Metatranscriptome Sequencing

What Is Metatranscriptomics?

Metatranscriptome sequencing is the ultimate solution for answering "How are microorganisms actively behaving?" By analyzing the entire pool of actively expressed RNA (mRNA) in a microbial community, this technology provides a dynamic snapshot of real-time gene expression and functional dynamics.

Why Is Metatranscriptomics Important?

This service reveals which genes are being transcribed under specific conditions, linking the community's genetic potential (DNA) to its functional reality (RNA). It is crucial for understanding host-microbe crosstalk, immediate environmental responses, and active metabolic pathways.

Why choose metatranscriptome sequencing?

Active Functional Insight

Directly quantify active gene expression, moving beyond genetic potential to measure the community's phenotypic response.

Dynamic Data Capture

Obtain a precise snapshot of metabolic activities and stress responses at the moment of sampling.

High Resolution Gene Expression

Generate detailed analysis on the transcription levels of thousands of microbial genes and pathways.

Technical Specifications

RNA sequencing requires meticulous handling and high-depth sequencing. Psomagen uses optimized protocols featuring an advanced depletion strategy that targets rRNA from diverse organisms, including human (cytoplasmic/mitochondrial rRNA, beta-globin), mouse, and rat rRNA, plus diverse microbial species (E. coli, B. subtilis, ATCC standards).

This comprehensive removal of non-target transcripts, combined with the latest Illumina platforms, ensures maximum sensitivity and data quality.

Target Molecule

Total RNA (mRNA after rRNA depletion).

Custom options are available for total RNA, non-coding RNA, and small RNA — book a consultation to learn more.

Sequencing Platform

NovaSeq X Plus

QC Measures

RNA Quantification: assessing RNA concentration as the primary QC method to ensure sufficient input material.
rRNA Depletion: highly abundant ribosomal RNA is removed to maximize sequencing depth on the messenger RNA (mRNA).
Library Preparation: Stranded library preparation maintains directional information of transcripts.

Read Length

2 x 150 bp

Deliverables

Raw FASTQ file

Basic or advanced analysis results

Recommended Depth

Highly dependent on complexity (consultation recommended)

Bioinformatics and Analysis Options

Our bioinformatics pipeline is optimized for handling metatranscriptome complexity, focusing on quantification and statistical significance. We offer three possible deliverables depending on your project's needs:

	File Format	Content
Raw Data	FASTQ	Final sequencing data
Basic Analysis Report	HTML, XLSX	QC statistics (quantification/rRNA depletion) Read mapping stats Gene expression table (raw counts/TPM)
Advanced Analysis Report	HTML, PNG	Differential gene expression (DEG) table Functional pathway analysis (KEGG/COG) Statistical visualization (volcano plots, heatmaps)

Gene Expression Quantification & Functional Annotation

Reads are mapped against microbial functional databases to quantify active gene expression and annotate their functions.

Host Transcript Removal: Host RNA transcripts are meticulously filtered out to ensure accurate focus on microbial activity.
Gene Expression Measurement: Quantifying the expression levels of individual genes across the entire microbial community using RSEM or similar tools.
Functional Annotation: Active transcripts are annotated against major functional databases (e.g., KEGG, COG, Pfam) to reveal the actively utilized metabolic and regulatory pathways.

Differential Gene Expression (DEG) Analysis

This is the core analysis for comparing the functional states of different groups (e.g., treated vs. control, healthy vs. diseased).

Statistical Analysis: Statistical methods and tools (e.g., DESeq2, edgeR) are used to identify genes that are significantly up- or down-regulated between experimental groups.
Key Outputs: Identification of genes and pathways that drive the phenotypic differences between groups.
Visualization: Volcano plots and MA plots are generated to visualize the statistical significance and magnitude of fold-change for thousands of transcripts.

EXPERT SUPPORT FROM START TO FINISH

Book a Consultation

Due to the complexity of RNA stability and statistical analysis in metatranscriptomics, customized consultation is highly recommended. Our experts are ready to assist with experimental design (including RNA preservation methods), complex statistical modeling, and data interpretation.

Reach Out

SERVICES // METAGENOMICS