16S/18S/ITS Amplicon Sequencing

We work with a wide variety of sample types and have extraction and purification protocols for more than 50 different matrices, including several low-biomass sample types. Each sample type presents its own challenges such as contaminants or inhibitors, which must be addressed appropriately to obtain high-quality DNA for library preparation.

Some examples of sample types include: human samples (faeces, saliva, nasopharyngeal and oropharyngeal swabs, skin and mucosal samples, tape strips), veterinary samples (faeces, biopsies, swabs, and urine), environmental and agricultural samples (soil, rhizosphere and root samples, filtered freshwater and seawater, sediments and filtered air), surface and biofilm samples, and food ingredients and products.

Biological samples should be collected, transported, and stored according to the downstream analyses to be performed. Different sampling options are available, including the use of bacteriostatic agents to minimise sampling bias.

We also offer optimisation services for novel sample types.

16S amplicon sequencing (and 18S/ITS for eukaryotes and fungi) provides a taxonomic profile of the microbial community, including relative abundances for each sample and study group.
The analysis includes alpha and beta diversity metrics, comparisons between experimental conditions, and identification of differential taxa that may serve as potential biomarkers. Taxonomic resolution is usually at the genus level (at species level when supported by the region/database, e.g. SILVA or UNITE). Detection limits depend on the sample type and sequencing depth.

Throughout the process, you will be supported by a Project Manager who will keep you informed of your project’s status. Once the analysis has been completed, you will receive a PDF guide together with login credentials to access and download the results from the Microomics server. You will receive the raw sequencing data, a report detailing the materials and methods used in the project, and an HTML report that allows you to explore the results using dynamic tables and graphs as well as download figures and perform comparisons between analytical models.

Project turnaround times vary considerably depending on the stages carried out by Microomics (DNA extraction, library preparation, sequencing, and bioinformatics analysis) as well as the number and type of samples analysed. Delivery times typically range from 4 to 12 weeks for amplicon sequencing studies. We recommend contacting our team for a more accurate estimate.

16S/18S/ITS amplicon sequencing uses PCR amplification of a marker gene to generate taxonomic profiles with relative abundance data. It is faster and more cost-effective but provides lower taxonomic resolution, generally at the genus level.
Shotgun metagenomics sequences all DNA present in a sample without targeted PCR amplification, enabling species- and strain-level identification, functional analysis of genes, and recovery of metagenome-assembled genomes (MAGs). It requires greater sequencing depth, bioinformatics processing and budget.
In summary, amplicon sequencing is best suited for efficient comparative microbiome characterisation focused on taxonomy, whereas shotgun metagenomics is better when maximum taxonomic resolution and functional information are required. We recommend discussing your project objectives with the Microomics team to determine the most appropriate approach for your microbiome study.