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Microbiota of the Large Intestine

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The large intestine hosts the most densely populated microbial ecosystem in the human body. This complex community primarily consists of anaerobic bacteria, with Bacillota (formerly Firmicutes) and Bacteroidota (formerly Bacteroidetes) as the predominant groups. The distribution of these microbes varies along different sections of the large intestine, influenced by local environmental factors such as oxygen availability and nutrient composition.The cecum, located at the beginning of the large...

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The human gastrointestinal (GI) tract is characterized by distinct physicochemical conditions that shape its microbial communities. Among these, the stomach presents a particularly challenging environment for microbial colonization due to its highly acidic pH, ranging from 1 to 3. This extreme acidity effectively limits microbial density. However, certain acid-tolerant microorganisms are capable of surviving in this niche. Notably, Helicobacter pylori can colonize the gastric mucosa,...

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Related Experiment Video

Updated: May 22, 2026

Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging

Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging

Published on: July 9, 2021

A crypt-specific core microbiota resides in the mouse colon.

Thierry Pédron¹, Céline Mulet, Catherine Dauga

¹Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, Paris, France.

|May 24, 2012

Summary

The mouse colon and cecum crypts harbor a unique aerobic microbiota, termed crypt-specific core microbiota (CSCM). This CSCM may play protective and homeostatic roles in the gut, offering a reference for future studies.

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Three-Dimensional Culture of Murine Colonic Crypts to Study Intestinal Stem Cell Function Ex Vivo

Three-Dimensional Culture of Murine Colonic Crypts to Study Intestinal Stem Cell Function Ex Vivo

Published on: October 11, 2022

Area of Science:

Microbiology
Gastroenterology
Molecular Diagnostics

Background:

The gut microbiota influences epithelial regeneration, a critical process for gastrointestinal health.
Understanding the specific microbial communities within functional gut niches is essential for host-microbiota interaction studies.
Previous research has characterized the luminal microbiome, but niche-specific microbial compositions remain less understood.

Purpose of the Study:

To investigate the microbial content of functionally critical niches in the mouse gastrointestinal tract, specifically the crypts housing intestinal stem cells.
To identify bacteria involved in gut microbiota cross-talk related to epithelial regeneration.
To compare the composition and quantity of crypt-associated microbiota with its luminal counterpart.

Main Methods:

Molecular microbial diagnostics were employed to analyze the microbial content of mouse gastrointestinal crypts.
Focus was placed on cecal and colonic crypts, known sites of epithelial renewal.
Comparative analysis was performed regardless of mouse line and breeding origin.

Main Results:

Only cecal and colonic crypts were found to harbor resident microbiota in mice.
The bacterial population within these crypts was unexpectedly dominated by aerobic genera.
This identified microbiota, termed crypt-specific core microbiota (CSCM), resembles that found in invertebrate midguts.

Conclusions:

The presence of CSCM in mouse colonic crypts may indicate a coevolutionary process under selective conditions.
CSCM could potentially serve protective and homeostatic functions within the colon.
This study provides a cultivable reference microbiota for future research on crypt-specific microbial roles.