Shotgun Metagenomics

Our shotgun metagenomic analysis service is highly versatile and compatible with all types of samples.

• Human samples: gut, oral, skin and vaginal microbiome.
• Environmental samples: soil, water (marine and freshwater) and air microbiome.
• Agri-food samples: plant microbiome (endophytes and epiphytes), fermented foods, soils and industrial surfaces.
• Animal samples: ruminant, poultry and fish microbiome.

We process more than 50 validated sample types, ensuring high-quality DNA extraction and shotgun sequencing. Please do not hesitate to contact us regarding the sample types included in your study.

When necessary, it is used to answer both of the following questions: “Which microorganisms are present in this sample at species level?” and “What metabolic capacity do the microorganisms in this sample have?” It enables the identification of functional biomarkers with prognostic or diagnostic value in product evaluation studies, control versus treatment comparisons, longitudinal characterisation studies, descriptive studies, and other experimental designs.

This depends on sample complexity and project objectives: from 5–10 million reads per sample (basic taxonomic/functional profiling) to 20–50+ million reads for MAG recovery or fine-scale detection of low-abundance genes. Contact us using the enquiry form so we can assess your project as a whole.

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 file that allows you to explore the results in dynamic tables and graphs, download figures, and perform comparisons between alpha and beta diversity models.

Microomics has its own certified clean-room laboratory for DNA extraction. In addition, we use negative controls (extraction blanks/NTCs) and positive controls (mock communities), generating quality control checkpoints throughout the project. We maintain contact with the researcher during the entire process, providing updates on the progress of the samples throughout our workflow.

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, direct functional analysis of genes/pathways, 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 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.