Data_Sheet_2_Metagenomics reveals novel microbial signatures of farm exposures in house dust.DOCX

Indoor home dust microbial communities, important contributors to human health, are shaped by environmental factors, including farm-related exposures. Advanced metagenomic whole genome shotgun sequencing (WGS) improves detection and characterization of microbiota in the indoor built-environment dust microbiome, compared to conventional 16S rRNA amplicon sequencing (16S). We hypothesized that the improved characterization of indoor dust microbial communities by WGS will enhance detection of exposure-outcome associations. The objective of this study was to identify novel associations of environmental exposures with the dust microbiome from the homes of 781 farmers and farm spouses enrolled in the Agricultural Lung Health Study. We examined various farm-related exposures, including living on a farm, crop versus animal production, and type of animal production, as well as non-farm exposures, including home cleanliness and indoor pets. We assessed the association of the exposures on within-sample alpha diversity and between-sample beta diversity, and the differential abundance of specific microbes by exposure. Results were compared to previous findings using 16S. We found most farm exposures were significantly positively associated with both alpha and beta diversity. Many microbes exhibited differential abundance related to farm exposures, mainly in the phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. The identification of novel differential taxa associated with farming at the genera level, including Rhodococcus, Bifidobacterium, Corynebacterium, and Pseudomonas, was a benefit of WGS compared to 16S. Our findings indicate that characterization of dust microbiota, an important component of the indoor environment relevant to human health, is heavily influenced by sequencing techniques. WGS is a powerful tool to survey the microbial community that provides novel insights on the impact of environmental exposures on indoor dust microbiota. These findings can inform the design of future studies in environmental health.

室内家居尘埃微生物群落，作为人类健康的重要影响因素，其构成受多种环境因素制约，其中包括与农业相关的暴露。与传统的16S rRNA扩增子测序（16S）相比，先进的宏基因组全基因组鸟枪法测序（WGS）在室内建筑环境尘埃微生物群落的微生物检测与表征方面具有显著优势。本研究假设，通过WGS对室内尘埃微生物群落的改进表征将增强对暴露-结果关联的检测。本研究旨在识别来自781名农业劳动者及其配偶的家庭尘埃微生物群落的与环境暴露相关的新型关联，这些参与者均参与了农业肺部健康研究。我们考察了各种与农业相关的暴露，包括农场居住、作物生产与动物生产、以及动物生产类型，以及非农场暴露，包括家庭清洁度和室内宠物。我们评估了暴露对样本内α多样性和样本间β多样性的影响，以及特定微生物的暴露差异丰度。研究结果与使用16S的先前发现进行了比较。我们发现，大多数农场暴露与α多样性和β多样性均存在显著的正相关。许多微生物表现出与农场暴露相关的差异丰度，主要在放线菌门、拟杆菌门、厚壁菌门和变形菌门。与16S相比，WGS在鉴定与农业相关的差异属水平的新型分类群（如红球菌属、双歧杆菌属、棒杆菌属和假单胞菌属）方面具有优势。我们的研究结果表明，尘埃微生物群落的表征，作为与人类健康密切相关的室内环境的重要组成部分，深受测序技术的影响。WGS是调查微生物群落的有效工具，它为环境暴露对室内尘埃微生物群落的影响提供了新的见解。这些发现可为未来环境健康研究的规划提供信息。