Metatranscriptomics: A Tool for Clinical Metagenomics.

Area of Science:

• Bioinformatics
• Microbiome Research
• Molecular Biology

Background:

• 16S rRNA gene sequencing and shotgun metagenomics are established microbiome analysis methods.
• These techniques identify microbial community members and gene content but not their activity.
• Metatranscriptomics is emerging to study active gene expression within microbial communities.

Purpose of the Study:

• To critically examine computational metatranscriptomics tools for microbial community transcriptomes.
• To explain the necessity of community transcriptomics in microbiome research.
• To discuss the challenges and prospects of metatranscriptomic workflows.

Main Methods:

• Review of computational tools for metatranscriptomics.
• Examination of RNA isolation, sequencing, and bioinformatics approaches.
• Analysis of statistical methods for differential gene expression.

Main Results:

• Metatranscriptomics provides insights into active microbial genes and their expression profiles.
• The review details challenges in RNA isolation, sequencing, and bioinformatics analysis.
• Strengths and limitations of metatranscriptomics compared to other methods are discussed.

Conclusions:

• Metatranscriptomics is crucial for understanding microbial community responses to environmental changes.
• Computational tools are essential for analyzing complex metatranscriptomic data.
• Metatranscriptomics offers valuable applications, including in clinical metagenomics.