Zeineldin Mohamed M, Lowe James F, Grimmer Elsbeth D, de Godoy Maria R C, Ghanem Mohamed M, Abd El-Raof Yassein M, Aldridge Brian M
Integrated Food Animal Management Systems, Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, 241 LAC, 1008 W Hazelwood Dr, Urbana, IL, 61802, USA.
Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, USA.
BMC Microbiol. 2017 Jun 23;17(1):138. doi: 10.1186/s12866-017-1042-2.
The importance of upper airway structure in the susceptibility of the lower respiratory tract to colonization with potential pathogens is well established. With the advent of rapid, high throughput, next generation sequencing, there is a growing appreciation of the importance of commensal microbial populations in maintaining mucosal health, and a realization that bacteria colonize anatomical locations that were previously considered to be sterile. While upper respiratory tract microbial populations have been described, there are currently no published studies describing the normal microbial populations of the bovine lower respiratory tract. Consequently, we have little understanding of the relationship between upper and lower respiratory tract microbiota in healthy cattle. The primary objective of our study was to characterize the composition, structure and relationship of the lower and upper respiratory microbial communities in clinically healthy feedlot cattle. Nasopharyngeal swabs (NPS), and bronchoalveolar lavage (BAL) fluid, were collected from clinically healthy feedlot calves (n = 8). Genomic DNA from each sample was extracted, and the V3-V4 hypervariable region of the bacterial 16S rRNA gene was amplified and sequenced using Illumina Miseq platform.
Across all samples, the most predominant phyla were Proteobacteria, Actinobacteria and Firmicutes. The most common genera were Rathayibacter, Mycoplasma, Bibersteinia and Corynebacterium. The microbial community structure was distinct between these two biogeographical sites. Most of the bacterial genera identified in the BAL samples were also present in the NPS, but biogeographical-specific genera were enriched in both the NPS (Rathayibacter) and BAL (Bibersteinia) samples. There were strong associations between the presence of certain taxa at each specific location, and strong correlations between the presence of specific taxa in both the NPS and BAL samples.
The correlation between the presence of specific taxa in both the NPS and BAL samples, supports the notion of a mutualistic interrelationship between these microbial communities. Future studies, in large cohorts of animals, are needed to determine the role and clinical importance of the relationships of respiratory tract microbial communities with health, productivity, and susceptibility to the development of respiratory disease, in growing cattle.
上呼吸道结构在潜在病原体定植于下呼吸道易感性方面的重要性已得到充分证实。随着快速、高通量的新一代测序技术的出现，人们越来越认识到共生微生物群落在维持黏膜健康方面的重要性，并且意识到细菌会定植于以前被认为是无菌的解剖部位。虽然已经对上呼吸道微生物群落进行了描述，但目前尚无已发表的研究描述牛下呼吸道的正常微生物群落。因此，我们对健康牛的上、下呼吸道微生物群之间的关系了解甚少。我们研究的主要目的是表征临床健康的饲养场牛下呼吸道和上呼吸道微生物群落的组成、结构及关系。从临床健康的饲养场犊牛（n = 8）中采集鼻咽拭子（NPS）和支气管肺泡灌洗（BAL）液。从每个样本中提取基因组DNA，并使用Illumina Miseq平台对细菌16S rRNA基因的V3-V4高变区进行扩增和测序。
在所有样本中，最主要的菌门是变形菌门、放线菌门和厚壁菌门。最常见的菌属是 Rathayibacter、支原体属、Bibersteinia 和棒状杆菌属。这两个生物地理部位的微生物群落结构不同。在BAL样本中鉴定出的大多数细菌属也存在于NPS中，但生物地理特异性菌属在NPS（Rathayibacter）和BAL（Bibersteinia）样本中均有富集。在每个特定位置某些分类群的存在之间存在强关联，并且在NPS和BAL样本中特定分类群的存在之间存在强相关性。
NPS和BAL样本中特定分类群存在之间的相关性支持了这些微生物群落之间存在互利共生关系的观点。未来需要在大量动物群体中进行研究，以确定呼吸道微生物群落关系对生长牛的健康、生产力和呼吸道疾病易感性的作用及临床重要性。
