We conducted 1 in vitro experiment and 3 in vivo trials to unveil the 3D’omic changes triggered by pathogen infections in poultry. The trials included different pathogen challenges and different treatments to reveal information relevant for chicken breeding and nutrition programs, as well as microbiota modulation strategies. 

At ETH Zurich, we conducted in vitro trials investigating pathogen-synbiotic-microbiota interactions at micro- and conventional scale. Treatments were designed to represent the in vivo trial with Salmonella Infantis.
3 in vivo poultry pathogen challenges (i.e., viral pathogen (Fowl adenovirus), bacterial pathogen (Salmonella Infantis), and protozoan pathogen (Histomonas meleagridis)) were conducted with chicken (and in the case of Histomonas also turkey). 
Further, we used both the conventional and microsection (meta)genomic and (meta)transcriptomic profiles to build models of the sliced tissues. All the data will be inputted to generate in silico representation of the microbiota changes triggered by pathogen infections in poultry. The aim of this task is thus to produce models in a timely manner, including the dynamic changes upon infection.

Work Package 6 had a total duration of 46 months and concluded in December 2025.

Milestones 5 and we 6 of the project have been achieved: "Large-scale poultry trials accomplished" (MS5) and "Poultry system 3D’omic, multi-omic and complementary data are generated" (MS6).

The outcome of Work Package were 4 method reports, which were shared with the consortium and the European Commission.