Metatranscriptomic Profiling

Unlock the true  function of the microbiome through Metatranscriptomic Profiling. Characterizing the specific expression profiles of the microbes at time of sample collection, this research solution provides the most robust approach for exploring microbiome function. This solution can provide insight into the subset of genes required for a microbial community to survive, and when used in comparative analysis it can identify key functions and pathways that differentiate one community from another; potentially unlocking the role of microbiome in driving different clinical phenotypes.

Our Laboratory Process

Our laboratory recommends starting with at least 1mg of high quality total RNA for each sample. Precaution should be taken when collecting a sample to be used for an RNA analysis, as this nucleic acid is far less stable than DNA.  Accordingly, RNA samples should be immediately snap frozen upon collection or stored in an RNA preservation buffer.  Following a successful RNA isolation, host mRNA is removed using a polyA tail depletion. Because the majority of RNA in a sample is ribosomal RNA, a ribosomal RNA depletion is required for all transcriptomic projects.  Once successful depletion is completed a cDNA library is synthesized and the samples are index barcoded and pooled for high-throughput sequencing. 

Our Analysis

Our analysts focus on establishing the relative abundance of enzymes and pathways for each community.  Following this mapping effort,  we obtain an assessment of community-level pathway similarity or dissimilarity across all study groups. Assuming that microbial communities with similar pathway representation share similar ecology, this assessment can inform the broader function of the community. Differentially represented pathways are also highlighted to inform which pathways are over or underrepresented in the experimental groups.

When all annotations and community comparisons are complete, we compile a comprehensive final report, which includes publication-ready tables with a variety of analyses to explain the microbial community under investigation. Once we deliver the final report, the Second Genome Solutions team is available for a detailed report review.