Sequencing ServicesAmplicon Sequencing


Amplicon Sequencing Services & Solutions

Amplicon Sequencing has been an integral methodology for microbiologists and microbiome researchers for decades; enabling the generation of whole community analysis of bacteria or fungi in any complex sample. Like many metagenomic approaches, amplicon sequencing offers unique advantages to microbiome researchers, many of which are highlighted on this page.

The CosmosID team have extensive experience in supporting the design and execution of amplicon-based metagenomics projects for both industry and academia for a wide range of applications, using both human and non-human sample types. The advantages of an Amplicon-based approach are:

  • Cost-effective

  • Can be advantageous for swabs and other low biomass samples

  • Well suited for taxonomic profiling in new, under-studied or exotic sample types

  • Well-suited for large cohort, biobanking and population-based studies

  • Well-suited for routine testing, including microbiome-based diagnostics


Amplicon SequencingBacteria / Archaea - 16S rDNA Sequencing

The 16S rRNA gene is comprised of ~1500 base pairs, made up of 9 hypervariable regions (V1-V9) and universally present in all in prokaryotic organisms (Bacteria & Archaea). Through selecting specific hypervariable regions for PCR amplification & sequencing, such as V1-V3 or V3-V4, CosmosID generates bacterial community profiles for comparative analysis purposes for almost any sample type.

Amplicon SequencingFungi - ITS Sequencing

Internal transcribed spacer (ITS) regions are spacer DNA regions universally present in eukaryotic organisms such as fungi and thus adopted by the microbiome research field for PCR amplification and sequencing when analyzing the fungal community, or mycobiome, in a complex sample. Through selecting the ITS1 & ITS2 regions, CosmosID generates fungal community profiles for comparative analysis purposes for almost any sample type.

Amplicon SequencingSample Processing

CosmosID’s CLIA-certified, GCP compliant facility receives samples from all around the world. Whether you’re batch sending samples for a microbiome R&D project or coordinating with multiple clinical trial sites, your precious samples will be barcoded & accessioned using the CosmosID LIMS system for sample tracking and project management.

CosmosID uses DNA extraction protocols optimized by samples type resulting in minimal bias, optimum yield and purity.

So whether you’re sending a biopsy, skin swab, raw fecal matter or DNA, rest assured your precious samples are safe with us!

Amplicon SequencingPCR Amplification & Sequencing

CosmosID offers Illumina-based Amplicon sequencing workflows performed using the Illumina MiSeq platform (2x250bp) at competitive, per-sample rates:

  • 16S V1-V3 Sequencing

  • 16S V3-V4 Sequencing

  • ITS1 & ITS2 Sequencing

  • Other Amplicons available upon request

Amplicon SequencingBioinformatics & Other Deliverables

In addition to sample processing & sequencing, CosmosID includes:

  • Taxonomic classification via the CosmosID curated 16S database using a closed-reference OTU picker and 97% sequence similarity through the QIIME framework.

  • Interactive and user-friendly charts & visualizations with access to comparative analysis features including heat maps, PCA plots, Alpha Diversity & Beta Diversity PCoA

  • Fastq/Fasta file transfer via AWS s3 Bucket/Dropbox

Amplicon SequencingTurnaround Time & Customer Service

CosmosID offers different turnaround time options for projects where samples can be processed as fast as 1-2 weeks for amplicon sequencing. Simply let us know about any special requirements and we can tailor our service accordingly.

Once samples have arrived at the lab, our operations team will keep you updated on a weekly basis on the status of your project!

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Amplicon SequencingFrequently Asked Questions

When would I choose amplicon over shotgun?

Amplicon sequencing is a cost effective option for very low biomass or novel and/or alien samples types as well as samples like biopsies that would typically be high in non-microbial biomass, that may be otherwise costly or ineffective to test with shotgun metagenomics. Amplicon sequencing can also be useful for routine testing once shotgun-based R&D has been completed and high-level profiling is sufficient such as at the phylum or genus levels.

What data can be generated through Amplicon sequencing?

For amplicon sequencing, whilst seeing some species-level calls is common, depending on the sample type, it is typical that genus-level resolution should be expected. Furthermore, pipelines like PICRUST can be run to infer the functional potential of a metagenome based on the taxa present but please note, this analysis is not based on observed genes.

How are the hypervariable regions selected to analyse?

Depending on your sample type and what is widely accepted in the field, CosmosID offers a range of different hypervariable region combinations which give you the best chance to differentiate the organisms you would expect to see based on the divergence in their 16S rRNA gene sequences. For example, skin microbiome samples are typically abundant in staphylococcus species which can be most easily detected via the V1 and V3 regions. For stool samples which contain a very high diversity of organisms, V3 and V4 regions are typically targeted. Simply reach out with your sample type of interest and we’ll get your study methodology designed in no time!