McDaneld Tara G, Kuehn Larry A, Keele John W
USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE.
J Anim Sci. 2018 Apr 12;96(4):1281-7. doi: 10.1093/jas/sky032.
Bovine respiratory disease complex (BRDC) is a multifactor disease, and disease incidence may be associated with an animal's commensal bacterial populations (microbiome) in the upper nasal cavity. Identifying these commensal bacterial populations in the upper nasal cavity may help us to understand the impact of the microbiome on incidence of BRDC in cattle. Various sampling techniques have previously been utilized to evaluate the microbiome of different locations of the upper nasal cavity in cattle. Therefore, our objective was to determine whether bacterial populations of the nasal cavity vary based on these sampling locations. Two common sampling techniques were evaluated, including 6-inch nasal swabs and deep nasopharyngeal swabs. Nasal swabs from calves were collected when the animal was diagnosed with BRDC after weaning in the feedlot in addition to collection of samples from asymptomatic cohorts. Samples were pooled in groups based on year the animal was in the feedlot (2015 or 2016), when the animal was diagnosed with BRDC (1 to 5 weeks after weaning), type of sample (6-inch nasal swab or deep nasopharyngeal swab), and health status (diagnosis with BRDC or control). Variable regions 1 through 3 along the 16S rRNA gene were amplified by PCR and sequenced using next-generation sequencing (Illumina MiSeq) for identification of the bacterial taxa present. Overall, sampling site did not consistently influence diversity of the bacterial populations of the upper nasal cavity. However, the effect of disease incidence on the microbiome was depended on sampling time after weaning (P = 0.0462) for 2015, while the main effects of sampling time after weaning (P = 0.00992) and disease phenotype (P = 0.012) were significant for 2016. These data for 2016 demonstrate that in addition to bacterial profiles changing throughout weaning, calves diagnosed with BRDC have different bacterial profiles compared to their control cohorts. In addition, evaluation of the microbiome identified predominant bacteria genera in the upper nasal cavity included those previously reported to be associated with cattle diagnosed with BRDC including Mycoplasma sp., Psychrobacter sp., and Mannheimia sp. In summary, these results demonstrate that shorter, less invasive 6-inch nasal swabs produce similar results to deep nasopharyngeal swabs.
牛呼吸道疾病综合征（BRDC）是一种多因素疾病，其发病率可能与动物鼻腔上部的共生细菌群体（微生物群）有关。识别鼻腔上部的这些共生细菌群体可能有助于我们了解微生物群对牛BRDC发病率的影响。此前已采用各种采样技术来评估牛鼻腔上部不同位置的微生物群。因此，我们的目标是确定鼻腔细菌群体是否因这些采样位置而有所不同。我们评估了两种常见的采样技术，包括6英寸鼻拭子和深部鼻咽拭子。除了从无症状牛群中采集样本外，在饲养场断奶后诊断出患有BRDC的犊牛也采集鼻拭子。样本根据动物进入饲养场的年份（2015年或2016年）、被诊断为BRDC的时间（断奶后1至5周）、样本类型（6英寸鼻拭子或深部鼻咽拭子）以及健康状况（诊断为BRDC或对照）进行分组合并。通过PCR扩增16S rRNA基因的1至3可变区，并使用下一代测序（Illumina MiSeq）进行测序，以鉴定存在的细菌分类群。总体而言，采样部位并未始终如一地影响鼻腔上部细菌群体的多样性。然而，疾病发病率对微生物群的影响在2015年取决于断奶后的采样时间（P = 0.0462），而在2016年，断奶后采样时间（P = 0.00992）和疾病表型（P = 0.012）的主要影响是显著的。2016年的这些数据表明，除了在整个断奶过程中细菌谱发生变化外，诊断出患有BRDC的犊牛与对照牛群相比具有不同的细菌谱。此外，对微生物群的评估确定了鼻腔上部的主要细菌属，包括先前报道的与诊断为BRDC的牛相关的细菌属，如支原体属、嗜冷杆菌属和曼氏杆菌属。总之，这些结果表明，较短、侵入性较小的6英寸鼻拭子产生的结果与深部鼻咽拭子相似。
