16S/ITS Sequencing

The 16S and ITS amplicon approaches use PCR to amplify the hypervariable regions of rRNA gene found in nearly all bacteria and archaea or fungi, respectively. Conserved regions of rRNA allow for consistent and accurate alignment of sequenced data, while the variable “fingerprint” regions allow for the classification of amplicon sequence variants (ASVs). Identified ASVs are taxonomically assessed using the full-length Silva-138 (16S) and Unite-8 (ITS) databases. The result of this workflow is the taxonomic profiling of a microbial community to determine the abundance of unique taxa in each system. As this technology has grown, representative databases like the Silva database have served as essential resources for properly classifying microbes.

At SeqCenter, we utilize Zymo Quick-16S Plus or Quick-ITS Plus Library Prep methods to selectively amplify either the V3/V4 region (bacteria/archaea) or ITS2 region (fungi) of your metagenomic sample, with reads spanning roughly 600 bp and 480 bp, respectively. All 16S and ITS services come with taxonomic analyses and assessments of alpha and beta diversity. While the applications for this technology are great, the reliance on precompiled databases poses challenges for poorly classified communities not represented in the available databases. This has led to a surge in shotgun metagenomics studies which aim to capture all available genomic information for a given system, including gene content and increased specificity of identification, though it is more costly to attain comparative amounts of depth.

For an example version of our 16S methods including primers used, click here; for the ITS methods, click here; and for a downloadable example of the 16S analysis, click here.

Sample Requirements:

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

What You Will Receive:

  • Two fastq files (2 x 301bp) for each sample
  • Sequencing stats summary
  • Materials and methods summary
  • ASV representative sequence and raw counts file
  • Data shared via Box folder 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)
20k Reads (10k Read Pairs)
Either V3/V4 or ITS2 Region
50k Reads (25k Read Pairs)
Either V3/V4 or ITS2 Region
100k Reads (50k Read Pairs)
Either V3/V4 or ITS2 Region
*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.

16S and ITS2 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.

Go to Top