METAGENOMICS APPROACHES FOR IMPROVED WATER QUALITY MONITORING, MICROBIAL SOURCE TRACKING, AND PUBLIC HEALTH RISK ASSESSMENT

Suttner, Brittany

Title:

METAGENOMICS APPROACHES FOR IMPROVED WATER QUALITY MONITORING, MICROBIAL SOURCE TRACKING, AND PUBLIC HEALTH RISK ASSESSMENT

dc.contributor.advisor	Konstantinidis, Kostas T.
dc.contributor.author	Suttner, Brittany
dc.contributor.committeeMember	Pavlosthatis, Spyros G
dc.contributor.committeeMember	Brown, Joseph M
dc.contributor.committeeMember	DiChristina, Thomas
dc.contributor.committeeMember	Kirby, Amy E
dc.contributor.department	Civil and Environmental Engineering
dc.date.accessioned	2022-01-14T16:05:31Z
dc.date.available	2022-01-14T16:05:31Z
dc.date.created	2020-12
dc.date.issued	2020-12-03
dc.date.submitted	December 2020
dc.date.updated	2022-01-14T16:05:31Z
dc.description.abstract	Fecal contamination of water is a primary source of waterborne pathogens and is one of the most common impairments of water quality, affecting over a billion people worldwide. Because it is not practical to directly monitor the numerous pathogens that cause waterborne diseases, water quality and public health risk are assessed using fecal indicator bacteria (FIB) as proxies for pathogens. However, there are many known limitations associated with current methods that lead to inaccurate water quality and risk assessments, including low host-specificity and -sensitivity (e.g., not all members of a host type carry the marker), and false positive signals from “naturalized” populations of FIB that are commonly found in the extraenteric environment. Accordingly, identifying the source of fecal pollution (e.g., municipal sewage, livestock, or wildlife) remains challenging for current methods. To provide new, more robust biomarkers for microbial source tracking (MST), we used shotgun metagenomic sequencing to compare the decay kinetics of fecal microbes from different sources (i.e., cow, pigs, humans, and municipal sewage) in freshwater mesocosms simulating a pollution event. We identified several host-specific metagenome assembled genomes (MAGs) and functional genes as putative biomarkers for more robust MST and demonstrated the advantages of metagenomic methods over traditional qPCR and culture-based tests. Notably, the identified MAGs differed from the most commonly used FIB both taxonomically and functionally. Further, we provided evidence that FIB cannot be effectively distinguished from their naturalized counterparts based on our mesocosm incubations, an important limitation that is not applicable to the newly proposed MAGs. Finally, we applied our biomarkers and newly developed bioinformatics pipelines to time series metagenomics data from creek sediments in Salinas Valley (California) and showed that these sediment communities are robust against inputs from agricultural surface runoff and cattle ranching.
dc.description.degree	Ph.D.
dc.format.mimetype	application/pdf
dc.identifier.uri	http://hdl.handle.net/1853/66021
dc.language.iso	en_US
dc.publisher	Georgia Institute of Technology
dc.subject	microbial source tracking
dc.subject	metagenomics
dc.subject	microbial ecology
dc.title	METAGENOMICS APPROACHES FOR IMPROVED WATER QUALITY MONITORING, MICROBIAL SOURCE TRACKING, AND PUBLIC HEALTH RISK ASSESSMENT
dc.type	Text
dc.type.genre	Dissertation
dspace.entity.type	Publication
local.contributor.advisor	Konstantinidis, Kostas T.
local.contributor.corporatename	School of Civil and Environmental Engineering
local.contributor.corporatename	College of Engineering
relation.isAdvisorOfPublication	f66cc347-a0bd-44a1-ac96-d4f61b26368a
relation.isOrgUnitOfPublication	88639fad-d3ae-4867-9e7a-7c9e6d2ecc7c
relation.isOrgUnitOfPublication	7c022d60-21d5-497c-b552-95e489a06569
thesis.degree.level	Doctoral