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. To date, understanding the precise role of the intestinal microbiome in health and disease has been restricted by limited access to the ‘true’ (not fecal) intestinal microbiome. However, interpretation of bacterial communities of the small intestine by studying the rectal microbiome from stool samples has its limitations.


  1. Unravel our understanding of the small intestine microbiota and its evolution under normal and pathogenic conditions while following each pig individually.
  2. Set up and validate an in vivo sampling tool (e.g. capsule endoscopy) to collect small intestine content in living pigs.
  3. Determine to what extent the small intestine microbiome changes over time and to assess the temporal stability of an individual pig’s gut microbiome.
  4. Compare previous results with pathophysiologic conditions to evaluate the consequences of an ETEC infection, as a model for pathogens interference.


  • Study 1 (validation study): Pigs from 6 to 100 kg will be administered orally with capsule. The capsule passess through the stomach, opens in the small intestine, delivering indelible marker and takes the digesta sample. The capsule is excreted with feces, delivering content of pig’s small intestine. The pigs will be euthanized to compare the small intestine content at the site of the marker and content sampled by the capsule. Microbiome analysis of the two sampling methods will be performed.
  • Study 2 (comparative study): Pigs will be administered with the capsule, starting from 6 kg until they reach order to follow microbiome development through their life cycle. Piglets will be divided in two groups out of which, one will be infected with E.coli strain. The samples taken by the capsule from both groups will be analysed to compare the small intestine microbiome of the pig under physiological and pathological condition.

Expected results

  1. Novel in vivo sampling tool validated and standard operating procedure describing the animal model written.
  2. Extended knowledge on the evolution of phylotypes and/or bacterial species in the small intestine microbiome from birth to post weaning.
  3. Knowledge on the evolution of the small intestine microbiome before, during and after induced pathogenic conditions using a validated ETEC infection model.

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)