Journal article
Metagenomics reveals novel microbial signatures of farm exposures in house dust
Frontiers in microbiology, Vol.14, pp.1202194-1202194
06/21/2023
DOI: 10.3389/fmicb.2023.1202194
PMCID: PMC10321240
PMID: 37415812
Abstract
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.
Details
- Title: Subtitle
- Metagenomics reveals novel microbial signatures of farm exposures in house dust
- Creators
- Ziyue Wang - National Institute of Environmental Health SciencesKathryn R. Dalton - National Institute of Environmental Health SciencesMikyeong Lee - , , , , , , , , , , , , , , , ,Christine G. Parks - National Institute of Environmental Health SciencesLaura E. Beane Freeman - , , , , , , , , , , , , , , , ,Qiyun Zhu - Arizona State UniversityAntonio González - , , , , , , , , , , , , , , , ,Rob Knight - University of California SystemShanshan Zhao - National Institute of Environmental Health SciencesAlison A. Motsinger-Reif - , , , , , , , , , , , , , , , ,Stephanie J. London - National Institutes of Health
- Resource Type
- Journal article
- Publication Details
- Frontiers in microbiology, Vol.14, pp.1202194-1202194
- Publisher
- Frontiers Media S.A
- DOI
- 10.3389/fmicb.2023.1202194
- PMID
- 37415812
- PMCID
- PMC10321240
- ISSN
- 1664-302X
- eISSN
- 1664-302X
- Language
- English
- Date published
- 06/21/2023
- Academic Unit
- Occupational and Environmental Health
- Record Identifier
- 9984701826802771
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