Microbiome Analysis

What are Microbioms?

Microbiome is a community of different microorganisms that interact with each other and with the surrounding environment. These microorganisms, like bacteria, archaea, fungi, protozoans, and viruses, are tiny living organisms that can be found in everywhere like deep-sea and agriculture soils, artic and tropical environments. Each habitat has a specific microbiome.
The microbiome is the most important player in ecosystems being the drivers of several biochemical processes namely the nutrient mineralization, nitrogen fixation, carbon sequestration and degradation of organic compounds. These processes contribute to sustain the health of any ecosystem. Microorganisms are also responsible for many industrial processes in the field of energy, mining and environment. Due their metabolic versatility, they can contribute to produce biogas, extract metals from mines, remediate polluted sites and treat wastewaters. Microbiome characterization is performed using molecular tools namely the untargeted metagenomic analysis or a target analysis using qPCR.

How does Microbiome Analysis work?

For most of our microbiome studies, we deploy metagenomics workflows through Next Generation Sequencing (NGS). Metagenomics is the study of the genetic material (genomes) from a mixed community of organisms. It is usually done by a technique called metabarcoding that looks at variations in specific DNA sequences to identify different species in a sample.
NGS is a technique which allows for in depth sequencing of numerous small fragments of DNA in parallel. Due to this parallel approach, the automatic detection of the nucleotides and the possibility of computers to process and reorganize large amounts of data, NGS has become the fastest and most cost-effective method for sequencing DNA.
With this technology, we can detect all microbial species or taxonomic groups in virtually any sample type, allowing the characterization of the composition, abundance and diversity of the microorganisms that compose any microbiome. Through the use of bioinformatics and data analysis tools, we then use the data generated by NGS to compare different conditions and samples, both in terms of their microbial composition and in terms of their metabolic potential.
The microbiome characterization can also be performed by targeting a specific organism using the qPCR technology. With this approach, we can detect and monitor the microorganism of interest, such as the iron-oxidizing bacteria in bioleaching processes and sulphate-reducing bacteria in microbial- induced corrosion.