Identify and compare bacteria from complex microbiomes or environments

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

16S rRNA Sequencing

16S ribosomal RNA (rRNA) sequencing is a common amplicon sequencing method used to identify and compare bacteria present within a given sample. 16S rRNA gene sequencing is a well-established method for studying phylogeny and taxonomy of samples from complex microbiomes or environments that are difficult or impossible to study.

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 rRNA sequencing as a cost-effective technique to identify strains that may not be found using other methods.

Illumina offers products to support 16S 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 16S rRNA sequencing protocol.

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.

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.

MetaPhlAn

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

QIIME Preprocessing and QIIME Visualizations

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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High-Speed, Multiplexed 16S Metagenomics Studies
High-Speed, Multiplexed 16S Metagenomics Studies

Get species-level identification of complex microbial populations in 2 days with our simple workflow.

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16S rRNA Sequencing Protocol
16S rRNA Sequencing Protocol

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

View Protocol (PDF)
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