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Related Concept Videos

Introduction to the Human Microbiota01:22

Introduction to the Human Microbiota

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Microorganisms colonize various regions of the human body, including the mouth, nasal passages, throat, stomach, intestines, urogenital tract, and skin. The total number of microbial cells is estimated to range from 10¹³ to 10¹⁴—comparable to, or exceeding, the number of human somatic cells. This host–microbiome relationship has led to the conceptualization of humans as supraorganisms, wherein microbial communities perform vital roles in development, immunity,...
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Microbiota of the Stomach and Small Intestine01:27

Microbiota of the Stomach and Small Intestine

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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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Microbiota of the Large Intestine01:27

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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Inflammatory Bowel Disease II: Ulcerative Colitis01:20

Inflammatory Bowel Disease II: Ulcerative Colitis

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Ulcerative colitis is a chronic inflammatory disorder of the colon characterized by continuous mucosal inflammation that typically begins in the rectum and extends proximally in a uniform pattern. Its pathogenesis involves a complex interplay of genetic predisposition, immune dysregulation, and environmental influences. These factors converge to impair the colon’s epithelial defenses and promote an exaggerated inflammatory response against luminal contents.Breakdown of the Mucosal...
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Inflammatory Bowel Disease III: Crohn's Disease01:25

Inflammatory Bowel Disease III: Crohn's Disease

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Crohn’s disease is a chronic, relapsing form of inflammatory bowel disease characterized by segmental, transmural inflammation that can affect any part of the gastrointestinal tract. Its pathogenesis arises from a combination of genetic susceptibility, environmental exposures, epithelial barrier dysfunction, and immune dysregulation. Together, these factors lead to an exaggerated immune response against components of the gut microbiome.Genetic and Environmental InfluencesMultiple genetic...
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Related Experiment Video

Updated: May 5, 2026

Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging
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A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment.

Bokai Zhu1,2,3, Yunhao Bai2,3, Yao Yu Yeo4

  • 1Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.

Biorxiv : the Preprint Server for Biology
|March 18, 2024
PubMed
Summary
This summary is machine-generated.

Microbiome Cartography (MicroCart) enables simultaneous in situ study of host-microbiome interactions. This new framework reveals dynamic shifts in gut immunity and microbial communities during colitis.

Keywords:
GlycomicsGut MicrobiotaMultiplexed imagingSpatial ProteomicsSpatial TranscriptomicsSystems Immunology

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Last Updated: May 5, 2026

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Area of Science:

  • Microbiome research
  • Host-microbiome interactions
  • Spatial multiomics

Background:

  • Host immune system and microbiome interactions are dynamic and shift with intestinal environment changes.
  • Current in situ methods limit simultaneous, systems-level study of host and microbial communities.
  • Understanding these complex interactions is crucial for disease research.

Approach:

  • Introduced Microbiome Cartography (MicroCart), a novel framework for simultaneous in situ probing of host and microbiome features.
  • Utilized MicroCart with spatial proteomics, transcriptomics, and glycomics platforms.
  • Investigated alterations in gut host and microbiome components in a murine model of colitis.

Key Points:

  • MicroCart enables simultaneous spatial multiomics analysis of host and microbial communities.
  • Demonstrated comprehensive investigation of host and microbiome alterations during colitis.
  • Revealed systematic transformation in tissue immune responses and epithelial cell states.

Conclusions:

  • MicroCart provides deep insights into the interplay between host tissue and its microbiome.
  • Identified localized inflammatory responses and metabolic alterations in the gut microbiome during colitis.
  • Highlights the potential of spatial multiomics for studying host-microbiome dynamics.