Date of Award

December 2013

Degree Type


Degree Name

Master of Science


Freshwater Sciences and Technology

First Advisor

Sandra L. McLellan

Committee Members

Harvey A. Bootsma, Matthew C. Smith


Brazil, Fecal Indicator Bacteria, Microbial Source Tracking, Microbiome, Waterborne Illnesses, Water Quality Monitoring


Waterborne illnesses, attributed to the ingestion or contact with contaminated water, present a significant global health concern. Surface water sources can be impacted by wide array of pollution inputs, but fecal pollution generates the most significant and acute threat to human health. Therefore, the detection of fecal bacteria in surface water sources remains an important public health objective. Current surface water monitoring employs the use of fecal indicator bacteria (FIB) including E. coli and enterococci as proxies for pathogenic organisms carried in fecal pollution. These traditional indicators, detected by culture-based microbiological methods, do not discriminate fecal sources from another. New molecular approaches in pathogen surveillance, such as microbial source tracking (MST) and fecal-associated signatures, are culture-independent and are better suited for both the detection and identification of fecal pollution sources. By identifying fecal pollution sources, human health risks can be more accurately assessed and remediation strategies can be effectively implemented.

This paper examines a variety of MST markers, and the basis for these by integrating in host source microbiome studies. Chapter 2 describes work with Catellicoccus marimammalium, where next generation sequencing demonstrates this marker is a dominant member of the gull microbiome. This work has important implications for reconciling high fecal indicator levels at beaches with health risk. Chapter 3 extends MST work to areas of poor sanitation in Jenipapo, Brazil. The distribution of human specific indicators in surface water fecal contamination and prevalence of the waterborne illness schistosomiasis is described. Lastly, Chapter 4 explores the microbial community of humans and animals across different geographic regions, Brazil and the United States, to evaluate the applicability of existing MST methods, assess host-specific organisms and fecal-associated bacterial groups, and investigate the potential to develop new and geographically-appropriate markers.