Elucidating the faecal microbiota of mammalian and avian hosts as a foundation for microbial source tracking

01.01.2010 - 31.12.2012
Stipendium
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 α-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.

Personen

Projektleiter_in

Institut

Grant funds

  • Österr. Akademie der Wissenschaften (National) Austrian Academy of Sciences

Forschungsschwerpunkte

  • Environmental Monitoring and Climate Adaptation: 50%
  • Efficient Utilisation of Material Resources: 50%

Schlagwörter

DeutschEnglisch
fäkale Verunreinigungfaecal pollution
genetische Markergenetic markers
intestinale mikrobielle Gemeinschaftenintestinal microbiota
Verursacheridentifizierungmicrobial faecal source tracking
WasserqualitätWater Quality

Externe Partner_innen

  • Forschungsinstitut für Wildtierkunde und Ökologie Veterinärmedizinische Universität Wien
  • Department of Chemistry and Biochemistry, University of Colorado at Boulder,
  • Cornell University Department of Microbiology Ithaca, NY

Publikationen