Come meet the team in Los Angeles at the ASM Microbe Conference, Booth #1222, June 19-23!

Full-Length 16S (V1-V9)

16S/ITS Sequencing Full-Length 16S (V1-V9) Shotgun Metagenomics

Supported by PacBio’s CCS technology, SeqCenter’s Full-Length 16S services provides high accuracy reads spanning both conserved and hypervariable regions (V1-V9) of the 16S rRNA gene, which can be leveraged to identify and differentiate a wide range of bacterial taxa within diverse bacterial communities.

Historically, traditional short-read 16S sequencing methods have been limited in taxonomic resolution and often yielded ambiguous classifications, because they focus on one or two hypervariable regions roughly 500bp in length. In contrast, full-length 16S sequencing encompasses the entire 1500bp 16S gene.

The increased coverage significantly enhances the 16S amplicon approach’s ability to resolve closely related taxa, allowing for more accurate and detailed microbial community characterization. This makes full-length 16S sequencing particularly valuable for applications requiring precise microbial identification, where short read technologies have proved lacking.

In environmental microbiology, full-length 16S gene sequencing enables better understanding of microbial diversity, ecosystem function, and biogeochemical processes. In microbiome research, especially in human health and disease studies, it allows for more confident detection of clinically relevant species, supporting efforts in diagnostics, therapeutics, and personalized medicine. Full-length 16S sequencing, enabled by advances in long-read sequencing technologies, represents a powerful tool for advancing microbiological research across a wide range of scientific domains.

Similar to its short-read predecessor, the power of the analysis can still be limited by the breadth of the taxonomic database used. To that end, SeqCenter is excited to be fueling the diversification of these data repositories as powerful, cost-effective sequencing, like full-length 16S reaches a wider range of researchers.

Sample Requirements:

  • Total volume of 20 µL or more
  • Minimum of 1 ng/µL concentration
  • Sample eluted into water or dilute Tris/TE buffer

What You Will Receive:

  • One fastq file for each sample
  • Sequencing stats summary
  • Materials and methods summary
  • ASV representative sequence and raw counts file
  • Data shared via Globus within 2 weeks
  • Analysis reports include:
    • Species abundance tables
    • Alpha and beta diversity
    • Taxonomic assignment
    • Diversity barplots by taxonomic rank

Packages and Pricing

Sequencing Package
(Minimum Read Count Per Sample)		 Price*
10k PacBio Long Reads
16S V1-V9 Region		 $45.00
25k PacBio Long Reads
16S V1-V9 Region		 $55.00
50k PacBio Long Reads
16S V1-V9 Region		 $75.00
*Orders >48 Samples receive 5% discount

We offer convenient DNA extraction services using ZymoBIOMICS DNA extraction kits. This protocol can extract DNA even from tough-to-lyse cells using a bead bashing tube for consistent mechanical lysis. We are able to accommodate all organisms up to BSL2+ and do not accept BSL3 or higher classified organisms for extraction services. We cannot accept soil samples from outside of the US.

Full Length 16S samples requiring DNA extraction can be submitted as frozen environmental samples or as aspirated cell pellets shipped frozen on dry ice.

Please note that while this kit is broadly applicable to many sample types, we cannot guarantee its efficacy for a given organism. More information about the ZymoBIOMICS kit can be found here.

16S/ITS Sequencing

The 16S/ITS amplicon approach uses targeted PCR amplification and sequencing of the hypervariable regions of rRNA genes. The results are then binned and queried against a database to provide a taxonomic abundance profile.

Explore

Shotgun Metagenomics

Our Shotgun Metagenomics packages sequence randomly spread eDNA fragments within a sample and attempt to create metagenomic assemblies for the members of the community. This can provide a survey of functional genes within the community and a plethora of analytical opportunities.

Explore

Contact:
91 43rd Street, Ste. 250
Pittsburgh, PA 15201
(878) 227-4915

Services:

About:

Resources:

Full Flowcell:

We offer full flowcell sequencing services for libraries that have been prepared outside of our lab. For each library, we will need to know the loading concentration, phiX spike-in, and run structure. Data is delivered as a complete run folder and can be demultiplexed upon request if a sample sheet is provided.

SARS-CoV-2 Sequencing:

Our SARS-CoV-2 Sequencing services include an assembly on the SARS-CoV-2 reference genome as a scaffold. These packages provide roughly 200Mbp of paired end reads (2×151 bp) as fastq files and the assembly in fasta format.

We require a minimum sample volume of 15 µL of extracted material (or 250µL for VTM samples) and recommend that only samples with Ct values below 35 are sent (because submissions are not measured for viral load before processing). We offer services for both purified RNA and samples in VTM media that require viral RNA extraction. Please see our SARS-CoV-2 Sequencing page for more detailed information.

Microbiome Sequencing:

Please see our Microbiome Sequencing page for package details, including distributables and sample requirements.

Nanopore Sequencing:

Our Oxford Nanopore sequencing packages provide reads equal to the length of input DNA, delivered as a fastq file.

For each sample, we require a minimum volume of 60 µL, and at least 40 ng/µL dsDNA quantified by Qubit or other dye-based method (100 ng/µL by Nanodrop). Variant calling add-on analysis requires an annotated reference file. DNA extraction services are available for only specific categories of microbes.

Please see our DNA Sequencing: Long Read Sequencing page for more detailed information about the package, variant calling analysis, and extraction requirements.

PacBio:

Our PacBio services deliver HiFi reads with an average read length of 8-12kb for standard offerings and up to 25kb for full flowcell runs. All package names are listed by the minimum number of >Q20 reads that will be delivered. Both assembly and annotation are included with all packages.

For each sample, a minimum volume of 60 µL and at least 35 ng/µL dsDNA (quantified by Qubit or other dye-based methods) are required. SeqCenter strongly recommends utilizing our HMW DNA Extraction service for best results; however, we will also accept samples that are shipped on dry ice to avoid DNA integrity issues caused by the shipping process.

Please see our PacBio Sequencing page for more detailed information about our services.

RNA Sequencing:

We offer both rRNA depletion RNA squencing and polyA-tail enrichment mRNA sequencing. Both provide stranded, paired end reads (2x 151bp) as fastq files.

For each sample, we require a minimum volume of 20µL and at least 50ng/µL RNA. We also recommend, but do not require, that samples be DNAse treated and have a RIN score greater than 6. We also offer Basic and Intermediate RNAseq analyses, which require an annotated reference sequence.

Please see our RNA Sequencing page for more detailed information about both our RNA sequencing and analysis packages.

Illumina Sequencing:

The Illumina sequencing packages produce paired end reads (2×151 bp) delivered as fastq files.

For each sample, we require a minimum volume of 30 µL and at least 10 ng/µL dsDNA quantified by Qubit or other dye-based method (20 ng/µL by Nanodrop). Variant calling add-on analysis requires an annotated reference file. DNA extraction services are available for only specific categories of microbes.

Please see our DNA Sequencing: Whole Genome Sequencing page for more detailed information about the package, variant calling analysis, and extraction requirements.

For additional information about variant calling and short read assemblies, please see our Bioinformatics page.

Go to Top