Sequencing the Microbiome of Agricultural Household Dust: Characterizing Community Structure

Thesis (Master's)--University of Washington, 2022Intro: Understanding how indoor environments can not only affect but also shape human health is a new area of emerging research. Considering that we spend a large portion of our daily lives indoors, dust is a major complex environmental mixture we are exposed to every day. While we already know from previous studies that several factors can influence the indoor dust microbial community, few studies have examined the effects of agricultural activities on the indoor dust microbiome, especially through the perspective of occupational pesticide exposures. Methods: We performed shotgun metagenomic sequencing on 104 household dust samples collected from a longitudinal agricultural cohort from the Lower Yakima Valley of Washington. After successfully sequencing our dust samples, not only did we compare the indoor dust microbial community structure between farmworker (FW) and nonfarmworker (NFW) households, but we also evaluated how the indoor dust microbiome changed over time since we collected these samples throughout the course of two time periods (2005 and 2011) and across two agricultural seasons (Thinning and Nonspray Season). Additionally, since we also had total dust organophosphates (OPs) concentrations for each of our household dust samples, we also examined how the indoor dust microbial community changed in relation to organophosphates exposures. Results: We observed significant longitudinal and occupational effects on the indoor dust microbiome. We found that for both Alpha and Beta diversity the indoor dust microbial community structure significantly changed between CHC2 and CHC3, with the difference in total dust OP concentrations between the two cohort years playing a significant role in the observed Shannon diversity differences. Additionally, when assessing differential taxa abundance using ANCOM-BC we found that 7 Orders and 40 Genera were significantly impacted by total dust OP concentrations as some taxa decreased when total dust OP concentrations increased and other taxa showed the inverse relationship. Furthermore, we also observed significant Occupational effects on individual taxa abundances at the Order, Family and Genus level. Although only one Order had significantly higher abundances in NFW households compared to FW households, both of our significant Family members as well as our significant Genera each had higher abundances within FW households. Conclusion: These results have demonstrated that the indoor dust microbial community is influenced by agricultural activities. While we not only provided evidence of the occupational take-home pathway by showing that in addition to pesticide residues being brought into the home, environment bacteria can also be introduced, we also showed that organophosphates found within household dust can directly affect the indoor dust microbiome. While researchers are still uncovering the many functions of all these unique and different bacteria, considering that household dust is a significant reservoir and route for indoor microbial exposures, understanding whether these microbes can positively or negatively influence human health will be an important next step for future public health, especially for the many families and children residing within these farm exposed households