Diet and Human Microbiota clinical trials

Microbiota and Related Metabolome in Omnivore, Vegetarian or Vegan Diets

The human body houses a huge microbial ecosystem, including the intestinal and oral microbiota. Both these ecosystems, and, in particular, the intestinal one, are responsible for maintaining human health. The response of the organism to the diet and the relative alteration of the susceptibility to disease are worth of investigation to comprehend the role of the microbiota to maintain the state of well being in humans. This concept, which is the overall scientific basis of the entire project, perfectly fits with the declared scopes of Horizon 2020. Understanding the impact of omnivore, vegetarian and vegan diets on human intestinal microbiota is aligned to the Grand Societal Challenge of the Horizon 2020 scheme, which is addressing the human nutritional needs and the impact of food on human physiological functions. In particular, studying the link between dietary habits and the intestinal microbiota activity will be pivotal to improve the food-based promotion of health and well being. The project aims at studying how the omnivore, vegetarian and vegan diets may affect the oral intake of microorganims, and the composition of the oral and fecal microbiota. With the aim to build up a permanent European platform for such type of studies, ten Research Units (RUs) are involved in the proposal, with the partnership of 16 National and, especially, foreign Institutions, covering 12 different countries. About 50 omnivore, vegetarian and vegan volunteers, for a total of 150 subjects will be recruited. Volunteers will be asked to fill in diaries, describing their dietary habits, and to collect biological samples (saliva, feces and urine), once a week for three weeks. For obvious ethical constraints, biopsies will be not available in this study. RUs will share their tasks, mainly depending on the nature of the samples to be studied, namely foods and biological samples. Based on the different dietary habits, the presumptive intake of microorganims will be estimated using literature data and, especially, culture-dependent methods. Typing and antibiotic resistance of some food related microbial communities or foods will be also investigated. The microbial diversity of foods, whose microbiota has never been studied in depth, will be characterized by PCR-DGGE and deep sequencing. The metabolome characterization will complete the overview on foods. After collecting and preparing biological samples from the three diet groups, the oral and fecal microbiota will be studied. The viable cell number of several microbial groups will be estimated in fecal samples, before freezing. Preliminarily, the microbial diversity of saliva and fecal ecosystems will be analyzed through PCR-DGGE. PCR assessment of genetic basis of antibiotic resistance will be also carried out. Selected numbers of biological samples will be further subjected to next generation sequencing, aiming at determining representative individuals/samples of the three types of diet. Only for feces, representative samples (e.g., 4/5 for each diet) will be subjected to meta-omics analyses based on meta-genomic, meta-transcriptomic and meta-proteomic approaches. An integrated and iterative workflow will be also developed, by assembling an in house synthetic meta-genome. The functionality of fecal samples and/or of isolates from feces will be characterized based on fecal genotoxic and anti-genotoxic activities, and modulation of the immune response. In agreement with an holistic approach, the metabolome analysis of saliva, feces and urine will complete the characterization of biological samples. All data available from the different RUs will merge into a common database, whose structure will be developed during the project. Based on the literature data (ISI Web of Knowledge), this is the first study that aims at correlating the effect of the main dietary habits on the oral and fecal microbiota through integrated meta-omics analyses.