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Metatranscriptome Sequencing

Leveraging Illumina sequencing technology, BMKGENE’s metatranscriptome sequencing service unveils the dynamic gene expression of a diverse array of microbes, spanning eukaryotes to prokaryotes and viruses, within natural environments such as soil, water, sea, stool, and the gut. Our comprehensive service empowers researchers to delve into the entirety of gene expression profiles within complex microbial communities. Beyond taxonomic analysis, our metatranscriptome sequencing service facilitates exploration into functional enrichment, shedding light on differentially expressed genes and their roles. Uncover a wealth of biological insights as you navigate the complex landscapes of gene expression, taxonomic diversity, and functional dynamics within these diverse environmental niches.

Service Details


Demo Results

Featured publications

Service Features

● rRNA depletion followed by directional mRNA library preparation.

● Sequencing on Illumina NovaSeq.

Service Advantages

●  Study the changes of complex microbial communities: at the transcriptional level and explore potential new genes.

● Explaining microbial community interactions with the host or environment.

● Comprehensive bioinformatic analysis: providing insights on community taxonomic and functional compositions, as well as differential gene expression analysis.

● Extensive gene annotation: using up-to-date gene function databases for informative gene expression information of microbial communities.

● Post-Sales Support: Our commitment extends beyond project completion with a 3-month after-sale service period. During this time, we offer project follow-up, troubleshooting assistance, and Q&A sessions to address any queries related to the results.

Service Specifications

Sequencing platform

Sequencing Strategy

Data recommended

Data Quality Control

Illumina NovaSeq




Sample Requirements

Concentration (ng/µL)

Total amount (µg)

Volume (µL)








Service Work Flow

sample delivery

Sample delivery

Library Preparation

Library construction



Data analysis

Data analysis

After sale Services

After-sale services

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    Includes the following analysis:

    ●  Sequencing data quality control

    ●  Transcript assembly

    ●  Taxonomic annotation and abundance

    ●  Functional annotation and abundance

    ●  Expression quantification and differential analysis

    Taxonomic distribution of each sample:



    Beta diversity analysis: UPGMA




    Functional annotation – GO abundance



    Differential taxonomy abundance – LEFSE



    Explore the advancements facilitated by BMKGene’s meta transcriptomics sequencing services through a curated collection of publications.

    Lu, Z. et al. (2023) ‘Acid tolerance of lactate-utilizing bacteria of the order Bacteroidales contributes to prevention of ruminal acidosis in goats adapted to a high-concentrate diet’, Animal Nutrition, 14, pp. 130–140. doi: 10.1016/J.ANINU.2023.05.006.

    Song, Z. et al. (2017) ‘Unraveling core functional microbiota in traditional solid-state fermentation by high-throughput amplicons and metatranscriptomics sequencing’, Frontiers in Microbiology, 8(JUL). doi: 10.3389/FMICB.2017.01294/FULL.

    Wang, W. et al. (2022) ‘Novel Mycoviruses Discovered from a Metatranscriptomics Survey of the Phytopathogenic Alternaria Fungus’, Viruses, 14(11), p. 2552. doi: 10.3390/V14112552/S1.

    Wei, J. et al. (2022) ‘Parallel metatranscriptome analysis reveals degradation of plant secondary metabolites by beetles and their gut symbionts’, Molecular Ecology, 31(15), pp. 3999–4016. doi: 10.1111/MEC.16557.

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