Bacterial RNA Sequencing
What Is Bacterial RNA Sequencing?
Bacterial RNA sequencing (prokaryotic RNA-seq) provides a genome-wide snapshot of prokaryotic gene expression, regulatory RNAs, and transcript architecture—enabling studies of differential expression, operon structure, and small RNA function. At AUGenomics, our bacterial RNA-seq workflows combine:
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Efficient rRNA Depletion: Probe-based capture (e.g., Ribo-Zero™ for bacteria), RNase H–mediated removal, or Terminator 5′-phosphate exonuclease to deplete > 95% rRNA and enrich mRNAs and sRNAs.
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Strand-Specific Library Prep: dUTP second-strand marking preserves transcriptional orientation for sense/antisense and untranslated region analysis.
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Host Depletion (if needed): Custom probes remove mammalian rRNA/transcripts in infected‐tissue or microbiome samples.
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Mixed Community Support: Compatible with pure cultures, synthetic communities, environmental microbiomes, and infected tissues.
This brings you the tools you need for transcript discovery, operon mapping, profiling transcription start/stop sites for regulatory network reconstruction, detecting regulatory RNAs and riboswitches, and monitoring condition-specific shifts under antibiotic, nutrient, or environmental stresses.
By tailoring depletion and library strategies, we capture both abundant mRNAs and regulatory small RNAs from as little as 50 ng total RNA—delivering high‐resolution, reproducible data across diverse bacterial systems.
Advantages of Bacterial RNA Sequencing
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Maximized mRNA & sRNA Coverage: > 95% rRNA removal lets you see low-abundance transcripts and small RNAs.
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Strand Specificity: dUTP-based methods retain transcript directionality for antisense and UTR studies.
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Low Input & Degraded Samples: Work with ≥ 10–50 ng total RNA, including FFPE and environmental extracts.
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Operon & TSS Mapping: Full-length coverage reveals operon structures, transcription start sites, and termination signals.
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High Dynamic Range & Sensitivity: Detect transcripts from housekeeping genes to rare regulatory RNAs in a single run.
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Reproducible Quantitation: ERCC spike-in support and UMIs (optional) ensure accurate molecule counting.
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Scalable Throughput: Dual-index barcoding supports 96–384 libraries per sequencing lane.
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Rapid Turnaround: Complete from RNA receipt to data delivery in 7–10 business days.
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Operon & TSS Resolution: Full-length, strand-specific reads map operon structures, TSS, and termination sites.
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Small RNA Detection: Annotate sRNAs (50–200 nt), riboswitches, and CRISPR RNAs alongside mRNAs.
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Novel Transcript Discovery: Uncover unannotated coding sequences, alternative transcripts, and small peptides.
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Mixed-Sample & Host Depletion: Profile pure cultures, metatranscriptomes, or infected tissues with dual bacterial/host RNA removal.
Bacterial RNA sequencing is valuable for:
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Differential Gene Expression in Bacterial Strains: Compare mutants, stress responses, or growth phases.
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Host-Pathogen Interaction: Profile bacterial and host transcripts simultaneously; track in vivo virulence gene expression.
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Antibiotic Resistance & Drug Response: Monitor gene regulation underlying resistance mechanisms and drug targets.
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Microbiome Function: Assign functional roles in complex communities; link species-specific expression to metabolic pathways.
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Small RNA & Regulatory RNA Discovery: Identify sRNAs, riboswitches, CRISPR RNAs, and antisense regulators.
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Synthetic Biology & Engineering: Validate promoter activity, pathway flux, and circuit behavior in engineered microbes.
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Stress & Nutrient Limitation Studies: Uncover regulatory networks activated by pH, temperature, or starvation.
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Regulatory RNA Studies: Map sRNA targets, riboswitch activity, and antisense regulation.
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Transcriptome Annotation & Network Modeling: Build complete gene regulatory and interaction networks for systems biology.
Our workflows are designed for both pure cultures and complex communities, offering sensitive and reproducible expression insights from even difficult or low-yield samples.
What is Bacterial RNA Sequencing Used For?
Bacterial RNA Sequencing with AUGenomics
Sample Submission
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Accepted Sample Types: RNA from bacterial cultures, mixed microbial samples, infected tissues, or environmental sources
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Input Requirement: ≥50 ng total RNA (≥10 ng for ultra-low input protocols)
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Sequencing Recommendations:
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rRNA depletion required for optimal bacterial RNA signal
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10–30 million reads/sample depending on genome size and complexity
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Supports both strand-specific and total RNA workflows
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Please refer to our Shipping Guidelines for project-specific guidance.
Turnaround Time
Typical turnaround is 7-10 business days from sample receipt. Expedited options are available depending on project scope and sequencing depth.
Frequently Asked Questions (FAQs)
Q: Can I sequence bacteria from complex or environmental samples?
A: Yes. We offer workflows compatible with both pure cultures and mixed microbial communities, including environmental microbiomes and infected tissue.
Q: Do you support strand-specific bacterial RNA-seq?
A: Yes. Strand-specific protocols are available and recommended for regulatory studies and antisense transcript analysis.
Q: How is bacterial RNA-seq different from eukaryotic?
A: Bacteria lack poly(A) tails, so we use rRNA depletion (not oligo(dT)) and random priming with strand-specific prep—also enabling operon and sRNA analyses.
Q: What depth is needed for metatranscriptomes?
A: For single-species bacterial transcriptomes, 10–20 M reads/sample suffice; for metatranscriptomes or mixed infections, we recommend 20–30 M reads/sample.
Got more questions? Contact our team and get a free consultation anytime. info@augenomics.com
Glossary of Terms
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Bacterial RNA-seq: Sequencing of the complete transcriptome of a bacterial species
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rRNA Depletion: Removal of abundant ribosomal RNA to enhance sequencing depth for mRNA and other RNAs
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Host-Pathogen Interaction: Study of molecular interactions between bacteria and host cells
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Strand-Specific RNA-seq: A sequencing method that preserves information about the direction of transcription
