Time series of chicken stool metagenomics and egg metabolomics in changing production systems: preliminary insights from a proof-of-concept

Abstract

Background Diferent production systems of livestock animals infuence various factors, including the gut microbiota. Methods We investigated whether changing the conditions from barns to free-range chicken farming 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. Results Over the six time points, 12 taxa—mostly lactobacilli—changed signifcantly. 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 profles of the egg white and yolk to profles of eggs from commercial suppliers. Here, we observed signifcant diferences between commercial and fresh collected eggs as well as diferences between the former barn chicken and free-range chicken. Conclusion Our data indicate that the gut microbiota can undergo alterations over time in response to changes in production systems. These changes subsequently exert an infuence on the metabolites found in the eggs. The preliminary results of our proof-of-concept study motivate larger scale observations with more individual chicken and longer observation periods.