Fig. 1

Study design and sample collection. a Cohort design, fecal sample collection and subsequent analyses. Barn chicken (depicted as brown chicken) were released from an industry barn and divided into two cohorts. H1-H3 were released into a free range, isolated from existing free-range chicken (depicted in white). H4-H6 were released and grouped together with existing free-range chicken. Samples were also collected from long-term existing free-range chicken H7 and H8. Fecal samples were collected from all cohorts on several days and subjected to whole-genome DNA extraction and subsequent whole-genome sequencing. b Anatomy of the chicken gastrointestinal tract. During sampling fecal samples will contain contain traces from the foregut but also from the ceca. c From all cohorts, eggs were collected 97 days past study begin and the egg white and egg yolk of each egg were analysed by mass spectrometry. Results were compared to eggs and eggs from barn chicken from a local supermarket. Additionally, an egg from a newly relocated former barn chicken (entered the environment the day of egg collection), which was transferred into a free-range environment and grouped with H7 and H8 was analyzed