Metagenomics reveals novel microbial signatures of farm exposures in house dust

Ziyue Wang; Kathryn R Dalton; Mikyeong Lee; Christine G Parks; Laura E Beane Freeman; Qiyun Zhu; Antonio González; Rob Knight; Shanshan Zhao; Alison A Motsinger-Reif; Stephanie J London

doi:10.3389/fmicb.2023.1202194

Metagenomics reveals novel microbial signatures of farm exposures in house dust

Front Microbiol. 2023 Jun 21:14:1202194. doi: 10.3389/fmicb.2023.1202194. eCollection 2023.

Authors

Affiliations

¹ Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, United States.
² Genomics and the Environment in Respiratory and Allergic Health Group, Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, United States.
³ Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States.
⁴ School of Life Sciences, Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States.
⁵ Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States.
⁶ Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States.
⁷ Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.
⁸ Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, United States.

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.

Keywords: agricultural health study; environmental microbiology; farming environmental exposures; home dust microbiota; indoor microbiome; whole genome sequencing.