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  3. A Multi-omics Spatial Framework For Host-microbiome Dissection Within The Intestinal Tissue Microenvironment.
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  3. A Multi-omics Spatial Framework For Host-microbiome Dissection Within The Intestinal Tissue Microenvironment.

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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

View abstract on 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.