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.

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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

NextSeq 550 System

Combine proven NGS technology with tunable output to enable sequencing and array capabilities across a range of applications.

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.

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Metatranscriptome FAQs

Metagenomics is the study of all the genes found within a microbial population sample.5 In contrast, metatranscriptomics is the study of expressed genes, or the transcriptome, of a population.1

/ Results

16S rRNA sequencing is a specific method that targets the 16S rRNA gene, which is only found in prokaryotes (ie, bacteria and archaea).6 Unlike metatranscriptomics or metagenomics, 16S rRNA sequencing cannot detect other microbes such as viruses and fungi. Although this method is not as susceptible to host DNA contamination, it is limited in detecting functional information and identifying strains/variants compared to metatranscriptomic or metagenomic sequencing methods.

/ Results

RNA extraction can be achieved using commercially available microbiome RNA extraction kits that provide an RNA Integrity Number (RIN) that's greater than or equal to 5.

/ Results

The BaseSpace Microbiome Metatranscriptomics app is included with the Ribo-Zero Plus Microbiome Depletion Kit and offers bioinformatics tools to perform comprehensive metatranscriptome analyses.

/ Results

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.

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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.