Boissy Robert J, Romberger Debra J, Roughead William A, Weissenburger-Moser Lisa, Poole Jill A, LeVan Tricia D
University of Nebraska Medical Center, Department of Pathology and Microbiology, Omaha, Nebraska, United States of America.
Veterans Nebraska Western Iowa Healthcare System, Omaha, NE, USA and University of Nebraska Medical Center, Pulmonary, Critical Care, Sleep Medicine & Allergy Division, Omaha, Nebraska, United States of America.
PLoS One. 2014 Apr 18;9(4):e95578. doi: 10.1371/journal.pone.0095578. eCollection 2014.
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.
吸入农业粉尘会引发炎症反应以及头痛、发烧和不适等症状，这些症状可能会发展为慢性气道炎症及相关疾病，如哮喘、慢性支气管炎、慢性阻塞性肺疾病和过敏性肺炎。尽管在许多农业环境中，饲料颗粒是这些粉尘的主要成分，但它们引发的炎症反应可能归因于与颗粒相关的细菌、古细菌、真菌和病毒。在本研究中，我们对来自养猪场或谷物升降机的粉尘DNA进行了鸟枪法焦磷酸测序宏基因组分析，并与无宠物家庭的粉尘进行了比较。DNA序列比对显示，分别来自养猪场或家庭粉尘的鸟枪法焦磷酸测序宏基因组DNA序列读数中，有19%或62%分别来自猪或人类。相比之下，来自谷物升降机粉尘的此类读数中只有2%来自哺乳动物。在我们对农业粉尘微生物群的分析中，排除了这些来自哺乳动物的宏基因组鸟枪法读数。与谷物升降机或家庭粉尘相比，在养猪场中鉴定出的十种最普遍的细菌类群分别由75%、16%和42%的革兰氏阳性菌组成。养猪场粉尘中排名前五的属中有四个是可分类的（梭菌属、乳杆菌属、瘤胃球菌属和真杆菌属，相对丰度从4%到19%不等）。在谷物升降机或无宠物家庭的粉尘中，这四个属的相对丰度较低。这些分析还突出了养猪场粉尘在门水平上厚壁菌门（70%）、在纲水平上梭菌纲（44%）和在目水平上梭菌目（41%）的优势。总之，对农业粉尘的鸟枪法焦磷酸测序宏基因组分析表明，它们在存在的微生物类群水平上在质量和数量上存在差异，并且用于此类研究的生物信息学分析必须经过精心设计，以避免非微生物DNA（例如来自常驻哺乳动物的DNA）的潜在贡献。
