Functional metagenomics: a powerful tool for discovering new molecules of therapeutic interest and decoding bacterial-intestinal cell interactions.
The actions of intestinal bacteria are still poorly defined to this day. However, a better understanding of these bacteria and their function has become a major challenge, with the ambition of being able to use them to improve our health and well-being. Understanding the mechanisms by which the intestinal microbiota interacts with our cells is essential in order to identify the genes and bacterial metabolites involved in this dialogue. On the one hand, the identified metabolites may constitute new targets with therapeutic potential. On the other hand, the possible receptors or signalling pathways identified in the host may represent targets for new drug antibodies or pharmacological molecules. One of the technological challenges in decoding these bacterial-intestinal cell interactions is the difficulty in culturing the bacteria present in our intestinal microbiota. Those that can be cultivated in the laboratory represent only a small part of them. These intestinal bacteria are in fact very sensitive to oxygen, which is harmful to them and is virtually absent in our colon.
In order to decode these interactions, MetaGenoPolis-INRAE has set up a cutting-edge technology called functional metagenomics. Functional metagenomics allows us to better understand the function of each of the bacteria in the intestinal microbiota, to decode host-microbiota interactions and to identify new molecules/targets of therapeutic interest without prior culture. In this way, it enables us to get as close as possible to the interactions that exist between bacteria and intestinal cells in the natural environment.
What does it consist ?
Functional (meta)genomics is based on a set of high-throughput screening technologies.
It targets all the genes present in a bacterial genome or in a more complex sample such as a stool sample. The DNA is extracted and then fragmented into 40kb pieces. Each 40kb metagenomic insert is cloned and integrated into an easily cultivable bacterium (e.g. Escherichia coli).
Libraries of metagenomic clones, from 20,000 to 70,000 clones, are then obtained. High-throughput screening is then developed with the aim of identifying genes with the desired function. The clones are then placed in the presence of human cells in order to identify the metabolic pathways that have been activated. The positive clones, carriers of the genomic sequence of interest, are sequenced with the aim of identifying the genes and knowing from which bacterium the metagenomic insert is derived. As the number of clones to be tested is large, a high-throughput approach is used for the growth and lysis of the metagenomic clones, cell culture, processing and analysis of the data obtained.
All the samples studied have enabled the MetaGenoPolis-INRAE to produce 18 metagenomic banks from, among other things, faeces from healthy donors, Crohn's disease patients or patients suffering from obesity, i.e. a total of 575,000 clones ready to be tested.