Student theses on microbiology of the built environment of interest

I have some automated Google Scholar searches for MoBE related topics and recently a few theses came up in the searches and I thought Iwould post about them here

Here is one: Indoor biological exposures : what can HVAC filter dust tell us?

Author: Jennings, Wiley Charles from Kerry Kinney’s lab.


Because people in the US spend an estimated 80-90% of their time indoors, much of it at home, understanding the potential health impacts of biological exposures that occur in the home is crucial. Recently, rapid advances in high-throughput DNA sequencing technology have spurred increased study of the relationships between the human and built environment microbiomes. HVAC filters hold promise as long-term, spatially integrated, high volume samplers to characterize the airborne home microbiome. In order to optimize HVAC sampling protocols and improve comparability between studies employing HVAC filters for bacterial community analysis, three HVAC filter dust sampling methods were compared. These three methods, vacuuming the filter surface, swabbing the filter surface, and eluting filter dust in a buffer, were selected as representative of previously published methods. Our findings suggest that vacuum and swab samples produced more repeatable and representative bacterial communities than did elution. Furthermore, given the reduced labor and cost of vacuum and swab methods, and the additional advantage that these two methods may also be applied to sampling dust from other home surfaces, vacuum and swab sampling of HVAC filter dust are found to be superior to elution.
It is estimated that on average people spend more than 90 percent of their time indoors. And yet, when we think about our health and how the environment affects it, most are unaware that indoor environments may have a larger impact on our health and well-being than even the outdoor environment. Given the amount of time we spend indoors, what are we exposed to indoors? Can we design indoor environments that are not only not harmful to us, but actually good for us? And can we do this in an energy efficient manner? What does a “healthy building” look like?

To start answering these questions, we focused on studying how various building characteristics and interventions affected indoor air microbiology and energy efficiency, two qualities that are critical when designing a healthy building. This work is split into three parts: (1) Investigating a healthy building intervention: cooling coil ultraviolet germicidal irradiation (UVG-CC), (2) investigating the microbiology of indoor air quality in a university dormitory and its effect on student health, and (3) a review of the role of mechanical ventilation in the airborne transmission of infectious agents in buildings.

Part (1) (Chapter 2) investigates the effect of ultraviolet germicidal coil cleaning (UVG-CC) technology on building energy efficiency and indoor air microbiology. Cooling coil surfaces within building ventilation systems are ideal sites for biofilm formation due to the presence of adequate nutrients (i.e. deposited particles) and moisture (i.e. condensate). Biofouling of cooling coils can contribute to decreased heat transfer efficiency and possible contamination of indoor air by releasing toxins or allergens into the air entering the building. We found that, in mild condensing conditions, UVG-CC increased heat transfer effectiveness by 3—6.4%, with an uncertainty of ± 2.7% resulting from the accuracy of our instrumentation. Microbial results showed increased airborne cell counts downstream of the coil one month after UVG-CC installation. This increase coincided with drastic (80—90%) decreases in surface cell counts, which suggests that UVGI inactivated biofilms from the surface of the coil and these clusters were then re-entrained into the airstream. Overall this study suggests that UVG-CC is most effective at reducing microbial contamination and increasing heat transfer effectiveness in humid climates with high latent loads but care must be taken one month after installation, especially in the case of retrofits, as inactive biological material may re-entrain into the air. Installation of this technology should be carefully considered depending on the climatic region, and may not need to be operated during non-condensing states. Future studies of UVG-CC should pay careful attention to the sensitivity and detection limits of their instrumentation, and would benefit from studying environments prone to excessive biological fouling so that differences between UV and non-UV coils are more pronounced.

Part (2) (Chapter 3) of this dissertation investigates the microbiota in indoor air in a student dormitory. We have long known that human occupants are a major source of microbes in the built environment. What remains undetermined is what, if anything, we can learn about the occupants of a building by analyzing the microbial communities found in indoor air. We investigated bacterial and fungal diversity found in settled dust samples and dust collected onto HVAC air filters from 91 rooms within a university dormitory in Boulder, CO. The sex of the room occupants had the most significant effect on the bacterial communities found in both the settled dust and air filter samples, while the room occupants had no significant effect on fungal communities. By examining the abundances of taxa at the genus level, we can predict the sex of room occupants with 79% accuracy, a finding that demonstrates the potential forensic applications of studying indoor air microbiology. We also identified which taxa at the OTU level were most different in abundance and frequency of occurrence between female and male rooms, and found that taxa often identified as members of the vaginal microbiome were more common in female-occupied rooms while taxa associated with human skin or the male urogenital microbiota were more common in male-occupied rooms. Measurement methods used to characterize the dormitory HVAC system and methods of health data collection are also described.

Part (3) (Chapter 4) is a comprehensive literature review of the role of mechanical ventilation in the transmission of infectious agents in buildings. Infectious disease outbreaks and epidemics such as those due to SARS, influenza, measles, or tuberculosis have raised concern about the airborne transmission of pathogens in indoor environments. There are insufficient data to quantify how various parameters controlled by HVAC systems may affect the airborne transmission of infectious agents. To improve our understanding and design of HVAC systems to promote better infection control, our review reveals a strong need for more epidemiologic studies and meta-analyses. Specifically, we call for well designed prospective observational or intervention studies in buildings to establish causal relationships between airborne exposures and outcomes and between building factors and exposures. Future studies will benefit greatly from improved experimental design, standardized measurement methods, and better collaboration between epidemiologists and HVAC engineers.

The work presented here provides a glimpse into the complex and interdisciplinary nature of indoor air and building science and makes connections across building energy systems, HVAC science, and microbiology to demonstrate the nuances of how building characteristics or design decisions can affect indoor exposures.

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Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. My lab is in the UC Davis Genome Center and I hold appointments in the Department of Medical Microbiology and Immunology in the School of Medicine and the Department of Evolution and Ecology in the College of Biological Sciences. My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis (see my lab site here which has more information on lab activities).  In addition to research, I am heavily involved in the Open Access publishing and Open Science movements.