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Simultaneous profiling of host expression and microbial abundance by spatial metatranscriptome sequencing
1Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
Genome Research
|June 13, 2023
Summary
We created a spatial metatranscriptome (SMT) pipeline to analyze microbial and host gene expression in tissues. This method reveals spatial host-microbe interactions, advancing spatial biology and microbiome research.
Area of Science:
- Microbiome research
- Spatial biology
- Transcriptomics
Background:
- Spatial transcriptomic (ST) data typically focuses on host gene expression.
- Understanding the spatial distribution of microbes within host tissues is crucial for studying host-microbe interactions.
- Current methods lack the ability to simultaneously analyze host and microbial spatial information.
Purpose of the Study:
- To develop and validate a computational pipeline for extracting and analyzing microbial sequences from ST data.
- To enable simultaneous analysis of host gene expression and microbial abundance in a spatial context.
- To investigate host-microbe interactions at various spatial scales within tissues.
Main Methods:
- Developed the spatial metatranscriptome (SMT) analysis pipeline to extract microbial sequences and assign taxonomic labels from ST data.
- Generated a spatial microbial abundance matrix alongside the host expression matrix.
- Applied the SMT pipeline to human and murine intestinal sections and validated results with alternative assays.
Main Results:
- Successfully generated spatial microbial abundance matrices, enabling simultaneous analysis of host expression and microbial distribution.
- Validated the accuracy of spatial microbial abundance data using independent experimental methods.
- Identified novel biological insights into host-microbe interactions across different spatial scales.
- Optimized experimental conditions to enhance microbial capture while maintaining host expression quality.
Conclusions:
- The spatial metatranscriptome (SMT) pipeline is a feasible method for analyzing microbial and host spatial data.
- SMT analysis opens new avenues for investigating host-microbe interactions in situ.
- This work provides a foundation for further optimization and application of spatial microbiome analysis in biological research.
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