ESR2: Evolution of the small intestine microbiome in pigs from birth to post weaning under normal and stress conditions


Targeted manipulation of the gut microbiota is increasingly recognized as a mean to improve livestock health. We know that the interpretation of bacterial communities of the small intestine by studying the rectal microbiome from stool samples has its limitations. Thus, getting a more in depth understanding of the precise role of the intestinal microbiome in health and disease requires a method to access the ‘true’ (not fecal) intestinal microbiome.


  1. Set up and validate an in vivo sampling tool (e.g. capsule endoscopy) to collect small intestine content in living pigs.

  2. Determine to what extent the small intestine microbiome changes over time and to assess the temporal stability of an individual pig’s gut microbiome.

  3. Compare previous results with pathophysiologic conditions to evaluate the consequences of an ETEC infection, as a model for pathogens interference.


  • In a first step, the new in vivo sampling tool will be optimized and validated.

  • In subsequent steps, the microbiome development through pigs life cycle will be monitored under normal and pathophysiological conditions.

Expected results

  1. Novel in vivo sampling tool for small intestine content will be validated and standard operating procedure prepared (D2.1).

  2. Extended knowledge on the evolution of phylotypes and/or bacterial species in the small intestine microbiome from post weaning to slaughter (D2.4) under physiological and pathophysiological conditions (D3.7).

Planned secondments

  • At: UNIBO (7 mo); Bioinformatics for microbiome and metabolome data;
  • At: TwentyGreen (1 mo); training in specific microbiological analysis of prebiotics and get inside on how to develop customer information.

Enrolment in Doctoral degree:

ESR2 will be enrolled at the Department of Agricultural and Food Science (DISTAL) of University of Bologna.


Catherine Ollagnier (Agroscope), Giuseppe Bee (Agroscope), Paolo Trevisi (University of Bologna)