The microbiome consists of the whole mixture of genetic material belonging to the microbiota (the entire collection of microorganisms).
In environmental samples and environmental science, this mixture is often called eDNA.
One of Econumerics’ primary expertise is in the use of high-throughput Next Generation DNA Sequencing (NGS)-based approaches, for investigating the microbiome, from any biological- or environmental- sample. The use of NGS to investigate the microbiome is also called DNA metabarcoding.
eDNA bears invaluable information on the identity and functions of the organisms. In the simpler form, the approach is like collecting the fingerprints from a crime scene and comparing them to a database of previously identified suspects. However, information on what metabolic processes are carried out by the organisms can also be obtained.
DNA metabarcoding represents a powerful technique for rapid, comprehensive and cost-effective biodiversity assessments. Such audits provide qualitative and quantitative insights, into the composition and functioning of the microbial community. Examples of sample types that can be processed include blood, soil, swabs, stools, wastewater, roots, sludge, sputum, biofilm, sediments, water, food, wine, plankton etc. The method can be used to study bacteria, archaea, viruses, fungi, protozoa, pathogens, parasites etc.
Econumerics also offers robust and validated molecular assays based on PCR, that can be used for the detection, identification, quantification and typing of various organisms of interest. Compared to DNA metabarcoding, these tests are more targeted towards specific genetic markers, from any biological- or environmental- sample. We routinely use these assays for:
- targeting desired or undesired microorganisms (viruses, pathogens, parasites, fermenters, fungi, viruses etc.)
- monitoring biochemical functions (nitrogen metabolism, pollutants degradation, antibiotic resistance, nutrients removal etc.)
- quantifying any microbial species (e.g., over time, space or treatments etc.)
- comparing strains of organisms at sub-species level
- monitoring industrial processes or environmental impact and interventions (fermentation, wastewater treatment, land and water reclamation etc.)
- Biofilm investigations and biofouling (colonization or contamination of matrices, lifespan of membranes and filters etc.)
Sanger sequencing is the conventional method of DNA sequencing first developed in 1977. Sanger sequencing provides a high degree of accuracy, long-read capabilities, and the flexibility to support a diverse range of applications. Phylogenetic reconstructions based on the sequence of a single genetic locus obtained by this rapid and cost-effective method, can be used in broad range of disciplines, like agriculture, aquaculture, farming, forensics etc.
While hassle free Sanger sequencing services are available, meaningful, client-focussed interpretation of the data output is not. We routinely use Sanger sequencing and phylogenetic reconstructions to assist our clients in:
- genetically characterizing breeds, wildlife, pets, production animals, plants, crops etc.
- identifying desired or undesired microorganisms, including novel species, invasive alien pest etc.
- inferring the (phylogenetic) evolutionary relationships between an organism and its known relatives etc.