Mansour, Dina2023-11-302023-11-302023-08https://hdl.handle.net/11299/258846University of Minnesota M.S. thesis. August 2023. Major: Dentistry. Advisors: Ronald Zapata, Craig Noblett. 1 computer file (PDF); vi, 69 pages.Purpose: To identify genes encoding the bacterial chemotaxis and biofilm formation pathway in primary and secondary root canal infections using whole genome shotgun sequencing. Materials and Methods: Thirty-seven samples from patients with primary and secondary root canal infections were evaluated using Shotgun sequencing. The distribution were assessed of bacterial species and functional genes, including genes encoding for chemotaxis and biofilm pathway. Libraries were made using 1⁄4 Nextera XT reations and sequencing was done on the Novaseq with a target of 15-20M reads per sample. Taxonomic and functional annotations were made using MetaPhIAn3 and HUMAnN3. The Mann Whitney test was used to compare differences in gene abundance between primary and secondary infections. Results: The study identified 19 chemotaxis and 77 biofilm genes. Prevalent bacteria with chemotaxis genes were Fusobacterium nucleatum (62%), Pseudopropionibacterium propionicum (21.6%), Selenomonas sputigena (10.8%), Desulfobulbus oralis (8.1%), and Campylobacter curvus (8.1%). Top chemotaxis genes included K10540: methyl-galactoside transport system substrate-binding protein (26/37) 70%, K10439 ribose transport system substrate-binding protein (21/37) 56%, K03413: two-component system, chemotaxis family, response regulator CheY (19/37) 51%, K02556: chemotaxis protein MotA (16/37) 43%, K02557 chemotaxis protein MotB (14/37) 37%. The prevalent bacteria encoding biofilm genes were Fusobacterium nucleatum (45.9%), Desulfobulbus oralis (8.1%), Campylobacter curvus (24.3%), Selenomonas sputigena (13%), and Eubacterium infirmum (43%). The top biofilm-related genes were K00688: starch phosphorylase (30/37) 81%, K00975: glucose-1-phosphate adenylyltransferase (30/37) 81%, K03092: RNA polymerase sigma-54 factor (23/37) 62%,K07173: S-ribosylhomocysteine lyase (24/37) 64%, K00640: serine O-acetyltransferase (23/37) 62%. Heatmap figures illustrated the abundance of these genes in the samples. Conclusion: Bacteria carrying chemotaxis and biofilm pathway genes included Fusobacterium nucleatum, Pseudopropionibacterium propionicum, Selenomonas sputigena, Desulfobulbus oralis, and Campylobacter curvus. The study provides valuable insights into potential targets for future research and treatment in root canal infections.enBiofilm formationChemotaxisEndodonticsGenesRoot canal infectionswhole genome shotgun sequencingThesis or Dissertation