Elucidating faecal microbiota for source tracking

The contamination of water by faecal pollution has enoromous impacts on a global scale. Estimates state that 1.1 billion people worlwide lack access to save drinking water. For over a century the microbiological water quality has been tested by cultivation of indicator bacteria. Increasing demand for the ability to precisely describe the nature and extent of faecal contamination of water resources led to recent developments in the field of microbial faecal source tracking (MST). In contrast to standard faecal indicators these methods are designed for faecal sources identification. Genetic markers targeting host-specific intestinal bacteria of the phylum Bacteroidetes have recently be holding a lot of promise in this field. However the design of genetic MST approaches has been based on highly incomplete information about the faecal community composition. Available markers do not cover many important source groups and exhibit inappropriate levels of source-specificity. The aim of this project is the investigation of the qualitative and quantitative faecal bacterial community composition of mammalian and avian hosts. Host sampling will be guided by the hypothesis that coevolution of the host and its microbiota is the main factor influencing qualitative community composition. Consequently faecal samples will be taken from host animals from all orders of Mammalia and Avia with extant members accessible in the Austria in order to achieve a broad focus in host phylogeny. In addition sampling will take into consideration other environmental factors with a potential impact on the microbiota (diet, habitat, domestication) as well as the relevance of hosts as sources of faecal pollution. After DNA extraction and total bacterial community PCR, high- throughput sequencing will be used to compile a database of partial 16S rRNA gene sequences of faecal microbiota from ~200 samples. This ultra-deep amplicon sequences will yield more than four million sequence reads. Faecal microbiota will be basically characterised by determining a-diversity, phylotype richness abundance and frequency. Communities will be compared using advanced bioinformatics tools for calculating divergence-based ß-diversity measures such as UniFrac to investigate the role of coevolution and other factors in the shaping of the faecal communities. Consequently the compiled database and analysis will allow the identification of phylotypes or whole pyhlogenetic clades which are specific to certain groups of animals. The chosen approach will permit the formulation of markers on various levels of host-specificity e.g. general - Mammalia - Artiodactyla - Ruminantia - Bovidae - Bovinae. In this way the proposed project will establish a stable basis for the definition of candidate MST markers. It will be open to complementation by sequences from other geographical areas or samples from hosts not covered in this study.

Summary for public relations work The FWF project IntMicro focused on the elucidation of the bacterial community composition in the gut of mammals and birds. The two main aims of the project were: Firstly, to find and identify bacterial populations that are highly specialised to specific groups of host animals. The highly host-adapted symbionts are potentially critical for the health and survival of the host by providing essential nutrients or by serving as a barrier against pathogenic microorganisms. Secondly these host-associated bacteria are ideal target that can be used to track the source of faecal pollution in contaminated water and the environment.The contamination of water by faecal pollution has enormous impacts on a global scale. Estimates state that 750 million people worldwide lack access to save drinking water. For over a century the microbiological water quality has been tested by cultivation of indicator bacteria. Recent years brought the development of microbial faecal source tracking (MST) methods that allow the microbiological or molecular-biological identification of the source of faecal pollution directly in a water source.In the course of the IntMicro project faecal droppings were collected from almost 100 different species of mammals and 50 species of birds, ranging from common rodents and ruminants such as deer and cattle to rare carnivores and endangered animals such as rhinos and polar bears living in very different habitats. Bacterial DNA from these samples was sequenced to determine the bacterial community composition. This resulted in a DNA sequence database with more that 2 million sequences and 150 categories of background data on the host animals and sampling. The results of the project showed that the main factors determining the composition of the intestinal microbiota are the genetic ancestry of the host (host genotype) and the diet the animal is feeding on. The relative dominance of one of these two main drivers is varying between different groups of animals. One example for the strong influence of host physiology and genotype is the group of ruminant animals, which showed a highly distinct gut microbe composition when compared to other mammals. The results obtained in this study might have strong impact on the rapidly evolving research field of host-microbe interactions. On the other hand the host-associated bacteria found in the course of this study show strong promise for the development of molecular tools for faecal indication and source tracking. Therefore they will contribute to the assurance and improvement of the quality of water used for drinking and recreation and consequently to public health and disease prevention.