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Metatranscriptomics Sequencing Service

Reveal Microbial Dynamics with Gene Expression Profiling

Universal rRNA Depletion

Universal rRNA Depletion

Deplete host and bacterial ribosomal RNA (rRNA) from any sample type

Extreme Flexibility

Extreme Flexibility

Comprehensive gene expression analysis

Microbiome Master

Microbiome Master

Detect RNA from any kingdom (Bacteria, Archaea, Eukarya, and viruses)

High quality RNA from any sample type using unbiased mechanical lysis

Fragment size distribution and RIN score of RNA extracted using ZymoBIOMICS MagBead RNA Kit (R2137) or ZymoBIOMICS RNA Miniprep Kit (R2001).

Chart displaying high quality RNA

More relevant data with universal rRNA depletion

Ribosomal RNA depletion and RNA library prep was performed on ZymoBIOMICS Community Standard (D6300) and Fecal Reference Material (D6323) using Zymo-Seq RiboFree Total RNA Library Kit (R3000).

Chart displaying rRNA depletion

User-Friendly and Custom Bioinformatic Report Enables Actionable Insight

custom reports
Zymo Research has a dedicated team of experts excelling in creating user-friendly and custom bioinformatic reports. We ensure the data is presented in a clear and understandable format, tailored to the clients needs.

Metabolic Pathway and Gene Expression Analysis

Chart displaying gene analysis
The metabolic pathway profiling heatmap offers a visual representation of the abundance patterns of functional pathways across samples. Additionally, through hierarchical clustering organization, the report reveals samples with potential associations among functionally related pathways.

Multi-Kingdom Taxonomy Identification

Reveal Microbial Dynamics with Gene Expression Profiling









The Zymo Research database contains over 77,000 reference strains across all kingdoms (Bacteria, Archaea, Eukaryote and DNA Viruses). Proprietary algorithm eliminates the risks of false positives in taxonomy assignment.

Metatranscriptomics Sequencing Made Simple

How our Straightforward, User-Friendly Service Works

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Inquire Below

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Send Us Your Samples

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Receive A User-Friendly
Analysis Report

Multiple Payment Options Available

Trusted By Leading Institutions

We are honored to have collaborated and provided next-generation analysis services with the most prestigious institutions, agencies and companies in the world.

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  • Beckman Logo
  • Calysta Logo
  • Dana-Farber Logo
  • Forsyth Logo
  • Fred Hutchinson Logo
  • Harvard Logo
  • Johns Hopkins Logo
  • Massachusetts General Hospital Logo
  • Nestle Purina Logo
  • National Institutes of Health Logo
  • National Oceanic and Atmospheric Administration Logo
  • Novogene Logo
  • P & G Logo
  • Platiunum Performance Logo
  • Prolacta Bioscience Logo
  • USDA Logo

Technical Specifications

Sequencing Platform Illumina NovaSeq X™ 10B or 25B Reagent kit (2x150bp)
Sample Collection

Raw Sample

Various sample collection devices provided upon request

RNA sample

>10 ng/µl (by Fluorescence RNA quantification) with RIN score >7

Please ensure it is PCR inhibitor-free.

RNA Extraction
ZymoBIOMICS 96 Magbead RNA (R2137)
ZymoBIOMICS RNA Miniprep (R2001)
Library Prep
Zymo-Seq RiboFree Total RNA Library Kit (R3003)
Unique Dual Index (UDI)
Quality Control A positive control for RNA extraction (ZymoBIOMICS Microbial Community Standard, D6300) is included in each project as a quality control, without additional charge. Negative extraction controls and negative PCR controls are monitored and can be sequenced upon request.
Sequencing Analysis Kmer signature-based analysis using Sourmash with antimicrobial resistance using Diamond and functional pathway analysis using Humann3
Taxonomy Resolution
Bacteria and Archaea: strain-level
Fungi and Viruses: species-level
Reference Database Full GTDB database (R07-RS207) was used for bacterial and archaeal identification. Pre-formatted GenBank databases (v2022.03) provided by Sourmash were used for virus, protozoa, and fungi identification
Data Analysis

Taxonomy Profiling

Taxa abundance bar plot and heatmap

Alpha diversity boxplot

Various sample collection devices provided upon request

RNA sample

Antibiotics resistance identification

Virulence gene identification

Gene family profiling (UniRef)

Metabolic pathway profiling (MetaCyc)

Statistical Analysis LEfSe analysis uncovers taxa/traits that are differentially distributed among defined sample groups.
Example Report Our Sample Report can be viewed here.
Data Storage Raw sequencing data and analysis report are stored for up to 3 months.

Frequently Asked Questions

There is no sample minimum required in order to submit to our Metatranscriptomics Sequencing Service.

We recommend sending 200-500 mg for solid samples or 10-15mL of liquid samples in general. This may vary depending on the specific sample type.

The minimum volume of DNA required is 50 µl with a recommended concentration of 10-50 ng/µl. If the concentration is lower, we can often still successfully sequence as our pipeline is quite robust.

We have processed a wide variety of sample types, from human tissue samples, environmental samples, to food samples. If you have questions or concerns, please feel free to fill out an inquiry or contact us.

Because of our included quality control standard, it is possible to batch samples over time and have confidence that the samples were processed in the same way. We recently completed a project that had a total of >2,000 samples processed over a period of 6 months. By comparing the results from the standard for each group of samples, we had confidence that the results from different batches could be compared together.

Tell Us About Your Service Project

Please describe your project, and one of our scientists will be in touch to assist you.

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Why Partnering with Zymo Research for Microbiome Applications is Your Key to Success.

Metatranscriptomics has emerged as a powerful approach to unravel the functional dynamics of complex microbial communities. By capturing real-time gene expression patterns, metatranscriptomic sequencing offers unprecedented insights into microbial activities and ecological functions. At Zymo Research, we've harnessed this cutting-edge technique to provide a comprehensive metatranscriptomic sequencing service, revolutionizing microbiome analysis.

The metatranscriptomic sequencing workflow begins with sample collection, ensuring the preservation of microbial profiles. Total RNA isolation, rRNA depletion, library preparation, and high-throughput sequencing follow, each step optimized and validated to minimize bias and ensure accurate results. With stringent quality control measures in place, we guarantee the reliability of our data, empowering researchers with trustworthy insights.

Zymo Research's legacy in microbiome research is built on innovative products designed to meet the unique needs of researchers. Our DNA/RNA Shield ensures unbiased sample collection, while our ZymoBIOMICS RNA kits enable unbiased lysis. These products, coupled with our microbiome standards, ensure superior process quality control, laying the foundation for our metatranscriptomic sequencing service.

Central to our metatranscriptomic sequencing service is a comprehensive and user-friendly bioinformatics report. This report includes strain-level taxonomy profiling, metabolic gene family and pathway profiling, virulence gene and antibiotic resistance gene identification, and statistical analysis. Our advanced taxonomy assignment algorithm minimizes false positives, enhancing the accuracy of microbial identification.

The applications of metatranscriptome sequencing are vast and impactful. In microbial ecology research, it aids in characterizing functionally active bacteria and elucidating community metabolic interactions. In clinical research, it uncovers immune responses and autoimmune processes, while also offering insights into innovative drug delivery resources. Additionally, it improves food quality by providing data on microbial metabolic behaviors, paving the way for safer and healthier food products.

Zymo Research's metatranscriptomic sequencing service represents a leap forward in microbiome analysis. With a robust workflow, innovative products, and comprehensive bioinformatics analysis, we empower researchers to unlock the functional mysteries of microbial communities. From environmental studies to clinical applications, metatranscriptomic sequencing holds the key to transformative discoveries, and Zymo Research is at the forefront of this revolution.

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