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

IF 3.8 Q2 INFECTIOUS DISEASES One health outlook Pub Date : 2024-03-29 DOI:10.1186/s42522-024-00100-0
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
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Abstract

Background: Different production systems of livestock animals influence 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 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.

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 influence 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.

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不断变化的生产系统中鸡粪便元基因组学和鸡蛋代谢组学的时间序列:概念验证的初步见解。
背景家畜的不同生产系统会影响各种因素,包括肠道微生物群:我们研究了将鸡舍条件改为散养鸡三周内是否会对微生物群产生影响。我们比较了来自工业化鸡舍的鸡在集体或单独进入散养环境后的粪便微生物群:在六个时间点上,12 个分类群(主要是乳酸杆菌)发生了显著变化。不出所料,前谷仓鸡群对常见抗生素的耐药性更强。不过,在观察期间,这些抗生素的耐药性仍然呈阳性。研究结束时,我们收集了鸡蛋,并将蛋白和蛋黄的代谢组学图谱与商业供应商鸡蛋的图谱进行了比较。在这里,我们观察到了商业鸡蛋和新鲜鸡蛋之间的显著差异,以及谷仓鸡和散养鸡之间的差异:我们的数据表明,随着时间的推移,肠道微生物群会随着生产系统的变化而发生改变。这些变化会对鸡蛋中的代谢物产生影响。我们的概念验证研究的初步结果促使我们用更多的鸡和更长的观察期进行更大规模的观察。
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