A consistent and predictable commercial broiler chicken bacterial microbiome in antibiotic-free production displays strong correlations with performance

Defining the baseline bacterial microbiome is critical towards understanding its relationship with health and disease. In broiler chickens, numerous studies have aimed at defining the core microbiome, yet the core and its possible relationships with health and disease have been difficult to define due to lack of study power. Here, the most comprehensive microbiome-based effort to date in commercial broilers was undertaken. The primary goals of this study included understanding what constitutes core in the broiler gastrointestinal, respiratory, and barn environments; how these core players change across age, geography, and time; and which bacterial taxa correlate with enhanced bird performance in antibiotic-free flocks. Using 2,309 samples from 37 different commercial flocks within a vertically integrated broiler system, and metadata from 549 flocks within that system, the baseline bacterial microbiome was defined. The effects of age, sample type, flock, and successive flock cycles were compared, and results indicate a consistent, predictable, age-dependent bacterial microbiome, irrespective of flock. The tracheal bacterial microbiome of broilers was comprehensively defined for the first time, and interestingly, Lactobacillus was the dominant bacterial taxa in the trachea. Numerous bacterial taxa were identified which were strongly correlated with broiler chicken performance, across multiple tissues. While many positively correlated taxa were identified representing targets for future probiotic development, many negatively associated potential pathogens were identified in the absence of clinical disease, indicating subclinical dynamics occurring that impact performance. Overall, this work provides necessary baseline data for the development of effective antibiotic alternatives for sustainable poultry production.

明确细菌基线微生物组（bacterial microbiome），对于解析其与宿主健康和疾病的关联至关重要。针对肉鸡，已有大量研究致力于界定其核心微生物组（core microbiome），但由于研究统计效力不足，核心微生物组及其与健康、疾病的潜在关联始终难以明确。本研究针对商品肉鸡开展了迄今为止最为全面的基于微生物组的研究工作。本研究的核心目标包括：解析肉鸡胃肠道、呼吸道及养殖棚环境中的核心微生物组构成；明确这些核心类群如何随鸡龄、地域及时间推移发生变化；以及鉴定无抗鸡群（antibiotic-free flocks）中与肉鸡生产性能提升相关的细菌分类群（bacterial taxa）。研究依托垂直整合肉鸡养殖体系（vertically integrated broiler system）内37个不同商品鸡群的2309份样本，以及该体系内549个鸡群的元数据（metadata），最终明确了肉鸡的细菌基线微生物组。研究比较了鸡龄、样本类型、鸡群以及连续鸡群批次的影响，结果显示：无论鸡群背景如何，肉鸡的细菌微生物组均呈现出一致、可预测且随鸡龄动态变化的特征。本研究首次全面解析了肉鸡的气管细菌微生物组，有趣的是，乳杆菌属（Lactobacillus）是气管中的优势细菌分类群。研究在多种组织中鉴定出多个与肉鸡生产性能显著相关的细菌分类群。其中，既有多个可作为未来益生菌（probiotic）开发靶点的正相关分类群，也在无临床症状的鸡群中发现了多个与生产性能负相关的潜在致病菌，这提示存在影响生产性能的亚临床（subclinical）动态过程。综上，本研究为开发可持续家禽生产所需的高效抗生素替代方案（antibiotic alternatives）提供了必要的基线数据。