We are now aware that our commensal microbiota have a profound impact on the development of lymphoid tissue as well as the functional set-point of many innate and adaptive immune programs. This translates into a major influence on health and disease susceptibility. Indeed, we expect that the unique microbiota that we harbor in our gut and on our mucosal surfaces will carry information that will help predict our individual response to microbes. The LabEx MI proposes to verify this expectation and identify the correlations between immune phenotype variance, genetic polymorphisms and enterotype differences.
Defining commensal microbiota
Commensal microbiota represents an ensemble of microorganisms that reside in close proximity and in mutualistic relation with a host organism. Human beings have populations of bacteria, viruses and fungi in different parts of the body, such as in the surface or deep layers of skin (skin microbiota), the gut (gut microbiota), the nares (nasal microbiota), and so on.
Gut microbiota (formerly called gut flora) is the name given today to the microbe population living in our intestine. It contains tens of trillions of microorganisms, including at least 1,000 different species of known bacteria with more than 3 million genes (150 times more than the number of human genes). Microbiota can, in total, weigh up to 2 kg. One third of our gut microbiota is common to most people, while two thirds are specific to each one of us. In other words, the microbiota in our intestines can be used as an individual identity card – this is referred to as your enterotype.
Our power to identify association signals
In the context of the proposed project, we will establish correlations between the number and types of bacteria, fungi and viruses present within the commensal microbiota and the reactivity of the immune system in a panel of Immune Phenotypes. These associations will be further correlated to the host genotype. Finally, to provide an integrated view of the different interactions, we will be assessing the reactivity of the immune system using microbe or microbial components as stimuli (e.g. E. Coli vs. LPS) with measurements including cytokine / chemokine production, and changes in gene transcription and miRNA expression (see below). Correlations between bacterial strains and Immune Phenotypes will be further tested for causal relationships through the use of animal models.
The majority of symbiotic microbiota remain non-cultivable. Furthermore, the microbial diversity is estimated at approximately 104 unique strains of bacteria and unknown numbers of fungal and viral strains. These two constraints thus demand high-throughput sequencing technologies. While this is now possible through pyro-sequencing of PCR-amplified 16S rDNA (2nd generation sequencing technologies), the data remains semi-quantitative. We have therefore chosen to utilize the Ion Torrent PGM system as it provides long reads (> 500 base pairs in length) and it permits accurate quantitation of the different strains and species. Fungal diversity will be analyzed by single molecule sequencing of internal transcribed spacer (ITS) regions. Viral like particles (VLPs) will be purified by serial filtration and centrifugation, followed by DNA or RNA extraction and single molecule sequencing.
The concept of a variable human microbiome. The core human microbiome (red) is the set of genes present in a given habitat in all or the vast majority of humans. Habitat can be defined over a range of scales, from the entire body to a specific surface area, such as the gut or a region within the gut. The variable human microbiome (blue) is the set of genes present in a given habitat in a smaller subset of humans. This variation could result from a combination of factors such as host genotype, host physiological status (including the properties of the innate and adaptive immune systems), host pathobiology (disease status), host lifestyle (including diet), host environment (at home and/or work) and the presence of transient populations of microorganisms that cannot persistently colonize a habitat. The gradation in color of the core indicates the possibility that, during human microevolution, new genes might be included in the core microbiome, whereas other genes might be excluded. This LabEx will exploit the variable human microbiome in order to explore connections between host genetics and immune responsiveness. [Figure take from Turnbaugh et al. (1)]