Optimizing mouse metatranscriptome profiling by selective removal of redundant nucleic acid sequences.

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Metatranscriptome (MetaT) sequencing profiles microbiome metabolic functions and gene expression.
• High rRNA abundance (up to 99%) hinders accurate mRNA analysis in microbiome samples.
• Existing human-gut rRNA depletion probes are less effective for mouse cecal samples.

Purpose of the Study:

• To develop an efficient and consistent rRNA depletion method for mouse cecal samples.
• To refine a taxonomically-neutral probe design for improved MetaT analysis.
• To reduce the cost and bias associated with rRNA removal.

Main Methods:

• Designed and adapted rRNA depletion probes specifically for mouse cecal content.
• Utilized a taxonomically-neutral probe design strategy.
• Evaluated probe efficiency and consistency for MetaT analysis.

Main Results:

• Human-based rRNA depletion probes showed reduced effectiveness in mouse cecal samples.
• Adapted probes provided greater efficiency and consistency for mouse MetaT analysis.
• The refined method increased the number of mRNA-rich sequencing reads.

Conclusions:

• Targeted rRNA depletion probes are essential for accurate mouse microbiome MetaT analysis.
• The developed method offers an efficient, consistent, and cost-effective solution for rRNA removal.
• This advancement improves the functional profiling of mouse gut microbiomes.