Background and Objective: The human microbiome is recognized as essential for the maintenance of human health, but research suggests that chemical and biological [e.g., viruses, such as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)] exposures can elicit perturbations in the human microbiome communities. As demonstrated with the coronavirus disease 2019 (COVID-19) pandemic, the occupational environment impacts worker health in numerous ways, one of which may be through changes to the worker microbiome. Particularly, the agricultural environment presents both chemical and biological hazards (i.e., workplace environmental microbiome or envirobiome) that may affect the worker microbiome and ultimately worker health. The state of the science regarding the potential for the agricultural environment to impact worker microbiomes is presented herein.

Methods: A literature search using the PubMed database and the WorldWideScience and Google Scholar search engines was performed to identify English-language, peer-reviewed literature published on or before August 3, 2022 that evaluated microbiomes in the agricultural occupational setting.

Key Content and Findings: A total of 24 relevant publications meeting the inclusion criteria were identified in which the agricultural worker microbiome and/or envirobiome were assessed. The state of the science in this area was evaluated based on the methods and findings of these studies. Several themes emerged regarding the nature of the available of data. Most identified studies focused on animal exposures (especially swine) with very limited data regarding chemical exposures in the agricultural environment. The microbial identification methods employed were largely dominated by 16S sequencing, and the most common worker microbial communities examined were the nasal and gastrointestinal microbiomes. Nearly all studies examined the bacterial microbiome, with few studies examining the fungal or viral envirobiomes or worker microbiomes.

Conclusions: The impact of exposure to chemical and biological agents on the worker microbiome is becoming a central focus of research, including workers in agricultural operations. Based on this review, numerous studies evaluated the worker microbiome or envirobiome among agricultural workers; however, few studies have evaluated both simultaneously. The relationship of the agricultural worker microbiome and envirobiome with worker health outcomes remains understudied. Moving forward, research needs to assess the totality of workplace exposures while simultaneously assessing agricultural worker microbiomes holistically. Further, research should consider exposures, lifestyles, and diets outside of the workplace to fully understand short-term and chronic microbiome impacts and subsequent health effects.

Keywords: Microbiome; agriculture; occupational exposure; worker; envirobiome