AMPLICON SEQUENCING

16s rRNA & ITS
Gene Sequencing

Unlock precise bacterial and fungal taxonomic insights for environmental, agricultural, industrial studies, and more

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10-15 days

Standard TAT

US-only

All data on US soil

Flexible region coverage

V1–V9, V3–V4, V3–V5, V4, and customizable

OVERVIEW

What is 16S rRNA Gene & ITS Sequencing?

16S rRNA and ITS sequencing are marker gene-based amplicon sequencing approaches used to identify and quantify microbial communities directly from complex samples. These techniques sequence specific conserved-yet-variable regions of the genome that act as molecular barcodes for each organism.

The 16S ribosomal RNA gene is the gold standard for profiling bacteria and archaea. It’s nine hypervariable regions (V1–V9) carry enough sequence diversity to distinguish organisms at the genus and species level. Targeting specific regions such as V3–V4, V4 alone, V3–V5, or full-length V1–V9, lets researchers tune the breadth versus resolution of their survey.

The internal transcribed spacer (ITS) region serves the same purpose for fungi. Targeting ITS1 or ITS2 provides species-level resolution across a broad range of fungal taxa with minimal amplification bias, making it the standard approach for mycobiome profiling.

16S vs. ITS: which do you need?

If your sample contains bacteria or archaea, use 16S. If you're targeting fungi, use ITS. Many environmental and clinical samples benefit from running both assays in parallel to capture the full microbial picture

Our team here at Admera Health can coordinate within a single project.

Wondering whether 16S/ITS or shotgun metagenomics is right for your project?


16S and ITS are ideal for community composition and diversity. For functional depth and understanding what genes are present and what pathways are active, consider our metagenomics service.

OVERVIEW

16s rRNA & ITS Gene Sequencing Methods

Short-Read (High-Throughput)

  • Targeted sequencing of specific 16S rRNA or ITS regions

  • High-throughput approach ideal for microbial diversity profiling, community comparisons, and large-scale studies

  • Cost-effective and fast, suitable for high-volume projects

Full-Length 16S Amplicon-seq with PacBio

  • Sequences the entire 16S rRNA gene (~1.5 kb) for species- and strain-level resolution

  • Uses HiFi long reads for high accuracy and single-molecule resolution

  • Kinnex™ 16S rRNA kit enables multiplexing of up to 1536 samples per SMRT cell, reducing cost per sample

  • Ideal for studies requiring precise taxonomic profiling or tracking microbial dynamics

More on long-read sequencing

Applications of 16S rRNA & ITS Gene Sequencing

Microbiome Profiling

Identify and quantify microbial populations in environmental or gut microbiome samples

Taxonomic Profiling

Resolve closely related species or strains using full-length sequencing

Freshwater and Wastewater studies

Freshwater &
Wastewater Studies

Characterize microbial communities in rivers, lakes, and treatment plants to assess ecosystem health and contamination

environmental and industrial applications

Environmental & Ecological Studies

Monitor microbial diversity and ecosystem changes in soil, water, and environmental samples

Frequently Asked Questions

Sending samples? See our DNA sample submission guidelines for best practices on sample preparation, packaging, and shipment for the highest quality results.

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  • Short-read sequencing is a high-throughput method that targets specific regions, while full-length PacBio sequencing captures the entire gene for improved resolution and strain-level identification.

  • We support a wide range of primer sets to align with your study goals.

    • 16S rRNA: V1–V9, V3, V4, V5, and custom primer designs.

    • ITS: ITS1 and ITS2 for fungal community profiling.

    Custom primer sets can be validated upon request.

  • We accept microbial DNA, cells, gDNA, amplicons, environmental and FFPE samples.

    Contact us for specific questions regarding sample requirements.

  • Our standard recommendation for 16S rRNA gene sequencing is 0.1 million paired-end reads (PE 2×300) per sample. This depth provides reliable bacterial community profiling, supports diversity analyses, and meets typical publication standards.

    (We can adjust sequencing depth based on your sample type, cohort size, or resolution needs.)

  • Our standard turnaround time is typically 3-6 weeks, though this can vary depending on the sample type, project complexity, and required sequencing depth. Expedited services are available upon request.

    Please contact us for a detailed quote and timeline specific to your project.

  • We provide comprehensive, ready-to-use data.

    View our demo reports to get a feel for what you can expect when working with our team:

Get the Most out of Your Study

Maximize your project’s potential with advanced analysis solutions. Our team of expert bioinformaticians curate pipelines tailored to your project’s experimental design.

Data Analysis Services

See Metagenomics in Action
Admera Health provides comprehensive support for all projects, and delivers publication-ready data. Discover how researchers are using Admera Health to advance their environmental studies.

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