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.

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.

Featured webinars

Metatranscriptomic analysis of the skin and gut microbiomes

Discussion of the shift from using metagenomics to metatranscriptomics to understand the pathways driving health.

Functional profiling of human metatranscriptomes

Learn how to enable sensitive profiling of microbial diversity and metabolic activity with RiboZero Plus Microbiome in this presentation from Drs. Scott Kuersten and Brice Le François.

Microbiome sequencing in high-host and low biomass samples

Dr. Stefan Green addresses high-host and low microbial biomass issues, PCR-amplification bias, and alternatives for analyzing complex microbial communities.

Featured metatranscriptomic applications and publications

Identifying functional relationships in microbes and plants

Read how researchers used metatranscriptomics to learn about metabolically active microbial communities for biogas plants.

Uncovering RNA virus diversity

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

Characterizing lung RNA virome after transplantation

Learn how investigators used metatranscriptomics to shed light on the abudance and diversity of RNA viruses within the human pulmonary virome.

Studying rhabdovirus metatranscriptomics

See how this study provided a comprehensive phylogeny of rhabdoviruses to better understand their shared evolutionary relationships with plants.

Capturing dynamic shifts in the microbiome with metatranscriptomics

This paper uncovers the phylogenetic and functional diversity of microbial communities under the Antarctic ice shelf.

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

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.

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.

Analyze

BaseSpace Microbiome Metatranscriptomics

Perform taxonomic and pathway enrichment analysis on metagenomic samples.

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

Speak to a specialist

Questions on starting metatranscriptomics studies in your lab?

References

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.
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.
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.
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.
Metagenomics. National Human Genome Institute. genome.gov/genetics-glossary/Metagenomics. Accessed July 12, 2024.
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.

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Metatranscriptome sequencing

What is metatranscriptomics?

Discover the potential of community-level transcriptional information

NGS Workflow Finder

Featured webinars

Microbial profiling with metatranscriptomics

Featured metatranscriptomic applications and publications

Metatranscriptome sequencing workflow

Prep

Sequence

Analyze

Ribosomal RNA depletion for metatranscriptomic studies

Metatranscriptome FAQs

What is the difference between metatranscriptomics and metagenomics?

What is 16S rRNA gene sequencing and how is it different from metatranscriptomics or metagenomics?

How can I extract RNA from complex microbial samples for metatranscriptomic analysis?

How do I analyze metatranscriptomic data?