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Updated: Aug 18, 2025

Mesenchymal Stem Cell Regulation of Macrophage Phagocytosis; Quantitation and Imaging
Published on: July 16, 2021
Gut microbiota promotes stem cell differentiation through macrophage and mesenchymal niches in early postnatal
Ji-Eun Kim1, Bo Li2, Lijiang Fei3
1Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
Insights
Early life gut microbes are crucial for intestinal stem cell development. Disrupting this microbial exposure impairs stem cell differentiation and is linked to necrotizing enterocolitis (NEC), but probiotics can help.
Area of Science:
- Developmental biology
- Microbiology
- Gastroenterology
Background:
- Intestinal stem cell maturation is influenced by gut microbiota after birth.
- Early life microbial disruption can negatively impact intestinal development.
Purpose of the Study:
- To investigate how early life microbial exposure affects the intestinal stem cell niche.
- To understand the mechanisms by which microbiota regulate stem cell differentiation and niche maintenance.
Main Methods:
- Single-cell transcriptional analysis of intestinal cells.
- Mouse genetic models and organoid co-culture experiments.
- Investigating the role of CD206+ macrophages and Wnt ligands.
Main Results:
- Antibiotic treatment in early life impaired Paneth cell differentiation and macrophage specification.
- A CD206+ macrophage subset secreted Wnt ligands, maintaining mesenchymal niche cells for Paneth cell differentiation.
- Lactobacillus colonization or CD206+ macrophage transfer reduced necrotizing enterocolitis (NEC) severity.
Conclusions:
- Gut microbiota critically regulate intestinal stem cell niches during early postnatal development.
- Microbiota-derived signals, particularly from CD206+ macrophages, are essential for Paneth cell differentiation.
- Targeting the microbiota or specific immune cells may offer therapeutic strategies for NEC.
Abstract:
Intestinal stem cell maturation and development coincide with gut microbiota exposure after birth. Here, we investigated how early life microbial exposure, and disruption of this process, impacts the intestinal stem cell niche and development. Single-cell transcriptional analysis revealed impaired stem cell differentiation into Paneth cells and macrophage specification upon antibiotic treatment in early life. Mouse genetic and organoid co-culture experiments demonstrated that a CD206+ subset of intestinal macrophages secreted Wnt ligands, which maintained the mesenchymal niche cells important for Paneth cell differentiation. Antibiotics and reduced numbers of Paneth cells are associated with the deadly infant disease, necrotizing enterocolitis (NEC). We showed that colonization with Lactobacillus or transfer of CD206+ macrophages promoted Paneth cell differentiation and reduced NEC severity. Together, our work defines the gut microbiota-mediated regulation of stem cell niches during early postnatal development.
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