Schreuder Janneke, Velkers Francisca C, Bossers Alex, Bouwstra Ruth J, de Boer Willem F, van Hooft Pim, Stegeman J Arjan, Jurburg Stephanie D
Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.
Department of Infection Biology, Wageningen Bioveterinary Research, Lelystad, Netherlands.
Front Microbiol. 2021 Jan 28;11:626713. doi: 10.3389/fmicb.2020.626713. eCollection 2020.
Associations between animal health and performance, and the host's microbiota have been recently established. In poultry, changes in the intestinal microbiota have been linked to housing conditions and host development, but how the intestinal microbiota respond to environmental changes under farm conditions is less well understood. To gain insight into the microbial responses following a change in the host's immediate environment, we monitored four indoor flocks of adult laying chickens three times over 16 weeks, during which two flocks were given access to an outdoor range, and two were kept indoors. To assess changes in the chickens' microbiota over time, we collected cloacal swabs of 10 hens per flock and performed 16S rRNA gene amplicon sequencing. The poultry house (i.e., the stable in which flocks were housed) and sampling time explained 9.2 and 4.4% of the variation in the microbial community composition of the flocks, respectively. Remarkably, access to an outdoor range had no detectable effect on microbial community composition, the variability of microbiota among chickens of the same flock, or microbiota richness, but the microbiota of outdoor flocks became more even over time. Fluctuations in the composition of the microbiota over time within each poultry house were mainly driven by turnover in rare, rather than dominant, taxa and were unique for each flock. We identified 16 amplicon sequence variants that were differentially abundant over time between indoor and outdoor housed chickens, however none were consistently higher or lower across all chickens of one housing type over time. Our study shows that cloacal microbiota community composition in adult layers is stable following a sudden change in environment, and that temporal fluctuations are unique to each flock. By exploring microbiota of adult poultry flocks within commercial settings, our study sheds light on how the chickens' immediate environment affects the microbiota composition.
动物健康与生产性能以及宿主微生物群之间的关联最近已被确立。在家禽中，肠道微生物群的变化与饲养条件和宿主发育有关，但在农场条件下肠道微生物群如何应对环境变化却鲜为人知。为了深入了解宿主即时环境变化后的微生物反应，我们在16周内对四群成年产蛋鸡进行了三次监测，其中两群鸡可以进入室外活动场，另外两群则饲养在室内。为了评估鸡的微生物群随时间的变化，我们从每群中收集了10只母鸡的泄殖腔拭子，并进行了16S rRNA基因扩增子测序。禽舍（即鸡群饲养的鸡舍）和采样时间分别解释了鸡群微生物群落组成变异的9.2%和4.4%。值得注意的是，进入室外活动场对微生物群落组成、同一鸡群内鸡之间微生物群的变异性或微生物群丰富度没有可检测到的影响，但室外鸡群的微生物群随着时间的推移变得更加均匀。每个禽舍内微生物群组成随时间的波动主要由稀有而非优势分类群的更替驱动，并且每个鸡群都是独特的。我们鉴定出16个扩增子序列变体，它们在室内和室外饲养的鸡之间随时间差异丰富，但在一种饲养类型的所有鸡中，没有一个在所有时间内始终更高或更低。我们的研究表明，成年蛋鸡的泄殖腔微生物群落在环境突然变化后是稳定的，并且时间波动对每个鸡群都是独特的。通过探索商业环境中成年家禽群的微生物群，我们的研究揭示了鸡的即时环境如何影响微生物群组成。
