Time series of chicken stool metagenomics and egg metabolomics in changing production systems

Different production systems of livestock animals influence various factors, including the gut microbiota. We investigated whether changing the conditions from barns to free-range impacts the microbiome over the course of three weeks. We compared the stool microbiota of chicken from industrial barns after introducing them either in community or separately to a free-range environment. Over the six time points, 12 taxa - mostly lactobacilli - changed significantly. As expected, the former barn chicken cohort carries more resistances to common antibiotics. These, however, remained positive over the observed period. At the end of the study, we collected eggs and compared metabolomic profiles of the egg white and yolk to profiles of eggs from commercial suppliers. Here, we observed significant differences between commercial and fresh collected eggs as well as differences between the former barn chicken and free-range chicken. Our data suggest that the gut microbiota can change over time following a change in production systems. This change also influences the metabolites in the eggs. We understand the study as a proof-of-concept that justifies larger scale observations with more individual chicken and longer observation periods.