Date of Award
12-20-2024
Degree Name
Doctor of Philosophy (PhD)
Degree Type
Dissertation
Abstract
The microorganisms that are found in potable water and its treatment and supply systems are collectively considered as the drinking water microbiome. As part of the built environment, potable water can play a role in seeding the human commensal microbiomes. At the same time, certain opportunistic pathogens are enriched in the water plumbing systems and could lead to public health concerns. Despite its importance, very little is known about the diversity and functions of the drinking water microbiome, nor the forces that shape their variations. In particular, many microorganisms found in the drinking water environment do not have a reference genome, making it difficult to assign taxonomy or infer functions. In addition, while genome resources for pathogens are relatively abundant, genome resources of opportunistic pathogens in their environmental reservoirs are rarely available, limiting the development of source tracking technologies. To overcome these barriers, we systematically collected drinking water microbiome samples from individual households, using the St. Louis potable water as a model system. We applied 16S rRNA gene amplicon sequencing, shotgun metagenomic sequencing, and PacBio long read sequencing to examine the spatio-temporal variations of drinking water microbiomes and to investigate the forces driving the diversity of microbial communities in drinking water. The first study of this dissertation presents a pilot investigation in which daily sampling of the bathtub faucet water was conducted over the course of one week in eight households located in St Louis. We found that the species compositions of premise plumbing water microbiomes significantly differed by household and the household individuality was persistent across daily sampling of bathtub faucet water microbiomes. On the other hand, the functional compositions and the antimicrobial resistance profiles were more similar across different households. Community assembly analyses revealed that the household-level differences in bathtub faucet water microbiomes were mostly driven by stochastic processes. These findings highlight the importance of considering both household-level variation and species-level taxonomic compositions in assessing health risks associated with opportunistic premise plumbing pathogens over space and time. The second study of the dissertation expands to a larger sampling campaign involving 100 households in the St Louis area, utilizing a citizen scientist approach to collect samples and data. Both hot water samples from a bathtub faucet and cold water samples from a kitchen sink faucet were collected after overnight stagnation. Across all samples, we recovered 7,546 metagenome assembled genomes (MAGs) with medium and higher quality through hybrid assembly of Illumina shotgun metagenomic reads and PacBio long reads. Those MAGs were further de-replicated into 1,207 species-level genome bins (SGBs), representing 4 new families, 27 new genera, and 721 new species that are currently absent from the Genome Taxonomy Database. We found that the taxonomic compositions of microbial communities clustered more distinctively by sampling area (St Louis City vs St Louis County) than by sample type (bathtub faucet vs kitchen faucet). Models incorporating water chemistry parameters were built to understand the factors that contribute to the variation of the microbial community. In contrast, gene profiles exhibited stronger clustering by sample type than by sampling area, suggesting that different functions may be enriched in different types of water samples. The last study of this dissertation presents a tutorial review discussing phylogenetic relationships among non-tuberculous mycobacteria (NTM) as revealed by 16S rRNA gene, rpoB gene, hsp65 gene, and genome-based approaches. To study the association between the ecology and the phylogenetic relationships among NTM, a synthesis of data on the habitats of 189 mycobacterial species in a genome-based taxonomy framework was also performed. By visualization through the phylogenetic tree annotated with habitat information, none of the Mycobacterium complexes showed a strong association with drinking water, which provides justification for extending quantitative microbial risk assessment research to diverse complexes to further understand and manage the risks of NTM infections through water systems.
Language
English (en)
Chair
Fangqiong Ling
Committee Members
Daniel Giammar; Fuzhong Zhang; Jason Knouft; Jay Turner