CosmosID

Amplicon Sequencing Services & Solutions

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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.

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Bacteria / 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!

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