Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
Institute for Work and Health, University of Lausanne and University of Geneva, Epalinges, Switzerland.
Appl Environ Microbiol. 2018 Mar 1;84(6):e02470-17. doi: 10.1128/AEM.02470-17.
It has been hypothesized that the environment can influence the composition of the nasal microbiota. However, the direct influence of pig farming on the anterior and posterior nasal microbiota is unknown. Using a cross-sectional design, pig farms ( = 28) were visited in 2014 to 2015, and nasal swabs from 43 pig farmers and 56 pigs, as well as 27 air samples taken in the vicinity of the pig enclosures, were collected. As controls, nasal swabs from 17 cow farmers and 26 non-animal-exposed individuals were also included. Analyses of the microbiota were performed based on 16S rRNA amplicon sequencing and the DADA2 pipeline to define sequence variants (SVs). We found that pig farming is strongly associated with specific microbial signatures (including alpha- and beta-diversity), which are reflected in the microbiota of the human nose. Furthermore, the microbial communities were more similar within the same farm compared to between the different farms, indicating a specific microbiota pattern for each pig farm. In total, there were 82 SVs that occurred significantly more abundantly in samples from pig farms than from cow farmers and nonexposed individuals (i.e., the core pig farm microbiota). Of these, nine SVs were significantly associated with the posterior part of the human nose. The results strongly indicate that pig farming is associated with a distinct human nose microbiota. Finally, the community structures derived by the DADA2 pipeline showed an excellent agreement with the outputs of the mothur pipeline which was revealed by procrustes analyses. The knowledge about the influence of animal keeping on the human microbiome is important. Previous research has shown that pets significantly affect the microbial communities of humans. However, the effect of animal farming on the human microbiota is less clear, although it is known that the air at farms and, in particular, at pig farms is charged with large amounts of dust, bacteria, and fungi. In this study, we simultaneously investigated the nasal microbiota of pigs, humans, and the environment at pig farms. We reveal an enormous impact of pig farming on the human nasal microbiota which is far more pronounced compared to cow farming. In addition, we analyzed the airborne microbiota and found significant associations suggesting an animal-human transmission of the microbiota within pig farms. We also reveal that microbial patterns are farm specific, suggesting that the environment influences animals and humans in a similar manner.
人们假设环境会影响鼻腔微生物组的组成。然而，养猪直接影响鼻前部和鼻后部微生物组的情况尚不清楚。本研究采用横断面设计，于 2014 年至 2015 年期间访问了 28 个养猪场，采集了 43 名养猪场工人、56 头猪以及猪圈附近 27 个空气样本的鼻拭子。作为对照，还采集了 17 名奶牛场工人和 26 名非动物接触者的鼻拭子。使用 16S rRNA 扩增子测序和 DADA2 分析流程对微生物组进行分析，以定义序列变异（SVs）。我们发现，养猪与特定的微生物特征（包括α多样性和β多样性）密切相关，这些特征反映在人类鼻腔的微生物组中。此外，同一养猪场内部的微生物群落更为相似，而不同养猪场之间的微生物群落则更为不同，这表明每个养猪场都有特定的微生物群模式。总共发现 82 个 SVs 在养猪场工人的样本中比在奶牛场工人和非接触者的样本中更为丰富（即核心养猪场微生物群）。其中，有 9 个 SVs 与人类鼻腔的后部显著相关。结果强烈表明，养猪与人类鼻腔微生物群密切相关。最后，DADA2 分析流程得出的群落结构与 mothur 分析流程的结果非常吻合，这一点通过 Procrustes 分析得到了证实。关于动物饲养对人类微生物组影响的知识非常重要。以前的研究表明，宠物对人类的微生物群有显著影响。然而，动物饲养对人类微生物组的影响尚不明确，尽管已知农场，尤其是养猪场的空气中充满了大量的灰尘、细菌和真菌。在这项研究中，我们同时研究了猪、人和养猪场环境的鼻腔微生物群。我们发现，养猪对人类鼻腔微生物群的影响非常大，与奶牛养殖相比，这种影响更为明显。此外，我们还分析了空气中的微生物群，发现了一些显著的关联，这表明了在养猪场中存在动物与人类之间的微生物群传播。我们还发现，微生物模式具有农场特异性，这表明环境以相似的方式影响动物和人类。
