The factors affecting host-pathogen ecology in terms of the microbiome remain poorly studied. Chickens are a key source of protein with gut health heavily dependent on the complex microbiome which has key roles in nutrient assimilation and vitamin and amino acid biosynthesis. The chicken gut microbiome may be influenced by extrinsic production system parameters such as Placement Birds/m2 (stocking density), feed type and additives. Such parameters, in addition to on-farm biosecurity may influence performance and also pathogenic bacterial numbers such as Campylobacter. In this study, three different production systems ‘Normal’ (N), ‘Higher Welfare’ (HW) and ‘Omega-3 Higher Welfare’ (O) were investigated in an industrial farm environment at day 7 and day 30 with a range of extrinsic parameters correlating performance with microbial dynamics and Campylobacter presence. Our data identified production system N as significantly dissimilar from production systems HW and O when comparing the prevalence of genera. An increase in Placement Birds/m2 density led to a decrease in environmental pressure influencing the microbial community structure. Prevalence of genera, such as Eisenbergiella within HW and O, and likewise Alistipes within N were representative. These genera have roles directly relating to energy metabolism, amino acid, nucleotide and short chain fatty acid (SCFA) utilisation. Thus, an association exists between consistent and differentiating parameters of the production systems that affect feed utilisation, leading to competitive exclusion of genera based on competition for nutrients and other factors. Campylobacter was identified within specific production system and presence was linked with the increased diversity and increased environmental pressure on microbial community structure. Addition of Omega-3 though did alter prevalence of specific genera, in our analysis did not differentiate itself from HW production system. However, Omega-3 was linked with a positive impact on weight gain. Overall, our results show that microbial communities in different industrial production systems are deterministic in elucidating the underlying biological confounders, and these recommendations are transferable to farm practices and diet manipulation leading to improved performance and better intervention strategies against Campylobacter within the food chain.

中文翻译：

---

工业生产系统参数对鸡微生物组的影响：提高性能和减少弯曲杆菌的机制。

从微生物组角度影响宿主-病原体生态学的因素仍然缺乏研究。鸡是蛋白质的主要来源，肠道健康严重依赖于复杂的微生物群，而微生物群在营养同化以及维生素和氨基酸生物合成中发挥着关键作用。鸡肠道微生物组可能受到生产系统外在参数的影响，例如每平方米饲养密度（饲养密度）、饲料类型和添加剂。除了农场生物安全之外，这些参数还可能影响性能以及弯曲杆菌等致病细菌的数量。在本研究中，在工业化农场环境中对三种不同的生产系统“正常”(N)、“较高福利”(HW) 和“Omega-3 较高福利”(O) 在第 7 天和第 30 天进行了调查，将性能与微生物动力学和弯曲杆菌存在相关的外在参数。我们的数据表明，在比较属的流行程度时，生产系统 N 与生产系统 HW 和 O 显着不同。每平方米安置鸟类密度的增加导致影响微生物群落结构的环境压力减少。属的流行率，例如 HW 和 O 中的艾森伯格菌属（Eisenbergiella）以及 N 中的阿里斯贝属（Alistipes）具有代表性。这些属的作用与能量代谢、氨基酸、核苷酸和短链脂肪酸 (SCFA) 利用直接相关。因此，影响饲料利用率的生产系统的一致参数和差异参数之间存在关联，导致基于营养物质和其他因素的竞争而导致属的竞争性排除。弯曲杆菌是在特定的生产系统中发现的，其存在与微生物群落结构的多样性增加和环境压力增加有关。尽管添加 Omega-3 确实改变了特定属的流行率，但在我们的分析中并未将其与 HW 生产系统区分开来。然而，Omega-3 对体重增加有积极影响。总体而言，我们的结果表明，不同工业生产系统中的微生物群落在阐明潜在的生物混杂因素方面具有确定性，并且这些建议可转移到农场实践和饮食控制中，从而提高性能并针对食物链内的弯曲杆菌采取更好的干预策略。