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Research focuses on the indoor exposome, the complex mixture of microbes and chemicals that we are exposed to on a daily basis.

Our research group using molecular methods and –omics approaches to tackle important challenges in society.  Methods used include phylogenetics, metagenomics, proteomics, and transcriptomics for exploration of microbial communities and biological processes. The lab space is designed specifically for handling and analysis of precious samples to prevent ambient contamination, complete with a clean room. Our cutting-edge equipment includes a QuantStudio 6 real-time PCR machine, a QuantStudio 3D digital PCR machine, and a Synergy HTX microplate reader.

Previous work has been conducted in the following areas:

1. Demonstrate associations between microbial exposures and childhood asthma development and severity

Exposure to indoor dampness and visible mold is associated with negative health outcomes, although the causal microbial agent remains unclear. In collaboration with epidemiologists, we demonstrated that low fungal diversity exposure early in life was associated with later increased risk of childhood asthma development [a]. This finding expands beyond traditional assumptions that the concentration of one or more harmful fungal taxa are responsible for asthma development and supports integration of fungal diversity into future studies. In an additional study in collaboration with a group at Yale, we studied microbial exposure and effect on asthma severity. Research demonstrates that exposure to microbes is associated with asthma severity, and these associations are dependent on asthma subtype [b]. The powerful combination of cutting-edge techniques from engineering with skills of environmental epidemiologists provides the opportunity for significant scientific advances.

a. Dannemiller, K., et al., Next-generation DNA sequencing reveals that low fungal diversity in house dust is associated with childhood asthma development. Indoor Air, 2014. 24(3): p. 236-247.
b. Dannemiller, K. C., Gent, J., Leaderer, B., and Peccia, J. 2016. Indoor microbial communities: influence on asthma severity in atopic and non-atopic children. Journal of Allergy and Clinical Immunology, accepted.


2. Identify home characteristics that are associated with indoor microbial community structure

We spend 90% of our time indoors, and choices we make about our environment can impact our daily exposures. Our work has demonstrated novel results in regard to environmental processes in homes. This research made significant advances in regard to a long-standing question by demonstrating that moisture in homes was associated with increased fungal diversity in house dust [a]. Our work also shows that housing characteristics and occupants influence microbial communities with relevance to human health [b]. Additional work demonstrated that the allergen potency of fungal spores is dependent on temperature [c], and yet unpublished work utilized proteomics to demonstrate dependency on ozone concentration.

a. Dannemiller, K., et al., Next-generation DNA sequencing reveals that low fungal diversity in house dust is associated with childhood asthma development. Indoor Air, 2014. 24(3): p. 236-247.
b. Dannemiller, K. C., Gent, J., Leaderer, B., and Peccia, J. “Influence of housing characteristics on bacterial and fungal communities in homes of asthmatic children” Indoor Air. DOI: 10.1111/ina.12205
c. Low, S.Y., et al., The allergenicity of Aspergillus fumigatus conidia is influenced by growth temperature. Fungal Biology, 2011. 115(7): p. 625-632.


3. Improve quantification and ease-of-use of next-generation DNA sequencing results of the fungal ITS region

Indoor environmental contaminants are a complex mixture that represents an emerging environmental problem. The advent of next-generation DNA sequencing allows for full characterization of indoor microbial communities, but results were difficult to analyze and semi-quantitative at best. For the analysis of –omics measurements, we developed user-friendly software for bioinformatic analysis of fungal taxa in environmental samples [a] with over 150 downloads. Additionally, we developed methods to drive environmental microbial measurements from relative abundances toward more quantitative absolute concentrations [b].

a. Dannemiller, K.C., et al., Fungal High-throughput Taxonomic Identification tool for use with Next-Generation Sequencing (FHiTINGS). Journal of Basic Microbiology, 2013. 54(4): p. 315-321.
b. Dannemiller, K.C., et al., Combining real-time PCR and next-generation DNA sequencing to provide quantitative comparisons of fungal aerosol populations. Atmospheric Environment, 2014. 84: p. 113-121.


4. Determine associations between formaldehyde concentrations in homes and asthma severity in children

Formaldehyde is an indoor contaminant of concern that has gained increasing attention due high exposures of occupants in the FEMA trailers after Hurricane Katrina, as well as the recent demonstration of high exposure from flooring products. Relatively few studies exist to quantitatively study formaldehyde concentrations in the home and examine associations with asthma severity. We have designed an inexpensive measurement device and used this to demonstrate associations between formaldehyde exposure and asthma severity in children [a]. Our background incorporates both chemical and microbial experience and provides the ideal foundation for future research on the interactions of these two systems.

a. Dannemiller, K.C., et al., Formaldehyde concentrations in household air of asthma patients determined using colorimetric detector tubes. Indoor Air, 2013. 23(4): p. 285-294.