From genomes to metagenomes: Big data analysis of microbes related to public health

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.

Level thesis:degree_level

Doctoral

Department dc:contributor.department

Biology

Grantor dc:publisher

Georgia Institute of Technology

Year dc:date.issued

2018

Author dc:creator

• Soto Giron, Maria Juliana

Advisor dc:contributor.advisor

• Konstantinidis, Kostas T.

Committee members dc:contributor.committeemember

• Levy, Karen
• Jordan, Irving K.
• Hammer, Brian
• Stewart, Frank

• Metagenomics
• Microbial ecology
• Genetic exchange
• Genomics

Language dc:language.iso

en_US

Handle dc:identifier.uri

http://hdl.handle.net/1853/62227

OAI identifier oai:identifier

oai:repository.gatech.edu:1853/62227