Microbiome analysis

The microbiome is a collection of living microorganisms (microbiota) that interact with each other, live in the same habitat, and form their ecological niche.

Microbiome research has evolved rapidly over the past few decades and has been linked to many aspects of human and animal health and to the functioning of ecosystems.

A fundamental paradigm shift in our understanding of microorganisms is that eukaryotes are meta-organisms and must be considered together with their microbiota as an inseparable functional unit.

Understanding the complex relationships among microbiomes across diverse hosts and habitats and their associations with the health of humans, animals, and plants, unfolds the potential for innovative and holistic approaches to diagnosis, treatment, and intervention within the context of the One Health concept. 

The CGR provides the following services to assess the microbial potential (learning about available microbiota in the given habitat) and the metabolic potential (deciphering available genetic material).


Back to: Centre for Genomic Research

Amplicon Sequencing

At CGR we have developed a pipeline targeting the V4 region of the 16S rRNA gene. Researchers can submit DNA samples, and we will perform library preparation, sequencing and analysis to generate a comprehensive report. However, we can offer assistance to identify bacteria, archaea, fungi, algae, and protists by targeting their 16S and 18S rRNA genes, internal transcribed spacer (ITS), or specific functional regions of genes. 

Metagenomic Sequencing

Whole-genome sequencing of microbial DNA from any environment can provide functional information and facilitate de novo genome assembly of genomes. We offer automated and miniaturised protocols to minimise the initial input required in the library preparation. Moreover, we provide short reads (Illumina) and long reads (Pacbio) sequencing platforms depending on the aim of your project. 


Metatranscriptomics involves sequencing the complete (meta)transcriptome of the microbial community and provides a snapshot of the gene expression in a given sample at a given moment and under specific conditions.At CGR we offer the complete process from RNA to data analysis. We can assist with experimental design and the integration of metagenomics data. 


At CGR we have a talented and experienced bioinformatics team. In conjunction with our powerful HPC, we can accommodate bioinformatics analysis of microbiome data from the above sequencing applications. We are very adept at analysing amplicon sequencing with QIIME2, one of our team being a moderator on the QIIME2 forums. We can run published tools and develop custom pipelines to create bespoke analyses for your project.