Publication Date
Spring 2026
Degree Type
Master's Project
Degree Name
Master of Science in Bioinformatics (MSBI)
Department
Computer Science
First Advisor
Dr. Cleber Ouverney
Second Advisor
Dr. Philip Heller
Third Advisor
Dr. William Andreopoulos
Keywords
Metagenomics, human oral microbiome, CRISPR-Cas9 enrichment, ASV
Abstract
Studying the oral microbiome is vital because its health implications are not contained to the mouth. Cariogenic bacteria cause tooth demineralization and oral microbes that translocate to extra-oral organ systems are linked to conditions like Alzheimer’s disease, heart disease, diabetes, and cancer. Some of these pathogens belong to the most abundant phyla in the oral cavity: Bacillota, Pseudomonadota, Bacteroidota, Actinomycetota, Spirochaetota, and Fusobacteriota, which together comprise 94% of the oral microbiome. This project uses CRISPR-Cas9 to deplete sequences from highly abundant phyla and the Eubacteria domain, enriching the remaining 6% of rarer taxa. Paired with NanoASV for single-nucleotide resolution, this enrichment method successfully isolates underrepresented phyla, including Synergistota, Patescibacteria, Spirochaetota, and Deinococcota. Uncovering hidden microbial groups has potential to complete our understanding of oral microbiome diversity and its health impacts.
Recommended Citation
Sevilla Alvarez, Gilma Ruth, "Combining CRISPR and NanoASV to Uncover the Rare Bacterial Communities of the Human Oral Microbiome" (2026). Master's Projects. 1748.
https://scholarworks.sjsu.edu/etd_projects/1748
Included in
Bioinformatics Commons, Biotechnology Commons, Environmental Microbiology and Microbial Ecology Commons
