At Microbiome Insights, we are now pleased to offer metatranscriptomic sequencing services, providing information on gene expression and associated functional outcomes for a microbial community. Our metatranscriptomic sequencing services are backed by cutting-edge high-throughput sequencers, sequencing strategies, and advanced bioinformatics pipelines.
What is metatranscriptomics?
Metatranscriptomics is the study of all RNA molecules (the transcriptome) produced by all the microorganisms present in a particular environment, such as soil, water, or the human gut. High-throughput RNA sequencing can provide insights into the gene expression patterns, and information on metabolic activities and functional roles of different microbial species in an ecosystem. Metatranscriptomics focuses on messenger RNA analysis, though rRNA gene analysis is also possible if interested in targeting only active communities.
There are two options for RNA library preparation:
- rRNA depletion OR
- poly(A) mRNA selection.
Option 2 is the preferred method (certainly for prokaryotic/bacterial organisms), as it preserves snoRNA as well as rRNA and mRNA.
Following total RNA extraction and purification, including the removal of residual DNA by DNase treatment, mRNA must be depleted to obtain adequate sequencing coverage. QC checks must be carried out after these processes given that RNA is a fragile and transient molecule.
Prior to sequencing, RNA is generally fragmented, size-selected, and converted to double-stranded cDNA using single-strand cDNA conversion and second-strand preparation. This process eliminates strandedness; analysis depending on strand selection (e.g. Anti-sense Adaptors and barcodes) are then ligated to the cDNA fragments during library preparation.
Bioinformatic pipelines in metatranscriptomics are the next part of analyzing the expression profiles of microbial communities in diverse environments. The processing and analysis of metatranscriptomic data will ultimately depend on the questions being addressed in a particular study. A typical pipeline includes several steps, which are outlined below:
Irene Yang, PhD, RN
Assistant Professor at Emory University
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