells and granulocytes. Layer and broiler organoids showed significant differences in cell-specific transcriptome, most pronounced in epithelial cells, pointing to divergent selection on intestinal physiology. Our analysis finally provides a catalogue of novel cell marker genes to enable future research of chicken intestinal organoids.

AB - Studies of the avian gastrointestinal tract, where nutrient absorption and key host-pathogen interactions occur, have been strongly enabled by the development of intestinal organoid models. Here we report a single cell transcriptomic atlas of intestinal organoid cells derived from embryos of broiler and layer chickens, capturing mesenchymal, epithelial, endothelial, immune and neuronal cell lineages. Eight inferred mesenchymal subpopulations reflect anatomically distinct intestinal layers, including fibroblasts, telocytes, myofibroblasts, smooth myocytes, pericytes, and interstitial cells of Cajal. Identified heterogeneity within the epithelial lineage included enterocytes, goblet cells, Paneth cells, tuft cells, and diverse enteroendocrine cell subtypes. Additionally, we identified candidate macrophages, monocytes, γδ T cells, NK cells and granulocytes. Layer and broiler organoids showed significant differences in cell-specific transcriptome, most pronounced in epithelial cells, pointing to divergent selection on intestinal physiology. Our analysis finally provides a catalogue of novel cell marker genes to enable future research of chicken intestinal organoids.

KW - Animals

KW - Cell Lineage

KW - Chick Embryo

KW - Chickens/genetics

KW - Gene Expression Profiling

KW - Intestinal Mucosa/metabolism

KW - Intestines/cytology

KW - Organoids/cytology

KW - Single-Cell Analysis/methods

KW - Transcriptome

U2 - 10.1038/s41598-025-95721-4

DO - 10.1038/s41598-025-95721-4

M3 - Article

C2 - 40175530

SN - 2045-2322

VL - 15

SP - 1

EP - 17

JO - Scientific Reports

JF - Scientific Reports

IS - 1

M1 - 11362

ER -

Cellular landscape of avian intestinal organoids revealed by single cell transcriptomics

Abstract

Keywords / Materials (for Non-textual outputs)

Access to Document

Fingerprint

Projects

Defining genome activity

ISP 1 2023/28 Genes & Traits for Healthy Animals

Understanding the origins of animal phenotypes

Equipment

Genomics Platform

Cite this