Metagenomics and metagenetics

Metagenomics and metagenetics



Genomics is the study of all the genetic information (genome) contained in an organism and stored within the DNA. We distinguish the parts of the DNA coding for a function (the genes) of the other parts involved in the structure of DNA, polymorphism and regulation of functions. Genomics can identify the known functions available in an organism, the manner in which they are ranged (synteny), the specific areas of a taxon and those more accessories. Metagenomics is the study of all genetic information contained in an environment (hence the Greek prefix meta). The environmental DNA is first extracted and then sequenced for analysis. It differs from metagenetics that allows the identification of taxa present in a sample. Here a genetic marker is targeted within environmental DNA to be sequenced and associated with a reference taxon.

Medical field

The field of application of metagenomics and metagenetics in human (or animal) health is limited to microbiomes (ie all the microbes present on a tissue). Microbiomes are located within the human body on the integumentary, respiratory, digestive, visual and reproductive apparatus. Medical disciplines impacted by these technologies are therefore numerous. Many scientific studies show since the 1980s the involvement of commensal bacteria (friendly bacteria) in tissue maintaining. These works started with the digestive system, because humans do not have all the genetic material to digest and / or transform certain foods into usable and indispensable molecules (like the cow or rabbit that can not metabolize plant cellulose). There are therefore symbiotic interactions between commensal microbes and the human body. These interactions can be functional in nature (an enzyme to degrade a food) but also, and quite simply, the occupation of an ecological niche in order to prevent invasion of pathogenic organisms. These balances have been studied extensively since the advent of high-throughput sequencing. In some diseases, scientists have found microbiome imbalances by metagenetics. Metagenomics has allowed to identify the genetic functions impacted by these changes. Thus some lipases or lantibiotics could be characterized.
Since the 2010s, several laboratories have been working on microbe-based drugs that allow a rebalancing of the microbial flora. In this context, it seems likely that in the context of certain diseases (eg Crohn's disease), a diagnosis of the microbiome may be necessary to choose the combination of microorganisms best suited to ingest daily.

Food sector

In the agri-food sector, the applications of metagenetics and metagenomics are broader. They first affect the quality service in the context of the contamination monitoring. Currently, the methodology for identifying a health risk is carried out from the analysis of several probable contaminants, pre-emption beams, gathered at the level of standards. So in the field of water, specific monitoring of enterobacteria and proteobacteria is provided. We only see what we are looking for. This approach can lead to interpretation biases but also not to address the problem of contamination and risk management. In addition, the presence of certain bacteria taxa is not necessarily linked to a health risk in humans. Indeed, it is necessary that the bacteria is competent to infect an organism. In the wild, it is estimated that only a part of the populations of a species bacteria are pathogenic. In Vibrio cholerae , 50% of the environmental strains are not pathogenic. Metagenetics allows a more exhaustive approach (warning: this method does not guarantee 100% perfect completeness) of the composition of microbial flora an environment. Metagenomics will also provide information on the presence of pathogenic functions, production of biofilms, etc.
Another service impacted is the production by fermentation processes. Metagenomics and metagenetics offer better control of biological parameters by a finer control of fermentation flora. It is possible to follow taxa or functions according to the variation of physical and / or chemical parameters or the conclusions of the organoleptic tests.
Finally, the R&D department will also benefit from the support of metagenetics and metagenomics in many fields. In particular, it will find a real springboard in a context of the next green revolution in agriculture. The latter will go through several phases:

It will therefore be necessary to develop an increased monitoring of soil microbial flora, which can be very diverse.

Environment sector

The environment sector is a very heterogeneous field. There are industries of de-pollution, certain branches of industries in energy, construction or water management. Here, the needs will be almost similar to those of the production and R&D services of the agri-food sector (eg characterization sewage sludge). The difference lies mainly in the specificity of the requests and the difficulty understanding between the actors of the industrial and biological world.

The innovations needed for massive deployment

The era of metagenomics and metagenetics is gradually opening up. They make it possible to carry out studies and improvements which have not been possible in recent decades. Nevertheless, several areas of improvement are necessary to obtain 100% of the expected efficiency by these technologies:

Currently, all projects are launched and each new year brings significant progress on these various points. In our core business, we are driven by electronic innovation that allows us to use brute force in algorithmic resolution. In addition, advances in the semantic world (driven by companies like Google) also offer us solutions in data mining biology databases.
In terms of wet biology, annual innovations are important, but they also have a perverse effect for companies in the analysis sector. Sequencing technologies and kits developed for these systems are quickly becoming obsolete in favor of new features. However, investments are important and present a strong source of risk in the field of biotechnology.