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Unraveling gene expression in microbial populations

Unlock the power of NGS to explore microbial communities

What is metatranscriptome sequencing?

Metatranscriptomics is the collective study of expressed mRNA from complex microbial communities.1 Using sequencing to study gene expression in a community, 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 community’s behavior and function, metatranscriptomics can also provide valuable information about its 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

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
Library prep

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

A fast, integrated whole-exome enrichment and sequencing library preparation workflow for a wide range of applications.

2
Sequencing

NextSeq 550

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
Data Analysis

BaseSpace Microbiome Metatranscriptomics

Perform taxonomic and pathway enrichment analysis on metagenomic samples. 

Ribosomal RNA depletion for metatranscriptome sequencing

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 using Illumina Ribo-Zero Plus Microbiome. Download this app 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 16S rRNA sequencing 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 by using commercially available microbiome RNA extraction kits that provide an RNA Integrity Number, or RIN, greater than, or equal to, five.

/ 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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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.