The contamination of water by faecal pollution has enormous impacts on a global scale. Estimates state that 1.1 billion people worldwide lack access to save drinking water. For over a century the microbiological water quality has been tested by cultivation of indicator bacteria. Microbial hazard- and risk assessment increasingly demand for comprehensive faecal pollution analysis including the quantification of total microbial faecal pollution and a reliable identification of its major contributing sources. However, sole application of standard faecal indicators cannot sufficiently meet these challenges. The abundant intestinal bacterial populations are very promising alternative targets. There is growing evidence that intestinal microbial communities from vertebrate hosts possess populations distinct from those of non-intestinal habitats. In addition it seems that co-evolution has led to a co-diversification of vertebrate hosts and their intestinal microbiota. However, microbial populations in intestinal and non-intestinal systems exhibit a dazzling array of diversity which could not be resolved in the past due to methodical constraints. As a consequence molecular analysis of microbial faecal pollution has been based on a fragmentary puzzle of very limited sequence information. The AIM of the proposed research programme is to establish a unifying eco-phylogenetic framework for intestinal communities from vertebrate faecal excreta and to evaluate its robustness as a future foundation for molecular bacterial faecal indicator diagnostics. The realisation of the project becomes feasible for the first time by combining state-of-the-art sequencing technologies, novel bioinformatics and a hypothesis driven study design. PHASE 1 - will establish a defined 16S-rRNA-gene ultra-deep sequencing database covering a representative sample selection from faecal excreta of endothermic (mammals and birds) and ectothermic vertebrates (fish, amphibians and reptiles) and representatively chosen non-intestinal habitats. Sampling design for intestinal communities will be guided by phylogenetic vertebrate relationships, intestinal physiology and diet. Selection of non-intestinal habitats will cover carefully chosen and well-defined soil habitats. Non-intestinal habitats will be selected to exhibit a defined gradient of faecal pollution levels covering locations with only a ¿pristine¿ background level caused by wild-life to sites with intensive agricultural fertilisation using large amounts of faecal excreta. PHASE 2 - will focus on community sequence data analysis using comparative and multivariate statistics. The hypotheses on the distinctness of intestinal vertebrate populations as well as the co-diversification of vertebrate host groups and their intestinal populations will be reviewed as a foundation of molecular detection of total faecal pollution and source allocation, respectively. Finally, the possibility will be evaluated whether the established eco-phylogenetic framework supports the design of a modular molecular bacterial faecal indication system with nested levels of specificity (i.e. markers for total faecal pollution and respective vertebrate sub-groups). In conclusion, the proposed research will provide the first scientific basis to systematically understand the occurrence of abundant intestinal bacterial populations in the environment. The eco-phylogenetic framework will be open for iterative adaptations and expansion towards the global scale supporting water quality testing for tomorrow¿s generation.