Full-Length 16S Sequencing

Studying microbial communities using long-read sequencing

The 16S ribosomal RNA (rRNA) gene is approximately 1.5 kb long and contains several conserved and hypervariable regions (V1-V9) that vary between different bacteria. These hypervariable sequences can be used to identify and characterize microbial diversity. Therefore, the 16S rRNA gene is a common marker to characterize microbial communities in various specimens.

Using the PacBio single molecule real-time (SMRT) technology, we accurately sequence the full-length 16S rRNA gene, covering all variable regions with an average HiFi read length of about 1.5 kb. The extraordinary accuracy and length of PacBio HiFi reads generated using circular consensus sequencing (CCS) mode allows microbial taxa detection at high resolution.

Applications of full-length 16S sequencing are diverse and include:

  • characterization of different microbial communities
  • microbial biomarker detection
  • disease monitoring
  • drug development

Our Full-Length 16S Sequencing product provides interesting insights for diverse research questions.

CeGaT Is the Best Partner for Sequencing Your Project


Scalable for different sample types, quantities, and requirements


Processing according
to highest quality

Customer Service

Constant scientific supervision of all
project steps

Made in Germany

In-house processing to maintain our reliable and trusted quality

Our Commitment to You

Fast Processing

Turnaround time
≤ 15 business days

High Quality

Highest accuracy for all processes

Secure Delivery

Secure provision of sequenced data via in-house servers

Safe Storage

Safe storage of samples and data after project completion

Our Service

We provide a comprehensive and first-class project support – from selecting the appropriate product to evaluating the data. Each project is supervised by a committed scientist. You will have a contact person throughout the whole project.

Our service includes:

  • detailed project consulting
  • product selection tailored to your project
  • detailed bioinformatic evaluation of your data
  • detailed project report with information about sample quality, sequencing parameters, bioinformatic analysis, and results

Benefit from our dedicated support and accredited workflows.

Explore Our Product for Full-Length 16S Sequencing

We offer Full-Length 16S Sequencing to address a variety of research questions. Would you like to have bioinformatic analyses performed on your data in addition to the included deliverables? Our product can be supplemented with further services. We are happy to advise you.

Full-Length 16S Sequencing


Sample types
Isolated DNA & various other sample types upon request

Complete 16S rRNA gene (V1-V9 regions)

Read length
Approx. 1.5 kb

Sequencing platform

15,000 HiFi Reads per sample

Included deliverables
Project report & files in FASTQ format


Raw sequencing data are automatically processed. We offer different levels of bioinformatic analysis. The default level is Level 1. With increasing bioinformatic level, more data are delivered. The higher level includes the data from the lower level. In addition to the data, and independent of the analysis level, a project report is generated.

Level 1:

  • demultiplexing of the sequencing data (HiFi reads, FASTQ format)

Level 2:

  • taxonomic classification down to species level (if possible)
  • mapping of the sequencing data against microbiome database (FASTA, RMA)
  • generation of taxonomic tables including sequence counts and relative abundances (XLSX, TSV, and BIOM format)
  • generation of barplots showing relative abundances (PNG format)

Technical Information

At CeGaT, sequencing is performed using the PacBio Sequel IIe platform. If you require other sequencing parameters, please let us know! We can provide further solutions.

We are pleased to offer you our specifically designed stool sampling kit, which provides convenient and unbiased self-collection of fecal material combined with our DNA isolation service. Please also reach out to us to discuss sampling and DNA extraction of various starting material.

Our Workflow

Hier finden Sie den gesamten Prozessablauf

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Support & Offer

Support &

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Sample Receipt & Quality Control

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Library Preperation & Sequencing

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Bioinformatic Analysis & Data Delivery

Further Information about Full-Length 16S Sequencing

The 16S ribosomal RNA, also known as 16S rRNA, is part of the 30S subunit. This 30S subunit is the small subunit of the 70S ribosome, which occurs in prokaryotes. Ribosomes are macromolecular complexes that facilitate protein synthesis. The 16S rRNA has a unique role, as it is crucial for initiating the translation by binding to the Shine-Dalgarno sequence. This sequence is generally located upstream of the start codon and complementary to a segment in the 16S rRNA. The genes coding for this crucial component of the ribosome are referred to as 16S rRNA genes. The 16S rRNA gene shows slow rates of evolution. These slow evolutionary rates make them valuable for phylogenetic reconstructions. Thus, the 16S rRNA gene can give valuable insights into phylogenetics, the evolution of life, and the investigation of the relationships between different organisms.

The full length of the 16S gene measures approximately 1500 bp. The highly conserved sequence comprises nine variable regions. Targeting only a few of these variable regions was previously done due to technological restrictions. Different primers were available to sequence only a subregion of the 16S gene using short-read sequencing. With the advancements in third-generation sequencing, the sequencing of the full length of the 16S gene is feasible.

The PacBio sequencing platform and circular consensus sequencing (CCS) enable the full-length sequencing of the 16S gene and not only of sub-regions. The CCS mode allows the generation of so-called high-fidelity reads, short HiFi. During this process, single-molecule real-time (SMRT) libraries are prepared using double-stranded high-quality DNA and hairpin adapters on both sides of the double-stranded DNA.  The resulting circularized DNA is sequenced in repeated passes. The adapters of the repeated passes are trimmed, and the resulting subreads are merged into a consensus read. Such consensus reads with a sufficient quality are then called HiFi reads. The sequencing errors that naturally and randomly occur are rapidly diminished with an increasing number of passes, leading to a high read accuracy for long reads.

Our Full-Length 16S Sequencing product can cover the complete 16S rRNA gene with all nine variable regions. The circular consensus sequencing mode generates long HiFi reads with a high read accuracy. Thus, Full-Length 16S Sequencing can, amongst others, enhance phylogenetic studies and the detection of microbial biomarkers.


Full-Length 16S Sequencing Flyer (EN)
Full Length 16 S Sequencing Description

Contact Us

Do you have a question or are you interested in our service? Feel free to contact us. We will take care of your request as soon as possible.

Start Your Project with Us

We are happy to discuss sequencing options and to find a solution specifically tailored to your clinical study or research project.

When getting in contact, please specify sample information including starting material, number of samples, preferred library preparation option, preferred sequencing depth and required bioinformatic analysis level, if possible.