MTD

MTD quantifies host and meta-transcriptomes from RNA-seq data to enable integrative analysis of host–microbiota gene expression interactions at tissue and single-cell resolution.

Key Features:

• Simultaneous Quantification: Quantifies both host transcriptomes and meta-transcriptomes from the same RNA-seq sample for joint measurement of gene expression.
• Broad Microbiome Identification: Identifies and quantifies microbial entities including viruses, bacteria, protozoa, fungi, plasmids, and vectors within host-associated RNA-seq data.
• Correlative Analysis: Correlates microbiome activity and microbial gene expression profiles with host transcriptomic responses using statistical analyses.
• Versatile Data Compatibility: Supports analysis of both bulk RNA-seq data and single-cell RNA-seq data for tissue- and single-cell-level investigations.

Scientific Applications:

• Immune Response Dynamics: Characterizes host molecular responses to microbial communities by integrating host and microbial transcriptomes.
• Microbial Community Profiling: Profiles and quantifies diverse microbiome components within host tissues or cells using RNA-seq–derived transcripts.
• Disease Mechanisms: Investigates roles of microbiota in disease progression and host–pathogen interactions through joint host and microbial expression analyses.

Methodology:

Data preprocessing including handling and normalization of raw RNA-seq data; simultaneous transcriptome quantification of host and microbial gene expression; and statistical correlation analysis to relate microbiome activity to host transcriptomic responses.