Microbial Genomics
    • Microbial Genomics

    Metatranscriptome sequencing

    Unraveling gene expression in microbial populations with the power of NGS 

    What is metatranscriptomics?

    Metatranscriptomics is the collective study of expressed mRNA from complex microbial communities.1 Using metatranscriptome sequencing to study gene expression in a microbial population, researchers can gain important insights on how microbes respond to a given environment at a specific time. Sequencing RNA from microbiomes can reveal not only which microbes are present, but also their functional activities.

    sequencing library prep

    Discover the potential of community-level transcriptional information

    Powered by next-generation sequencing (NGS) technologies, metatranscriptomics is a research field that spans diverse applications in agriculture, biotechnology, medicine, and more.1-4 In addition to providing data about a complex microbial community’s behavior and function, metatranscriptome sequencing can also provide valuable information about the community's environment or host.

    Given the vast number (millions) of genes whose regulatory systems are not yet understood, metatranscriptomics is poised to make critical biological insights at the community level from native environments.

    NGS Workflow Finder

    Take the guesswork out of your next workflow. The NGS Workflow Finder provides personalized solution recommendations and resources so you can sequence with confidence.

    Find your NGS workflow today

    Featured webinars

    Microbial profiling with metatranscriptomics

    See how Diversigen and DNA Genotek scientists developed workflows for metatranscriptomic studies and read their views about this research area’s potentially impactful future.

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    Featured metatranscriptomic applications and publications

    Uncovering RNA virus diversity

    Explore the role metatranscriptomics played in revealing what turned out to be a stunningly vast world for RNA viruses.

    SARS-CoV-2 and the microbiome

    Read how scientists used metatranscriptomics to detect, track, and identify biomarkers of SARS-CoV-2 and how the virus can affect the respiratory microbiome.

    Metatranscriptome sequencing workflow

    1
    Prep

    Illumina Stranded Total RNA Prep with Ligation, Ribo-Zero Plus Microbiome

    Streamlined RNA-Seq solution for clear and comprehensive analysis across the coding and non-coding transcriptome with exceptional study flexibility.

    2
    Sequence

    MiSeq i100 Series

    Our fastest, simplest benchtop system for metatranscriptomics research.

    NextSeq 1000 and 2000 Systems

    Empower discoveries with a comprehensive workflow from start to finish.

    NovaSeq X Series

    Achieve extraordinary throughput and accuracy to perform data-intensive applications at production scale.

    3
    Analyze

    BaseSpace Microbiome Metatranscriptomics

    Perform taxonomic and pathway enrichment analysis on metagenomic samples. 

    Ribosomal RNA depletion for metatranscriptomic studies

    Learn how to optimize an RNA sequencing workflow for complex microbial samples, with details on library preparation, sequencing, and using an intuitive software for metatranscriptomic analysis with Illumina Ribo-Zero Plus Microbiome. Download this application note and begin focusing on high-value portions of the transcriptome to understand the role of the microbiome in health and disease.

    Download app note

    Metatranscriptome FAQs

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    Microbiome studies and the impact on biotechnology

    Read how whole-genome shotgun sequencing and transcriptomics provide researchers with data to refine drug discovery and development.

    Read customer interview

    Speak to a specialist

    Questions on starting metatranscriptomics studies in your lab?

    References

    1. Mukherjee A, Reddy MS. Metatranscriptomics: an approach for retrieving novel eukaryotic genes from polluted and related environments. 3 Biotech. 2020; 10(2). doi: 10.1007/s13205-020-2057-1. 
    2. Sharuddin SS, Ramli N, Yusoff MZM, et al. Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review. Int J Mol Sci. 2022; 23(7). doi: 10.3390/ijms23073737.
    3. de Vos WM, Tilg H, Van Hul M, et al. Gut microbiome and health: mechanistic insights. Gut. 2022; 71(5). doi: 10.1136/gutjnl-2021-326789.
    4. Saarenpää S, Shalev O, Ashkenazy H, et al. Spatial metatranscriptomics resolves host-bacteria-fungi interactomes. Nat Biotechnol. 2023 Nov 20. doi: 10.1038/s41587-023-01979-2.
    5. Metagenomics. National Human Genome Institute. genome.gov/genetics-glossary/Metagenomics. Accessed July 12, 2024.
    6. Janda JM, Abbott SL. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J Clin Microbiol. 2007 Sep;45(9):2761-4. doi: 10.1128/JCM.01228-07.