Confident and unbiased transcript analysis

Study microbial transcriptomes and metatranscriptomes with next-generation RNA-Seq

Microbial Transcriptomics

Microbial transcriptome and metatranscriptome information is important for predicting resistance to specific antibiotics, understanding host-pathogen immune interactions, quantifying gene expression changes, and tracking disease progression. Next-generation RNA sequencing (RNA-Seq) of bacteria, viruses, and other microbes has become a standard method for analyzing transcriptome and metatranscriptome information.

The transcriptome is the comprehensive set of RNAs encoded by an organism's genome. Metatranscriptomes encompass all RNAs encoded by a group of organisms in a complex sample.

Bacterial, viral, and other microbial RNA-Seq experiments enable annotation and quantification of comprehensive microbial transcripts. Cellular RNA is extracted and converted to cDNA, which is used to prepare sequencing libraries. Sequence reads are then mapped back to the reference genome, providing qualitative information on features such as exon junctions and splicing sites, as well as quantitative transcript data that can be compared across many experimental sets.

Unlike hybridization-based methods such as microarrays, RNA-Seq enables unbiased strand-specific identification of common and novel transcripts. A wide dynamic range enables confident identification of both high and low expressors in a single bacterial, viral, or other microbial RNA-Seq experiment. Multiple samples can be processed at once with a streamlined workflow suitable for automation.

Microbial Transcriptomics with rRNA Depletion

The Ribo-Zero Plus rRNA Depletion Kit removes rRNA before RNA-Seq, enabling you to focus on high-value portions of the transcriptome. This technical note demonstrates rRNA depletion performance on microbial isolate and community samples, while comparing against previous kit versions.

Read Technical Note
Microbial Transcriptomics with rRNA Depletion

There are multiple ways to perform these experiments, but these are some suggested products for each step of the workflow.

Click on the below to view products for each workflow step.

TruSeq Stranded Total RNA Library Prep Kit

Streamlined, cost-efficient, and scalable solution for total RNA analysis.

Note: If you use a TruSeq RNA library prep kit, you will not need to extract RNA and transcribe to cDNA.

Nextera XT Library Prep Kit

Prepare sequencing ready libraries of bacteria, viruses, and other microbes to analyze transcriptome and metatranscriptome information.

Note: If you use an RNA extraction kit, you will need to generate dsDNA.

Benchtop Sequencing

MiSeq System

Speed, accuracy and simplicity for far-reaching applications in microbiology.

NextSeq 550 System

Flexible benchtop sequencer for exome, transcriptome, and whole-genome sequencing.

High-Throughput Sequencing
Power for high-throughput microbial transcriptomics and flexibility to scale based on your project or workflow needs.

NovaSeq 6000 System

High throughput and low cost for production-scale genomics.

BaseSpace Apps for transcript profiling

DRAGEN Reference Builder

This app accepts FASTA files, and builds the proprietary reference used by the DRAGEN apps.


Performs alignment, quantification, and fusion detection.

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