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Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
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Published on: December 22, 2014

Preparation and metatranscriptomic analyses of host-microbe systems.

Jarrad T Hampton-Marcell1, Stephanie M Moormann, Sarah M Owens

  • 1Argonne National Laboratory, Argonne, Illinois, USA; Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA.

Methods in Enzymology
|September 25, 2013
PubMed
Summary

Dual RNA-Seq analyzes host and microbial gene expression to understand how infections develop. This method provides insights into microbial-host interactions and is faster and cheaper than other omics techniques.

Keywords:
Host–microbeMetatranscriptomicsMicrobialNext-generation sequencingTranslation

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Area of Science:

  • Microbiology
  • Genomics
  • Systems Biology

Background:

  • Metatranscriptomics enhances understanding of microbial communities' functional significance and genetic diversity.
  • Limited data exists on how microbiome gene expression influences host interactions, particularly during pathogenic infections.
  • Deciphering host and microbiome functional responses (Dual RNA-Seq) is crucial for understanding host-pathogen dynamics.

Purpose of the Study:

  • To present a standardized method for processing and analyzing host-associated microbial metatranscriptomes.
  • To enable independent analysis of microbial communities within a host environment.
  • To facilitate a deeper understanding of host-microbiome interactions.

Main Methods:

  • Dual RNA-Seq technique for simultaneous host and microbial gene expression analysis.
  • Coupling metatranscriptomic analysis with metagenomic data and statistical models.
  • Standardized protocol for processing and analyzing host-associated microbial metatranscriptomes.

Main Results:

  • Dual RNA-Seq offers a fast and cost-effective alternative to proteomics and metabolomics.
  • Provides insights into potential functional interactions between microbes and with the host.
  • Enables in-depth systems biology approaches when combined with metagenomics and statistical models.

Conclusions:

  • The presented method allows for the analysis of host-associated microbial metatranscriptomes independently of the host.
  • Dual RNA-Seq is a valuable tool for studying host-microbiome interactions during health and disease.
  • This approach contributes to a comprehensive understanding of microbial community function in host-associated environments.