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

Featured Microbial Genomics Research

The Time is Now for Microbiome Studies
The Time is Now for Microbiome Studies

Whole-genome shotgun sequencing and transcriptomics provide researchers and pharmaceutical companies with data to refine drug discovery and development.

Read Article
Microbes and Metagenomics Research Review
Microbes and Metagenomics Research Review

A recent surge in microbial sequence information has inspired new appreciation for microbial populations and their impact on the environment and human health.

Read Review
NGS is Revealing the Mysterious World of Microbes
NGS is Revealing the Mysterious World of Microbes

Researchers at Microba are investigating the genomes of microbes to improve our understanding of human health, disease, and microbial evolution.

Read Article

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.

Illumina Stranded Total RNA Prep with Ribo-Zero Plus

Rapid library preparation from a broad range of sample types for studying the coding and non-coding transcriptome with unparalleled study flexibility.

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 2000 System

Groundbreaking benchtop sequencers allow you to explore new discoveries across a variety of current and emerging applications, with higher efficiency and fewer restraints.

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.

Interested in receiving newsletters, case studies, and information on microbial genomics? Enter your email address.
From Microarrays to RNA-Seq
From Microarrays to RNA-Seq

Expression analysis scientists discuss transitioning from microarrays to RNA-Seq.

Read Interview
RNA Resources
RNA Resources

Access comprehensive resources for RNA sequencing.

Learn More