Functional and genetic characterization of microbial communities in the gastrointestinal tract of pigs.

The ability to fully characterize the intestinal ecosystem is the cornerstone to understand the effectiveness of practical solutions to manage the intestinal homeostasis and to improve the health status and disease resistance of the animals. The main objectives of WG1 are to compare procedures to characterize the microbiome under the new light of the metagenomics approach in the GIT of pigs to define its composition and functionality at different production phases under experimental conditions (optimized housing and feeding conditions) and to define the status of eubiosis and dysbiosis. Due to the complexity of this scientific approach, the following further tasks have been identified for WG1:

  •  To critically highlight the specificities of each of the available NGS methods for studying the bacterial profile, comparing also the available data provided by the COST partners.
  • To standardize the microbiome sequencing techniques across laboratories and establish equivalence of different methodologies, without intention to restrict research to one technique. Detailed discussions, opinion exchange and research are required to develop a common strategy as it is a practice in consortia for human studies and in the National Institutes of Health (NIH) in the USA.
  •  To harmonize the NGS data by the use of shared bioinformatics tools.
  •  To establish shared protocols suitable for determining the “standard” and determine the “optimal” microbiome in the GIT of pigs.
  • To assess the microbiome across different pig production phases and experimental conditions, to obtain an overview in terms of composition and functionality, including analysis of metabolites on the gut ecosystem of healthy pigs.
  • To exchange experience and knowledge, protocols, experimental design and data analysis with other WGs ESRs in an international forum.