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

Michael E. G. Rosch, Jacqueline Rehner, Georges P. Schmartz, Sascha K. Manier, Uta Becker, View ORCID ProfileRolf Müller, Markus R. Meyer, Andreas Keller, Sören L. Becker, View ORCID ProfileVerena Keller
doi: https://doi.org/10.1101/2023.03.06.531264
Michael E. G. Rosch
1Medical Doctor program Human Medicine, Saarland University/ Saarland University Medical Center, Saarbrücken/Homburg, 66123/66421, Germany
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Jacqueline Rehner
2Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, 66421, Germany
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Georges P. Schmartz
3Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, 66123, Germany
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Sascha K. Manier
4Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Saarland University, Center for Molecular Signaling (PZMS), Homburg/Saar, 66421, Germany
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Uta Becker
5MIP Pharma GmbH, Sankt Ingbert, 66386, Germany
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Rolf Müller
6Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, 66123, Germany
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  • ORCID record for Rolf Müller
Markus R. Meyer
4Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Saarland University, Center for Molecular Signaling (PZMS), Homburg/Saar, 66421, Germany
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Andreas Keller
3Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, 66123, Germany
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Sören L. Becker
2Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, 66421, Germany
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Verena Keller
3Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, 66123, Germany
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  • ORCID record for Verena Keller
  • For correspondence: verena.keller@uks.eu
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ABSTRACT

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.

Competing Interest Statement

GPS, RM, and AK are co-founders of MooH GmbH, a company developing metagenomic based oral health testing. UB is head of microbiology and diagnostics at MIP Pharma GmbH, Sankt Ingbert, Germany. All other authors have no conflict of interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted March 08, 2023.
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Time series of chicken stool metagenomics and egg metabolomics in changing production systems
Michael E. G. Rosch, Jacqueline Rehner, Georges P. Schmartz, Sascha K. Manier, Uta Becker, Rolf Müller, Markus R. Meyer, Andreas Keller, Sören L. Becker, Verena Keller
bioRxiv 2023.03.06.531264; doi: https://doi.org/10.1101/2023.03.06.531264
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Time series of chicken stool metagenomics and egg metabolomics in changing production systems
Michael E. G. Rosch, Jacqueline Rehner, Georges P. Schmartz, Sascha K. Manier, Uta Becker, Rolf Müller, Markus R. Meyer, Andreas Keller, Sören L. Becker, Verena Keller
bioRxiv 2023.03.06.531264; doi: https://doi.org/10.1101/2023.03.06.531264

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