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Holstein cow in a field

 Dust and water samples are being collected at dairy farms for the microbiome project.

CHROME Project

Project Title: Collaborative Health Research on the Microbiome and the Environment (CHROME)


 Microbiome Team


Microbes are present in all corners of the world in staggering numbers. For example, the ocean floor is home to 1029 microbial cells, or approximately 0.6% of the Earth’s total living biomass. The human body harbors an astounding number of microbes; the gastrointestinal tract alone is colonized by trillions of interacting microbes. Furthermore, microbes are highly concentrated in the near-surface atmosphere—millions of cells may be present in one cubic meter of air.

Microbes are essential, and intimately linked, to fundamental processes that promote human, animal, and environmental health. Conversely, there are subsets of microbes that are known pathogens. Additionally, nonviable microbial particulate matter may also trigger allergic and inflammatory responses. Community alterations and environmental perturbations may facilitate and promote the presence and growth of these harmful species.

Our work focuses on the synergistic relationships between human, animal, and environmental health. With the advent of next-generation sequencing, we are shifting the traditional paradigm of microbiology and industrial hygiene to high-throughput metagenomic approaches to better characterize and understand microbial niches, co-occurrences, and competitive exclusions in the occupational and environmental setting. For example, one facet of our research focuses on inhalational exposures to particulates containing viable and nonviable in the occupational setting and pulmonary responses (e.g., immunogenic and inflammatory) to further our understanding of the etiology of bioaerosol exposure-related lung diseases.

​With the capabilities of bioinformatics and data pipelines, analytic approaches can move beyond basic descriptive statistics to better anticipate and develop interventions that effectively reduce or prevent occupational exposures and environmental stressors.

Current Research

Bioaerosol Exposures and Models of Human Responses in Dairies and Cattle Feedlots

Project PI: Stephen J. Reynolds

Research into respiratory disease and exposures in agricultural settings has focused primarily on Gram-negative bacterial endotoxins. However, endotoxins may explain only a small proportion of respiratory disease currently seen in agricultural workers. The objectives of this research are to apply novel molecular tools to better characterize bioaerosols in dairies and to compare three different approaches for measuring the effects of bioaerosols in the lung: a traditional model using, a novel model using an aerosol sampler which includes human lung cells, and nasal samples taken from workers in these environments. This project will develop better tools for understanding agricultural lung disease, and will help to develop effective interventions (e.g. modification of livestock diet to change gut flora).

Modeling and Predicting Microbiomes in Dairies: A Metagenomic Assessment of Bioaerosols

Project PI: Joshua W. Schaeffer

Dairy farmers in the U.S. and globally are at an increased risk for chronic lung disease. This research capitalizes on a current HICAHS study in Colorado dairies to increase the number of aerosols samples collected and employ bioinformatics. The objectives of this research are to comprehensively characterize the biodiversity of airborne microorganisms at dairies using high-throughput sequencing data and bioinformatics to develop a metagenomic model to predict co-occurrences and absences of microorganisms at dairies that can be applied to other industries.

Exposure Assessment of Bioaerosols in an Australian Dairy

Project PI: Sue Reed

The sampling and analysis of bioaerosols in Australia has been both problematic and expensive, making it difficult to undertake exposure assessments in remote regions. This pilot project will establish a method for the sampling, transportation and analysis of bioaerosols that can be used to establish typical worker exposures in the Australian dairy industry. The findings from this project will also facilitate an international collaboration to characterize variations in geographical diversity, and complexity of bioaerosol constituents in dairies using emerging molecular identification tools and bioinformatics.

E. coli O157 Shedding and Antimicrobial Susceptibility on Colorado Dairies

Project PI: Craig McConnel

Cattle are the primary hosts of E. coli O157, and play a major role in the epidemiology of human infections. Some cows excrete far more pathogens than other cows (“super-shedders”), though the factors that may influence shedding are not well defined. This pilot project aims to assess the quantity and duration of shedding in cattle, and identify factors potentially contributing to antimicrobial resistance among super-shedding animals.

Characterizing Biological Pollutants in Agricultural Runoff at Colorado Dairies

Project PI: Sheryl Magzamen

In most river valleys and floodplains in Colorado, the alluvial aquifer consists of groundwater that is connected to surface water, making agricultural runoff a critical environmental health issue. Multiple agricultural products and by-products may enter local watersheds. This pilot project will employ exposure assessment and sequence-based analysis to characterize the spatial and temporal patterns of bacteria, antibiotics, and antibiotic resistant genes at a sample of dairies.