Doctoral Dissertation Research - Humans as reservoirs: Historical microbiomes uncover hidden zoonotic pathways

Human populations have migrated to nearly every environment in the world, and as part of this process have modified and integrated with local ecologies. Human alterations to the environment, such as deforestation, contribute significantly to zoonotic disease transmission, including transmission of pathogens (bacteria, viruses, and other microorganisms) from animals to humans, and from humans to animals.

Less well studied are the impacts of the human-altered environment on marine mammal populations. This doctoral dissertation research project investigates the transmission of a human pathogen into marine mammal populations, uses preserved microorganisms on historical marine mammal remains as a unique resource to measure human-animal pathogen transmission, and explores the impact of human alterations on the marine environment.

This project and the dissemination of its results serve to build collaborative research among anthropologists, conservation biologists and environmental ecologists through publication and through outreach with the National Parks Service, Skype a Scientist, and STEM mentorship for the Oklahoma Louis Stokes Alliance for Minority Participation.

Coastal runoff increases the introduction of human pathogens and antibiotics into the environment. This can lead to the spread of zoonotic disease in wildlife and the environmental selection for antibiotic resistance. Of importance, Klebsiella pneumoniae, a common hospital acquired infection of humans, has become endemic among California sea lions along the California Channel Islands.

In addition, a hypervirulent strain of Klebsiella pneumoniae (hvKp), has been documented along the Pacific Rim. However, the origin of this transmission event is unknown. This project studies the introduction of Klebsiella pneumoniae into the California sea lion population using museum collections.

Museum collections can provide a timeline for studying environmental alterations as well as pathogen emergence. The investigators use metagenomic sequencing on California sea lion dental calculus to reconstruct the microbial community and link changes in microbial diversity to human activity. The investigators also perform in-solution DNA capture on specimens with Klebsiella pneumoniae to determine which strains are present.

By investigating the oral microbiomes of California sea lions across time, the investigators assess whether any human-mediated alteration to the microbiome allowed for easier transmission of Klebsiella pneumoniae into the sea lion population.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.