Metagenomics reveals novel microbial signatures of farm exposures in house dust

Abstract

Indoor home dust microbial communities, important contributors to human health outcomes, are shaped by environmental factors, including farm-related exposures. Detection and characterization of microbiota are influenced by sequencing methodology; however, it is unknown if advanced metagenomic whole genome shotgun sequencing (WGS) can detect novel associations between environmental exposures and the indoor built-environment dust microbiome, compared to conventional 16S rRNA amplicon sequencing (16S). This study aimed to better depict indoor dust microbial communities using WGS to investigate novel associations with environmental risk factors 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, and should be an important consideration in designing future studies in environmental health.

Occupational Farm Work Activities Influence Workers’ Indoor Home Microbiome

“…(24) (ALHS data release P3REL201209.00) Further details on the study design and inclusion criteria can be found elsewhere. (18,19) Of the full ALHS cohort (N=3301), 2871 participants completed a home visit between 2009 to 2013 with vacuumed bedroom dust collection. (25) The Institutional Review Board at the National Institute of Environmental Health Sciences approved the study.…”

“…A subset of 879 dust samples were sent for microbiome analysis, with sample selection described elsewhere. (18,19,25) DNA extraction followed standard protocols following manufactured kits and is described elsewhere. (18,19) Extracted DNA samples were sent to the University of California San Diego IGM Genomics Center for library preparation, multiplexing, and whole genome shotgun sequencing using standard techniques.…”

“…(18,19,25) DNA extraction followed standard protocols following manufactured kits and is described elsewhere. (18,19) Extracted DNA samples were sent to the University of California San Diego IGM Genomics Center for library preparation, multiplexing, and whole genome shotgun sequencing using standard techniques. ( 26) Details on the full library preparation, sequencing protocols, and quality control steps are described in Wang et.…”

“…al. (19) After quality control, 781 samples remained with 6,528 taxa for downstream analysis. A taxonomy chart was created that assigned all taxa to a taxonomic classification across the seven phylogenetic levels -kingdom, phylum, class, order, family, genus, and species.…”

“…The authors and others have previously shown altered home dust microbiota with living on a farm and by farm type. (18)(19)(20) However, it is unknown how different occupational tasks and exposures within farm work shape the microbes in workers' homes, which is important for their health and the health of cohabitants. There is some evidence that the host microbiome is impacted by pesticides and other chemicals used by farmers and other occupational groups.…”