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Applications of ribosome profiling
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Depletion of Ribosomal RNA for Mosquito Gut Metagenomic RNA-seq
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Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes.

Asako Tan1, Senthil Murugapiran2, Alaya Mikalauskas3

  • 1Illumina, Inc, Madison, WI, 53719, USA.

BMC Microbiology
|October 20, 2023
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Researchers developed a novel probe set for efficient enzymatic removal of microbial ribosomal RNA (rRNA), enabling accurate metatranscriptomic analysis of the human microbiome and its functional dynamics.

Keywords:
MetatranscriptomicsMicrobiomeNext-generation sequencingrRNA depletion

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • The human microbiome's composition and function are dynamic and vary significantly.
  • Metatranscriptomics offers insights into microbiome activity but is hindered by abundant microbial ribosomal RNA (rRNA).
  • Efficient and unbiased rRNA removal is crucial for accurate gene expression profiling of microbial communities.

Purpose of the Study:

  • To develop and optimize a probe set for efficient enzymatic removal of rRNA from human-associated microbial communities.
  • To validate the accuracy and efficiency of the rRNA depletion method for metatranscriptomic analysis.
  • To provide a tool for studying the transcriptional dynamics of the human microbiome.

Main Methods:

  • Design of a custom probe set targeting microbial rRNA.
  • Iterative refinement of the probe set for diverse human microbiome samples.
  • Enzymatic rRNA depletion using the developed probe set.
  • Assessment of quantitative accuracy using synthetic nucleic acid spike-ins.

Main Results:

  • The custom probe set achieved efficient enzymatic rRNA removal from complex human microbiome samples.
  • The rRNA depletion process did not introduce substantial quantitative errors in gene expression profiles.
  • Successful depletion enabled accurate characterization of taxonomic and functional profiles.
  • The method was effective in studying the developing human gut microbiome.

Conclusions:

  • The developed pan-human microbiome enzymatic rRNA depletion probes are a powerful tool.
  • This method facilitates the study of transcriptional dynamics and function in the human microbiome.
  • It overcomes a significant barrier in metatranscriptomic data acquisition.