Metagenomics reveals novel microbial signatures of farm exposures in house dust

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.

Association of milk microbiome with bovine mastitis before and after antibiotic therapy

“…Regarding Jeotgalibaca and Rikenellaceae dgA-11 gut group , there were no published data on correlation with various types of mastitis in cows. However, data have been reported on the association of Jeotgalibaca with cattle rumen and manure fermentation [ 76 ], as well as its uniqueness for dairy and beef cattle breeding [ 77 ]. Jeotgalibaca has also been reported to be a major genus identified in milk [ 78 ].…”

Effects of microbes in pig farms on occupational exposed persons and the environment

“…However, it is worth noting that farms generally exhibit higher levels of microbial diversity. When farmers bring these dust microbes home, the indoor microbiota can resemble that of a farm and play a crucial role in protecting children from developing asthma (Kirjavainen et al 2019;Wang et al 2023). Therefore, the influence of pig farms on microorganisms in the surrounding environment has long been a research hotspot.…”