Identify and compare microbial organisms from complex microbiomes or environment

NGS offers a culture-free method to identify microbes that may not be found using other methods

16S and ITS rRNA Sequencing

16S and Internal Transcribed Spacer (ITS) ribosomal RNA (rRNA) sequencing are common amplicon sequencing methods used to identify and compare bacteria or fungi present within a given sample. Both 16S and ITS rRNA gene sequencing are well-established methods for comparing sample phylogeny and taxonomy from complex microbiomes or environments that are difficult or impossible to study.

16S rRNA Sequencing with the iSeq 100 System

Using the 16S metagenomics workflow with the iSeq 100 System, you can achieve genus-level sensitivity for surveys of bacterial populations.

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Unlike capillary sequencing or PCR-based approaches, next-generation sequencing (NGS) is a culture-free method that enables analysis of the entire microbial community within a sample. With the ability to combine many samples in a sequencing run, microbiology researchers can use NGS-based 16S and ITS rRNA sequencing as a cost-effective technique to identify strains that may not be found using traditional methods.

eDNA Offers a Powerful Look at Biodiversity

Michael Bunce, PhD uses next-generation sequencing and metabarcoding methods to study environmental DNA (eDNA).

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Illumina offers products to support 16S and ITS rRNA sequencing, from sample and library preparation to data analysis and interpretation. Our demonstrated workflow can help take the guess work out of your experiments. View our demonstrated sequencing protocols for16S rRNA and ITS rRNA.

Click on the below to view products for each workflow step.

Nextera XT v2 Index Kits

Multiplex samples to drive greater sample throughput.

MiSeq System

Speed, accuracy and simplicity for far reaching applications in microbiology.

iSeq 100 System

Affordable, fast, and accessible sequencing power for targeted or small genome sequencing in any lab.

MiSeq v3 Reagent Kits

Improved chemistry to increase cluster density and read length. The 600 cycle kit is ideal for 16S rRNA sequencing.

MiSeq v2 Reagent Kits

Produce up to 7.5 Gb of data. The 500 cycle kit allows for 16S rRNA sequencing with up to 15 million reads.

BaseSpace Apps for taxonomic classification

16S Metagenomics

Performs taxonomic classification of 16S rRNA targeted amplicon reads using an Illumina-curated version of the GreenGenes taxonomic database.

Kraken Metagenomics

Assigns taxonomic labels to short DNA sequences with high sensitivity and speed using exact alignments of k-mers and a novel classification algorithm.

ITS Metagenomics

Performs taxonomic classification of fungal rRNA targeted amplicon reads using the UNITE taxonomic database.


The Metagenomic Phylogenetic Analysis (MetaPhlAn) tool profiles microbial community composition from metagenomic shotgun sequencing data.

QIIME Preprocessing 

Quantitative Insights into Microbial Ecology (QIIME) is designed to take users from raw sequencing data to publication quality graphics and statistics.

One Codex

Enables metagenomics analysis by rapidly assessing your samples from BaseSpace Sequence Hub with a fast, comprehensive, accurate data platform.

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MiSeq, 16S rRNA Sequencing and the American Gut Project
MiSeq, 16S rRNA Sequencing and the American Gut Project
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16S rRNA Sequencing Webinar
16S rRNA Sequencing Webinar
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Hospital Microbiome Projects
Hospital Microbiome Projects
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16S rRNA Sequencing Protocol
16S rRNA Sequencing Protocol

Demonstrated protocol for 16S rRNA amplicon sequencing. Read FAQs.

View Protocol (PDF)
Metagenomics to Map Ocean Biodiversity
Metagenomics to Map Ocean Biodiversity

An epic ocean expedition sequenced salt water samples from around the globe to survey plankton diversity in marine ecosystems.

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Sequencing a Mouthful of Microbes
Sequencing a Mouthful of Microbes

The Saca La Lengua project is using NGS to identify the variety of bacteria and fungi that live in the human mouth.

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High-Speed, Multiplexed 16S Metagenomics Studies
Fungal Sequencing and Classification 

Get genus level detection of fungi in diverse sample types with the ITS metagenomics workflow.

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ITS rRNA Sequencing Protocol
ITS rRNA Sequencing Protocol

Demonstrated protocol for ITS rRNA amplicon sequencing.

View Protocol