Benign steatohepatitis (Non Alcoholic Fatty Liver Disease / NAFLD) represents a spectrum of liver diseases encompassing simple fatty infiltration (steatosis), fat and inflammation (non-alcoholic steatohepatitis - NASH), and cirrhosis in the absence of excessive alcohol consumption, viral diseases or other identified etiologies. Due to the high prevalence and to the fact that NAFLD is a common condition that has significant adverse health consequences for those who are afflicted, NAFLD is considered a major public health problem throughout the world. Liver disease has been associated with changes in the intestinal microbiota and specific pathways in which microbiota is involved have been demonstrated to play a role in exacerbation of liver disease. Taking advantage of recently available high throughput sequencing technologies, the three partners involved in the project are currently working in close collaboration to develop a clinically validated biomarker platform to establish quantitative description of gut microbiota and correlations with disease phenotypes. In this context, MetaGenomic Species (MGS, sets of genes predicted to belong to the same microorganism, likely bacterial species) that are associated with NAFLD but are significantly less abundant in advanced liver disease (NASH) were identified. A biomarker is under development based on these results. This project aims at better understanding the biology beyond the biomarkers, i.e. identify which biological functions associated to the biomarkers could explain their potential beneficial effect, as described recently for Faecalibacterium prausnitzii. Since most gut bacterial species cannot easily be cultivated, an innovative strategy will be used. Briefly, specific probes targeting MGS of interest will be used to enrich stool fractions. DNA will then be extracted from these enriched fractions. A high throughput functional screening method of metagenomic libraries will be used to characterize the putative protective effect of molecules that could be encoded by genes belonging to these MGS. Mice will also be colonized with microbiota derived from patients and known to contain low or high proportions of “protective” MGS, then challenged with high fat/fructose diet to explore the effect of these selected microbiota on the onset of steatohepatitis. This project will make it possible for Enterome to validate the technological concept on which its overall activity is based. Indeed, if a functional link is demonstrated between the selected MGS species identified using Enterome’s technology and the development and/or maintenance of the disease, this would fully validate the relevance of the quantitative metagenomic analysis to accurately identify robust biomarkers. In addition the project will generate new IP such as new clones and new molecules of interest that will potentially be further developed in future projects. New technical tools and animal models colonized with MGS of interest will also be useful in future research projects aiming for example at isolating bacterial species corresponding to beneficial MGS. This will be an important asset in a very competitive field of research that has generated lot of interest from big pharmaceutical companies these last few years, thus supporting the international development of the company in a close partnership with its academic partners INRA-Micalis and INRA-Metagenopolis.

The future challenge in animal production will be to provide food to a growing human population by respecting a balance between quality products, consumer acceptance and safety, as well as animal welfare. In a perspective of safe and sustainable food systems, reducing the use of antibiotics in livestock is a major concern. In fact, antibiotic resistance is one of the major medical challenges of the 21st century. The transfer of genes conferring resistance through the environment and the food chain, the potential for development of resistant bacteria and the appearance of therapeutic failures in human medicine, notably due to zoonotic bacteria, constitute major health issues for livestock farming sectors. In the pig breeding industry, the weaning period is often accompanied by a decreased growth rate caused by disparate food intake and diarrhoea due to digestive disorders that might be associated with bacterial population disequilibrium (i.e. dysbiosis) and/or opportunistic intestinal infections. Alarmingly, during this transition period the prophylactic use of antibiotics is still very frequent in order to limit piglet morbidity and mortality. Thus, reducing the prophylactic use of antibiotics in weaning pigs is a main issue and there is a strong need for alternatives. In this context, we have built a public-private partnership that gathers INRA scientists and industries from economic sectors of both animal feeding and pig breeding. PigletBiota is a precompetitive project that will study the physiological and genetic bases of the piglet sensitivity at weaning, as a prerequisite to identify innovative actions to adapt animals and pig production systems to a reduction of antibiotic use. The global aim of the PIGLETBIOTA project is to develop research that will contribute to adapt pig production systems to a reduction of antibiotics. The project proposes an integrative biology approach to determine the main factors influencing the variability of the individual’s robustness at weaning. We will monitor piglets for health, immune, stress and zootechnical traits and will characterize the intestinal microbiota diversity and composition as well as the contribution of host’s genotypes. The experimental design will combine various environments, including experimental and commercial farms, and ages at weaning and all animals will be fed without antibiotics. Animals (n~1000) will be clinically surveyed, measured for various traits related to production, immunity and stress, and genotyped with high-density SNP chips. The genetic parameters of the sensitivity at weaning will be estimated and genetic association studies performed. Faecal samples before and after the weaning date will be collected for characterizing the dynamics of the gut microbiota and studying its influence on the individual sensitivity at weaning. Animal and microbiota data will be vertically integrated in order to better understand the interplay between the these two levels of this biological system, and to develop robust indicators of weaning sensitivity. Finally, a functional screening using INRA platforms dedicated to human studies will be performed in order to detect active molecules to be tested in vivo and by using an axenic pigs model. The PigletBiota public-private consortium will favor translational research and innovation.