TY - JOUR
T1 - Metagenomics reveals novel microbial signatures of farm exposures in house dust
AU - Wang, Ziyue
AU - Dalton, Kathryn R.
AU - Lee, Mikyeong
AU - Parks, Christine G.
AU - Beane Freeman, Laura E.
AU - Zhu, Qiyun
AU - González, Antonio
AU - Knight, Rob
AU - Zhao, Shanshan
AU - Motsinger-Reif, Alison A.
AU - London, Stephanie J.
N1 - Funding Information:
This work was supported by the Intramural Research Program of the National Institutes of Health (NIH), the National Institute of Environmental Health Sciences (NIEHS) (Z01-ES049030 and Z01-ES102385), the National Cancer Institute (Z01-CP010119B), and by American Recovery and Reinvestment Act funds. The Center for Microbiome Innovation at the University of California San Diego provided support by generating sequencing data.
Funding Information:
We appreciate all the study participants for their contribution to this research. We thank F. Day of NIEHS for expert computational assistance and J. Hoppin (North Carolina State University, Raleigh, NC) for her important contribution to the Agricultural Lung Health Study during her tenure at NIEHS. We also thank Gail Ackermann of UCSD for assistance with metadata curation, and Greg Humphrey for laboratory processing.
Publisher Copyright:
Copyright © 2023 Wang, Dalton, Lee, Parks, Beane Freeman, Zhu, González, Knight, Zhao, Motsinger-Reif and London.
PY - 2023
Y1 - 2023
N2 - 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.
AB - 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.
KW - agricultural health study
KW - environmental microbiology
KW - farming environmental exposures
KW - home dust microbiota
KW - indoor microbiome
KW - whole genome sequencing
UR - http://www.scopus.com/inward/record.url?scp=85164512665&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85164512665&partnerID=8YFLogxK
U2 - 10.3389/fmicb.2023.1202194
DO - 10.3389/fmicb.2023.1202194
M3 - Article
AN - SCOPUS:85164512665
SN - 1664-302X
VL - 14
JO - Frontiers in Microbiology
JF - Frontiers in Microbiology
M1 - 1202194
ER -