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Related Concept Videos

Introduction to the Human Microbiota01:22

Introduction to the Human Microbiota

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, and disease...
Development of Human Microbiota01:30

Development of Human Microbiota

The human microbiota begins developing at birth and undergoes continual change as we age. Infancy marks a critical period of microbial sensitivity, offering a “window of opportunity” during which beneficial microbes help mature the immune system. By age three, children typically develop a more stable and diverse microbial community. Newborns acquire microbes from their immediate environment; vaginal delivery favors maternal vaginal microbes, while cesarean births favor microbes from the skin...
The Oral Microbiota01:27

The Oral Microbiota

The oral microbiome includes a complex ecosystem comprising over 700 microbial species, identified through genomic sequencing and culture-based analyses to date. This community includes a core microbiome, found universally among individuals, and a variable component influenced by environmental factors such as diet, lifestyle, and host genetics. Site-specific conditions, including oxygen gradients, pH levels, and nutrient availability, determine the spatial distribution of these microorganisms...
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Microbiota of the Stomach and Small Intestine

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,...
Microbiota of the Large Intestine01:27

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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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Updated: Jun 13, 2026

Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging
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A multi-omics spatial framework for host-microbiome dissection within the intestinal tissue microenvironment.

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

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

Nature Communications
|January 31, 2025
PubMed
Summary
This summary is machine-generated.

Microbiome Cartography (MicroCart) offers a new way to study host-microbiome interactions in situ. This spatial multi-omics framework reveals dynamic immune and microbial shifts during intestinal inflammation.

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Area of Science:

  • Microbiome research
  • Host-microbiome interactions
  • Spatial multi-omics

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 interactions is crucial for studying gut health and disease.

Purpose of the Study:

  • Introduce Microbiome Cartography (MicroCart), a novel framework for simultaneous in situ probing of host and microbiome.
  • Enable multi-modal spatial analysis of host-microbiome interplay.
  • Investigate host and microbiome changes in a murine colitis model.

Main Methods:

  • Developed Microbiome Cartography (MicroCart) for simultaneous in situ spatial multi-omics.
  • Applied MicroCart using spatial proteomics, transcriptomics, and glycomics.
  • Studied a murine colitis model to analyze gut host and microbiome alterations.

Main Results:

  • Demonstrated MicroCart's capability for simultaneous in situ host and microbiome analysis.
  • Revealed systematic tissue immune response transformations during colitis.
  • Observed bacterial population shifts, localized inflammation, and metabolic alterations.

Conclusions:

  • MicroCart provides a powerful tool for deep, spatially resolved investigation of host-microbiome interactions.
  • The framework enables comprehensive analysis of tissue remodeling and cellular responses.
  • Facilitates understanding of the complex interplay between host tissue and microbiome in disease states.