I entered graduate school at Baylor College of Medicine in August 2011 as part of the Integrative Molecular and Biomedical Sciences graduate program. After five rotations encompassing a broad range of topics from Bacillus anthracis (the causative agent of anthrax) to nociception in bacterially infected Drosophila melanogaster larvae to simian immunodeficiency virus, I finally joined a lab focused on the human microbiome. My thesis work was divided into three main categories: the human microbiome and health, the human microbiome in disease, and the human microbiome and death:
The Human Microbiome and Health-Nitrate Reducing Oral Bacteria and Cardiovascular Health
The Human Microbiome and Disease-The Pulmonary Microbiome of Children with Bronchiolitis
Although I was really curious about how the human microbiome improves our everyday health, I also found it important to identify microbiome community alterations associated with disease-as did much of the microbiome community at the time that I was in graduate school, despite the Human Microbiome Project's focus on defining the healthy human microbiome. I jumped at the chance to work with collaborator Jonathan Mansbach at Harvard School of Public Health to use both marker gene and whole genome shotgun sequencing of the pulmonary microbiome in an effort to disentangle whether and how bacteria are associated with viruses and bronchiolitis-as well as the potential to develop wheezing disorders later in life-in children less than two years of age admitted to the hospital with bronchiolitis. While I did not find strong associations between specific bacterial species and the viral etiology of bronchiolitis (RSV, HSV, or both) I did find that children wheezing upon admission to the hospital did have significantly higher levels of bacterial species that had previously been implicated in asthma in older cohorts, as described in my 2013 Journal of Allergy and Clinical Immunology article (see my publications page). The children in this cohort will be followed until 6 years of age, the age at which most who will develop asthma develop this condition. I am disapointed that I won't be involved in the follow microbiome study; however, I am confident that whoever is will find a wealth of interesting connections between bronchiolitis, asthma, and the pulmonary microbiome.
The Human Microbiome and Death-The Microbiome Associated with Human Decomposition
Through a collaboration with Drs. Aaron Lynne and Sibyl Bucheli-microbiologist and entomologist-at Sam Houston State University in Houston, TX, I was able to provide some of the very first available information about the microbial communities associated with human decomposition. Although animal models such as mice and pigs have been used for years to study mammalian decomposition, the microbial communities associated with decomposition remain a new endeavour in the field, and studies with human subjects are even rarer. Aaron, Sibyl, Aaron's graduate student Daniel, and I had access to human cadavers through the Southeast Texas Applied Forensic Science Research Facility, a willed-donation center that enables researchers from various fields to study the forensics sciences. In our first study, published in PLoS One in October 2013 (see my publications page), we sampled two cadavers at two time points-pre- and post-bloat-to determine whether bacterial communities change betwen these two decompositional stages. Our results showed they bacterial communities indeed undergo drastic changes; therefore, we endeavoured on a more in depth study, again sampling two cadavers but leveraging more body sites and more time points to get a better look at microbial community changes during human decomposition. We published this work in the Journal of Forensic Science in 2014 (see my publications page). During this time, I reached out to Dr. Jessica Metcalf in Rob Knight's lab, who was working on mammalian decomposition using animal models, and a fruitful collaboration was born. Because of this collaboration I have been able to continue my forensics microbiome work as a post-doc.
As a postdoctoral researcher in Rob Knight's lab, I have worked on both the environmental and human microbiomes.
The Environmental Microbiome:
Beginning in 2014, when I first joint the Knight lab, I have been using bacterial and fungal marker gene sequencing and analysis to characterize the microbial communities present in the sap (latex) of the Euphorbia plant. This sap has traditionally been thought of as not only sterile, but inhibitory to microbial growth, so when my collaborators at Oak Crest Institute and Huntington Gardens in Pasadena, CA observed bacterial growth in the sap, they hypothesized that latex may actually be more microbially diverse than previously thought. Using samples collected from plants grown in a nursery, garden, and a greenhouse, we found both fungal and bacterial diversity in Euphorbia sap, with trends suggesting that the microbial communities may differ between plants grown in nurseries vs. gardens vs. greenhouses. This study was preliminary, and was recently accepted for publication in the Journal of Botany (see my publications page). The implications of our work have led us to collect a larger number of samples to more fully characterize the microbial community of Euphorbia latex.
Upon joining the Knight lab, I took on an orphan project that now represents one of my most passionate research topics-the effects of closed-space lifestyles on the microbiome of both humans and animals, and the potential connection between closed living, the microbiome, and disease. Also using bacterial marker gene sequencing and analysis, I characterized host-environment microbial sharing in three model systems: humans/pets and houses, captive Komodo dragons and their enclosures, and wild amphibians and their ponds. Through this work, I determined that host-microbial sharing in closed, built environments is different from that occuring in wild, open environments. Humans and their pets, as well as captive Komodos, share a significant proportion of their microbes with their living environments; this type of sharing is not seen among wild amphibians and their environments. The closed environment limits the amount of bacterial diversity that we or an animal is exposed to, and may play a part in the increased incidence of chronic diseases observed among humans in the last century as well as among captive animals but not their wild counterparts.
The Human Microbiome:
As a post-doc in the Knight lab, I had the privelege of continuing human decomposition studies that I had started as a graduate student at BCM. I've worked closely with Dr. Jessican Metcalf, who is leading the forensics microbiome work in the Knight lab, to not only continue to study the microbial (bacterial, eukaryotic, and fungal) communities associated with decomposition, but to study whether microbes can act as trace evidence at crime scences. In a paper recently published in Science (see my publications page), we demonstrated that microbial communities assemble on and around corpses in a predictable manner throughout decomposition, and we present the idea of using a microbial clock for time since death predictions. Our methods were applied both to animal and human corpses, and in both cases, we were able to predict time since death with very low error rates (within a few days). We are also building upon previous work done in the Knight lab showing that computer keyboards can be assigned to their owners through microbial signatures to determine whether microbial signatures left behind at a crime scene could connect perpetrators to locations of interest.
I recently joined a project aiming to characterize the affects of vaginal ring drug delivery systems on the vaginal microbiome of women. This work is crucial to testing the efficacy of a drug delivery system for HIV prevention in women. This project is in it's infancy and I will update this section as work progresses.
For more details on these and other projects that I have been involved in, please visit my publications page.