College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America.
University of Missouri Metagenomics Center, University of Missouri, Columbia, Missouri, United States of America.
PLoS One. 2020 Jan 28;15(1):e0228085. doi: 10.1371/journal.pone.0228085. eCollection 2020.
The lungs of people and companion animals are now recognized to harbor diverse, low biomass bacterial communities. While these communities are difficult to characterize using culture-based approaches, targeted molecular methods such as 16S rRNA amplicon sequencing can do so using DNA extracted from samples such as bronchoalveolar lavage fluid (BALF). Previous studies identified a surprisingly uniform composition of the microbiota in the lungs of healthy research dogs living in a controlled environment, however there are no reports of the lung microbiota of client-owned dogs. Moreover, compositional changes in the lung microbiota depending on disease status have been reported in people, suggesting that similar events may occur in dogs, a species subject to several respiratory disease mechanisms analogous to those seen in people. To address these knowledge gaps, BALF samples from client-owned dogs presenting to the University of Missouri Veterinary Health Center for respiratory signs between 2014 and 2017 were processed for and subjected to 16S rRNA sequencing. Based on specific diagnostic criteria, dogs were categorized as Chronic Bronchitis (CB, n = 53) or non-CB (n = 11). Community structure was compared between groups, as well as to historical data from healthy research dogs (n = 16) of a uniform breed and environment. The lung microbiota detected in all client-owned dogs was markedly different in composition from that previously detected in research dogs and contained increased relative abundance of multiple canine fecal and environmental bacteria, likely due to aspiration associated with their clinical signs. While inter-sample diversity differed significantly between samples from CB and non-CB dogs, the variability within both groups made it difficult to discern reproducible bacterial classifiers of disease. During subsequent analyses to identify other sources of variability within the data however, population-wide temporal dynamics in community structure were observed, with substantial changes occurring in late 2015 and again in early 2017. A review of regional climate data indicated that the first change occurred during a historically warm and wet period, suggesting that changes in environmental conditions may be associated with changes in the respiratory microbiota in the context of respiratory disease. As the lung microbiota in humans and other animals is believed to result from repetitive micro-aspirations during health and in certain disease states associated with dyspnea and laryngeal dysfunction, these data support the increased colonization of the lower airways during compromised airway function, and the potential for temporal effects due to putative factors such as climate.
现在已经认识到，人和伴侣动物的肺部存在着多样的、低生物量的细菌群落。虽然这些群落很难通过基于培养的方法来描述，但靶向分子方法，如 16S rRNA 扩增子测序，可以使用从支气管肺泡灌洗液 (BALF) 等样本中提取的 DNA 来实现。以前的研究表明，在受控环境中生活的健康研究犬的肺部微生物组组成惊人地一致，然而，目前还没有关于客户拥有的犬的肺部微生物组的报道。此外，据报道，在人类中，肺部微生物组的组成会因疾病状态而发生变化，这表明在狗中也可能发生类似的事件，狗是一种受到多种与人类相似的呼吸道疾病机制影响的物种。为了填补这些知识空白，对 2014 年至 2017 年间因呼吸道症状到密苏里大学兽医健康中心就诊的客户拥有的犬的 BALF 样本进行了处理，并进行了 16S rRNA 测序。根据特定的诊断标准，将犬分为慢性支气管炎 (CB，n = 53) 或非-CB (n = 11)。比较了各组之间的群落结构，并与具有统一品种和环境的健康研究犬的历史数据 (n = 16) 进行了比较。从所有客户拥有的犬中检测到的肺部微生物群在组成上明显不同于以前在研究犬中检测到的微生物群，并且含有多种犬粪便和环境细菌的相对丰度增加，这可能是由于与临床症状相关的吸入。虽然 CB 和非-CB 犬的样本之间的样本内多样性有显著差异，但两组内的变异性使得难以辨别疾病的可重复细菌分类器。然而，在随后的分析中，为了在数据中识别其他来源的变异性，观察到了群落结构的全人群时间动态，2015 年底和 2017 年初再次发生了重大变化。对区域气候数据的回顾表明，第一次变化发生在历史上温暖和潮湿的时期，这表明环境条件的变化可能与呼吸疾病背景下呼吸微生物群的变化有关。由于人们认为人类和其他动物的肺部微生物组是在健康状态下和与呼吸困难和喉功能障碍相关的某些疾病状态下，通过反复微吸入而产生的，因此这些数据支持在气道功能受损期间，下呼吸道的定植增加，以及由于气候等潜在因素而产生的时间效应的潜力。
