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Shotgun Pyrosequencing Metagenomic Analyses of Dusts from Swine Confinement and Grain Facilities

机译：散养和粮食设施产生的粉尘的弹枪焦磷酸测序元基因组分析

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Inhalation of agricultural dusts causes inflammatory reactions and symptoms such as headache, fever, and malaise, which can progress to chronic airway inflammation and associated diseases, e.g. asthma, chronic bronchitis, chronic obstructive pulmonary disease, and hypersensitivity pneumonitis. Although in many agricultural environments feed particles are the major constituent of these dusts, the inflammatory responses that they provoke are likely attributable to particle-associated bacteria, archaebacteria, fungi, and viruses. In this study, we performed shotgun pyrosequencing metagenomic analyses of DNA from dusts from swine confinement facilities or grain elevators, with comparisons to dusts from pet-free households. DNA sequence alignment showed that 19% or 62% of shotgun pyrosequencing metagenomic DNA sequence reads from swine facility or household dusts, respectively, were of swine or human origin, respectively. In contrast only 2% of such reads from grain elevator dust were of mammalian origin. These metagenomic shotgun reads of mammalian origin were excluded from our analyses of agricultural dust microbiota. The ten most prevalent bacterial taxa identified in swine facility compared to grain elevator or household dust were comprised of 75%, 16%, and 42% gram-positive organisms, respectively. Four of the top five swine facility dust genera were assignable (Clostridium, Lactobacillus, Ruminococcus, and Eubacterium, ranging from 4% to 19% relative abundance). The relative abundances of these four genera were lower in dust from grain elevators or pet-free households. These analyses also highlighted the predominance in swine facility dust of Firmicutes (70%) at the phylum level, Clostridia (44%) at the Class level, and Clostridiales at the Order level (41%). In summary, shotgun pyrosequencing metagenomic analyses of agricultural dusts show that they differ qualitatively and quantitatively at the level of microbial taxa present, and that the bioinformatic analyses used for such studies must be carefully designed to avoid the potential contribution of non-microbial DNA, e.g. from resident mammals.
机译：吸入农业粉尘会引起炎症反应和症状，如头痛，发烧和不适，可发展为慢性气道炎症和相关疾病，例如哮喘，慢性支气管炎，慢性阻塞性肺疾病和超敏性肺炎。尽管在许多农业环境中，饲料颗粒是这些粉尘的主要成分，但它们引起的炎症反应却可能与颗粒相关的细菌，古细菌，真菌和病毒有关。在这项研究中，我们对来自养猪场设施或谷物升降机的粉尘中的DNA进行了shot弹枪热测序的宏基因组分析，并将其与无宠物家庭的粉尘进行了比较。 DNA序列比对显示，分别来自猪场或家庭尘土的散弹枪焦测序宏基因组DNA序列读取的19％或62％分别来自猪或人。相反，从谷物提升机灰尘中读取的此类读物只有2％来自哺乳动物。这些对哺乳动物起源的宏基因组shot弹枪读数被排除在我们对农业尘埃微生物群的分析之外。与谷物升降机或家庭扬尘相比，猪场中确定的十种最普遍的细菌类群分别由75％，16％和42％的革兰氏阳性生物组成。前五个猪场粉尘属中有四个是可分配的（梭菌，乳杆菌，鲁米球菌和真细菌，相对丰度为4％至19％）。这四个属的相对丰度在谷物升降机或无宠物家庭的粉尘中较低。这些分析还突出显示了在门级的沙门氏菌（70％），在级别的梭菌（44％）和在订单级的梭菌（41％）的猪场粉尘中占主导地位。总而言之，对农用粉尘的shot弹枪热测序宏基因组学分析表明，它们在当前微生物分类群的水平上在质和量上都存在差异，并且必须认真设计用于此类研究的生物信息学分析，以避免非微生物DNA的潜在贡献，例如来自常驻哺乳动物。

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