{"id":{"repo_id":"gatech","oai_identifier":"oai:repository.gatech.edu:1853/62227"},"canonical_url":"https://search.dev.ndltd.org/etd/gatech/oai:repository.gatech.edu:1853/62227","repository":{"repo_id":"gatech","name":"Georgia Tech","base_url":"https://repository.gatech.edu/server/oai/request"},"display":{"title":"From genomes to metagenomes: Big data analysis of microbes related to public health","abstract":"Bacterial infections represent a major public health concern mainly in young children in the developing world and in immunocompromised individuals. Despite recent developments in clinical microbiology, our understanding of the molecular and ecological mechanisms underlying the pathogen-host-environment interplay, remains incomplete. In this work, we applied cutting-edge laboratory and bioinformatics techniques to profile microbial communities that might pose a risk for human health. Our objectives were to: (1) characterize the composition of microbial communities growing on hospital showerheads using shotgun metagenomics, (2) evaluate the response of the gut microbiome to acute diarrhea episodes along a rural-to-urban gradient in Northern Ecuador, and (3) detect and quantify recent gene transfer events among closely related genomes as the underlying mechanism of response and adaptation. The results showed, among other things, that showerhead biofilms could often serve as reservoirs for opportunistic pathogens, rural and urban gut microbiomes showed a differential response during diarrhea episodes, and recent genetic exchange is spatial and functional biased, it can be rampant, and is largely driven by selection pressures (e.g., antibiotic treatment). Therefore, these findings advance our knowledge on the diversity and dynamics of microbial communities and their potential links to public health.","abstract_html":"Bacterial infections represent a major public health concern mainly in young children in the developing world and in immunocompromised individuals. Despite recent developments in clinical microbiology, our understanding of the molecular and ecological mechanisms underlying the pathogen-host-environment interplay, remains incomplete. In this work, we applied cutting-edge laboratory and bioinformatics techniques to profile microbial communities that might pose a risk for human health. Our objectives were to: (1) characterize the composition of microbial communities growing on hospital showerheads using shotgun metagenomics, (2) evaluate the response of the gut microbiome to acute diarrhea episodes along a rural-to-urban gradient in Northern Ecuador, and (3) detect and quantify recent gene transfer events among closely related genomes as the underlying mechanism of response and adaptation. The results showed, among other things, that showerhead biofilms could often serve as reservoirs for opportunistic pathogens, rural and urban gut microbiomes showed a differential response during diarrhea episodes, and recent genetic exchange is spatial and functional biased, it can be rampant, and is largely driven by selection pressures (e.g., antibiotic treatment). Therefore, these findings advance our knowledge on the diversity and dynamics of microbial communities and their potential links to public health.","abstract_has_math":false,"creators":["Soto Giron, Maria Juliana"],"institution":"Georgia Institute of Technology","degree_name":null,"degree_level":"Doctoral","degree_discipline":null,"degree_department":"Biology","school":null,"contributors":[],"advisors":["Konstantinidis, Kostas T."],"committee_chairs":[],"committee_members":["Levy, Karen","Jordan, Irving K.","Hammer, Brian","Stewart, Frank"],"year":2018,"date_issued":"2018-11-07","date_published":"2018-11-07","updated_at":"2026-07-27T19:51:09Z","subjects":["Metagenomics","Microbial ecology","Genetic exchange","Genomics"],"languages":["en_US"],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/1853/62227","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Konstantinidis, Kostas T."]},{"key":"dc:contributor.committeemember","label":"Committee Member","values":["Levy, Karen","Jordan, Irving K.","Hammer, Brian","Stewart, Frank"]},{"key":"dc:contributor.department","label":"Department","values":["Biology"]},{"key":"dc:creator","label":"Author","values":["Soto Giron, Maria Juliana"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2020-01-14T14:43:09Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2020-01-14T14:43:09Z"]},{"key":"dc:date.issued","label":"Date","values":["2018-11-07"]},{"key":"dc:publisher","label":"Institution","values":["Georgia Institute of Technology"]},{"key":"dc:type","label":"Dc Type","values":["Text"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Doctoral"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Metagenomics","Microbial ecology","Genetic exchange","Genomics"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language.iso","label":"Language (ISO)","values":["en_US"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["http://hdl.handle.net/1853/62227"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Bacterial infections represent a major public health concern mainly in young children in the developing world and in immunocompromised individuals. Despite recent developments in clinical microbiology, our understanding of the molecular and ecological mechanisms underlying the pathogen-host-environment interplay, remains incomplete. In this work, we applied cutting-edge laboratory and bioinformatics techniques to profile microbial communities that might pose a risk for human health. Our objectives were to: (1) characterize the composition of microbial communities growing on hospital showerheads using shotgun metagenomics, (2) evaluate the response of the gut microbiome to acute diarrhea episodes along a rural-to-urban gradient in Northern Ecuador, and (3) detect and quantify recent gene transfer events among closely related genomes as the underlying mechanism of response and adaptation. The results showed, among other things, that showerhead biofilms could often serve as reservoirs for opportunistic pathogens, rural and urban gut microbiomes showed a differential response during diarrhea episodes, and recent genetic exchange is spatial and functional biased, it can be rampant, and is largely driven by selection pressures (e.g., antibiotic treatment). Therefore, these findings advance our knowledge on the diversity and dynamics of microbial communities and their potential links to public health."]},{"key":"dc:description.degree","label":"Dc Description Degree","values":["Ph.D."]},{"key":"dc:format.mimetype","label":"Dc Format Mimetype","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["From genomes to metagenomes: Big data analysis of microbes related to public health"]}]}],"canonical_facts":{"dc:contributor.advisor":["Konstantinidis, Kostas T."],"dc:contributor.committeemember":["Levy, Karen","Jordan, Irving K.","Hammer, Brian","Stewart, Frank"],"dc:contributor.department":["Biology"],"dc:creator":["Soto Giron, Maria Juliana"],"dc:date.accessioned":["2020-01-14T14:43:09Z"],"dc:date.available":["2020-01-14T14:43:09Z"],"dc:date.issued":["2018-11-07"],"dc:description.abstract":["Bacterial infections represent a major public health concern mainly in young children in the developing world and in immunocompromised individuals. Despite recent developments in clinical microbiology, our understanding of the molecular and ecological mechanisms underlying the pathogen-host-environment interplay, remains incomplete. In this work, we applied cutting-edge laboratory and bioinformatics techniques to profile microbial communities that might pose a risk for human health. Our objectives were to: (1) characterize the composition of microbial communities growing on hospital showerheads using shotgun metagenomics, (2) evaluate the response of the gut microbiome to acute diarrhea episodes along a rural-to-urban gradient in Northern Ecuador, and (3) detect and quantify recent gene transfer events among closely related genomes as the underlying mechanism of response and adaptation. The results showed, among other things, that showerhead biofilms could often serve as reservoirs for opportunistic pathogens, rural and urban gut microbiomes showed a differential response during diarrhea episodes, and recent genetic exchange is spatial and functional biased, it can be rampant, and is largely driven by selection pressures (e.g., antibiotic treatment). Therefore, these findings advance our knowledge on the diversity and dynamics of microbial communities and their potential links to public health."],"dc:description.degree":["Ph.D."],"dc:format.mimetype":["application/pdf"],"dc:identifier.uri":["http://hdl.handle.net/1853/62227"],"dc:language.iso":["en_US"],"dc:publisher":["Georgia Institute of Technology"],"dc:subject":["Metagenomics","Microbial ecology","Genetic exchange","Genomics"],"dc:title":["From genomes to metagenomes: Big data analysis of microbes related to public health"],"dc:type":["Text"],"thesis:degree_level":["Doctoral"]},"updated_at":"2026-07-27T19:51:09Z"}