Metagenomics Services

Explore bacterial and fungal communities in detail across a range of niches with NCIMB's next-generation sequencing (NGS) metagenomics services.

What is metagenomics?

Metagenomics is the study of genetic material recovered directly from environmental samples. It offers game-changing insight into the microbial diversity. NCIMB can analyse samples including water, soil and gut microbiomes, or samples from production facilities, fermenters and bioreactors.

Metagenomics provides new insights into the taxonomic makeup of the system under study and the relative abundances of microbes including differential abundance testing and extrapolating functional context.

Benefits and applications of metagenomics

Many microbes do not grow under laboratory conditions and culture-based techniques only identify a fraction of the whole community.  Metagenomics identifies culturable and non-culturable taxa in one assay.

At NCIMB we offer 16S or ITS based amplicon metagenomics and whole-genome shotgun approaches.

Amplicon approaches allow you to quickly understand taxonomic makeup and distribution in a cost-effective manner. The whole-genome approach enables a full interrogation of the underlying genes and pathways within the ecosystem.

16S Metagenomics - bacteria

Metagenomics based on PCR amplification of marker genes such as 16s rDNA offers a cost-effective and rapid way to understand the makeup of a bacterial community.

It can be a good option to consider when testing to identify food spoilage bacteria.

We use the V3-V4 regions of the 16S gene in our standard 16S metagenomics service. However, if you have specific requirements for other variable regions, we can take care of the whole process from primer design to data analysis.

16S metagenomics is semi-quantitative and deals with the relative abundances of taxonomic groups. For greater quantitative power, 16S metagenomics can be combined with qPCR, which  provides rapid quantitative information for an organism or group of organisms.

ITS Metagenomics - fungi

Fungal ribosomes have a a large and a small subunit. The ribosomal RNA operon, that is the DNA that codes for ribosomal RNA, has three rRNA sequences, and two internal transribed spacer regions ITS1 and ITS2.  Fungi can be identified through sequencing of either one or both of the internal transcribed spacer (ITS) regions, and metagenomics based on PCR amplification of the internal transcribed spacer regions (ITS) offers a cost-effect way to understand the makeup of a fungal community.

Whole genome shotgun metagenomics

Whereas 16S and ITS metagenomics sequencing use marker genes to examine a metagenome's taxonomic diversity, Whole-genome metagenomics sequences bulk DNA from an environmental niche. In other words it can be used to sample all genes within all of the organisms that are present in an environmental sample. This allows not only taxonomic identification, but also a full interrogation of the underlying genes and pathways within the ecosystem.


At NCIMB, we have the microbiological knowledge, together with the bioiformatics capability and expertise required to get the most from your NGS data, no matter what your research or commercial aim.

Using the latest software and algorithms for metagenomic community analysis we can analyse microbiome data rapidly and accurately. Our bioinformatics capability scales to your project’s requirements, with clearly summarised and visualised data.

Expert advice

We can advise you on the most appropriate approach for sampling and testing. Please contact us for more information.

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