Joongjae Kim Email & Phone Number

Calgary, Alberta, Canada

o Developing optimized novel methodologies and establishing laboratory and quality control procedures.- Developing standard protocols for handling/processing/storing targeted biomolecules (DNA, RNA, metabolites, and proteins) from the SIMBA capsules for multi-omics analyses.- Developing a new microbiome viability-preserving system for the SIMBA capsule.o Developing advanced next-generation microbiome-based diagnostics.o Leading R&D projects including protocol design, data analysis, and reporting for scientific presentations and manuscripts.o Training and mentoring junior laboratory personnel.

Calgary, Alberta, Canada

o Developed yeast platforms for biological production of ultraviolet A/B-protective isoprene natural products, phytoene, and phytofluene by using enzyme and metabolic engineering approaches (e.g., conventional yeast transformation and CRISPR/Cas9 system).o In silico prospecting key genes (enzymes) for phytoene and phytofluene biosynthesis from diverse species and assessing their catalytic efficiencies in yeast by using LC-MS.o Created mutant enzymes (phytoene synthase and phytoene desaturase) for alteration of product specificity and improvement of enzyme performance by directed evolution, e.g., error-prone PCR and site-directed mutagenesis.

Calgary, Canada Area

o Analyzed microbiome and their dynamic in the hydrocarbon reservoirs (oil sands process-affected water) and methane biofiltration systems by culture-dependent and –independent approaches such as enrichment culture, quantitative PCR (qPCR) and next-generation sequencing (in-house Illumina MiSeq platforms; 16S profiling, whole-genome sequencing, metagenomics; generate, analyze, interpret massive microbiota data sets) followed by QIIME data analysis and BaseSpace Sequence Hub built by illumina Itd., and measuring methane oxidation rates using gas chromatography (GC). (Collaborated with civil engineers, and oil & gas industry)o Discovered novel microorganisms and microbial consortia of interest such as hydrocarbon degrader and methane/H2S oxidizer for bioremediation of contaminated industrial settings (oil and gas sector, landfill, etc), and identified, characterized, and evaluated their microbial and physiological properties including monitoring the metabolic products with a gas chromatograph. (2 papers and 3+ annual reports published)o Developed new biomarkers and established new molecular testing assays for detecting/quantifying the microbial activities (e.g., methane-oxidation) and dynamics of specific groups of microbes from the methane biofilter system by using quantitative PCR (qPCR) and next-generation sequencing followed by QIIME data analysis. (collaborated with civil engineers; 1 paper published)o Monitored/analyzed biological and environmental factors (pH, BOD, COD, Microbial diversity, etc) of oil sands process-affected water and water/sediment samples from hot springs over time.o Supervised 4+ graduate and 3+ undergraduate students for their research: teaching and technical training. (3 papers published)

Calgary, Canada Area

o Analyzed microbial community structure in environmental samples such as Canadian hot springs (water and sediments) by culture-dependent and –independent approaches such as clone library construction, real-time quantitative PCR (qPCR) with customized specific primers, and next-generation sequencing (454 pyrotaq; 16S profiling, metagenomics) followed by QIIME data analysis. (Collaborated with Governmental research institute, Natural Resources Canada)o Isolated and identified novel microorganisms and microbial consortia useful for cellulosic bio-ethanol production (cellulose degrader, and ethanol producer, etc) from extreme conditions such as water and sediment from the hot springs and identified, characterized, and evaluated their microbial and hydrolytic properties. o Supervised 4+ graduate and 3+ undergraduate students for their research: teaching and technical training. (3 papers published) o Scheduled project progress to ensure milestones are achieved according to the timeline / Contributed yearly research updates to report to external partnerships and program sponsors / Maintained, purchased laboratory supplies and equipment. / Got trained for laboratory management, laboratory health and safety, WHMIS 2015, and H2S Alive.

Osaka, Japan

o Awarded a research grant for a 2-years research project to prospect novel microorganisms for bioremediation of hydrocarbon contaminated area, resulted in discovering 4+ novel microbes (cellulolytic, lipolytic, etc.) from the compost. (Research grant awarded approx. CAD 112,000; 2+ papers and 2+ annual reports published) o Isolated and identified novel cellulolytic and lipolytic microorganisms from the compost and characterized their microbial characterization, and purified their cellulolytic and lipolytic genes and enzymes using DNA analyzer, FPLC and characterized their enzymatic properties using HPLC.o Constructed fosmid library and conducted functional screening to prospect novel genes, resulted in discovering novel cellulolytic and lipolytic genes (2+ papers and 2+ annual reports published)o Got trained in writing research proposals. (Postdoctoral scholarship awarded with a topic of bioremediation of oil spill hydrocarbon contaminated area)o Supervised and mentored graduate and undergraduate students in their research. (2 papers published)o Provided a project-based training course for master students with the topic of “Identification of microorganism by 16S rRNA gene sequence analysis”.

Osaka, Japan

o Analyzed symbiotic interactions between commensal thermophile and its partner microbe; physiological studies such as growth behavior, metabolic pathway analysis, genome analysis by using AKTA-FPLC, 2-D electrophoresis coupled with MALDI-TOF-MS, LC-MS, whole-genome sequencing by using various bioinformatics tools, and molecular studies to understand molecular mechanisms responsible for uncultivability. (2+ papers published)o Discovered and purified novel growth-stimulating factors (proteins and metabolites) in symbiotic interactions between commensal microorganisms by using AKTA-FPLC and 2-D electrophoresis coupled with MALDI-TOF-MS, LC-MS analyses, and developed novel cultivation methods for the uncultured anaerobic bacteria which resulted in isolating 16 strains of novel anaerobic spore-forming thermophiles. (2+ papers published)o Analyzed proteomic profile of whole-cell proteins and extracellular proteins produced by the commensal microorganism by using 2-D gel analysis coupled with MALDI-TOF MS (Ultraflex, Bruker Co.), LC-MS (APEX IV, Bruker Co.), and various bioinformatics tools (MASCOT software, COGs database, KEGG database, SignalP, iPOST, TMHMM 2.0 software, SecretomeP, PSORT, SOSUIsignal, JVirGel 2.0, and so on) for the prediction of protein function and domain structure. (2+ papers published)o Involved in the genome sequencing project of the symbiotic microorganisms, Symbiobacterium toebii for the annotation, function prediction, and classification of individual genes with several bioinformatics tools such as Pedant-Pront-Pro, genome gambler, etc.

Yuseong-Gu, Daejeon, Korea

o Analyzed the biopolymer (poly-gamma-glutamic acid; PGA) biosynthetic machinery and constructed metabolically engineered microbial strains to increase the productivity of biopolymer, poly-gamma-glutamic acid (PGA) from Bacillus subtilis by means of knock-out mutation and DNA recombination techniques.o Developed and constructed E. coli, Bacillus, and lactic acid bacteria expression system (e.g., plasmid construction, soluble expression, protein purification using FPLC, western blotting, 2D-electrophoresis, etc.) for high-level (secretory) production of biologically active proteins (e.g., subtilisin E, lipase, etc).o Developed/launched new products using microbial resources in the food and feed industries (e.g., calcium-fortified feed additives to increase mineral absorption, edible vaccines using surface-displayed lactic acid bacteria, immune-enhancing probiotic agents for preventing swine/poultry diarrhea disease, and biological control of spoiling microbes). (2+ patents generated; collaborated with animal feeds company)o Produced recombinant proteins using bioreactor/fermenter system from 3L of lab-scale to 50L of pilot-scale, and 1-10 tons of industrial-scale.o Developed and maintained laboratory standard operating procedures (SOPs), work instructions, and technical documents and setup guidelines in compliance with the KFDA regulations.

Yuseong-Gu, Daejeon, Korea

o Analyzed the diversity of commensal anaerobic thermophiles by culture-dependent and -independent methods, such as clone library construction, PCR amplification, competitive quantitative PCR (qPCR), terminal restriction fragment length polymorphism (TRFLP), and PCR-denaturing gradient gel electrophoresis (PCR-DGGE), and DNA sequencing techniques.o Characterized commensal thermophile, Symbiobacterium toebii and its partner, Geobacillus toebii isolated from compost by using bioassay with a microplate reader and purified growth-supporting materials by using AKTA-FPLC. (3+ papers published; 1+ patent generated)o Purified and characterized fibrinolytic enzymes from Bacillus sp. isolated from Chungkookjang, Korean traditional fermented soybean food, and over-produced fibrinolytic enzymes in shake-flask and 3L jar fermentation systems.

Jeungpyeong-Gun, Chungcheongbuk-Do, Korea

o Operated, and took charge of, an environmental/water quality monitoring facility and monitored environmental parameters (e.g., pH, turbidity, BOD, COD, biosolids, etc.) of wastewaters.o Trained anti-terror task force team of the army, soldiers, and fire officers for the protection and detoxication under chemical-biological-radiological warfare and bio-terror situations.

Doctor Of Philosophy (Phd), Agricultural Biotechnology (Food Science And Technology)

Specific major of Microbial Ecology and Physiology Dissertation title: Analysis of commensal properties of commensal thermophile.

Master Of Science (Msc), Applied Microbiology

Thesis title: Purification and characterization of fibrinolytic enzymes in Bacillus sp. isolated from Chungkookjang (Korean traditional.

Bachelor Of Science (Bsc), Applied Microbiology

Worked as a research trainee in Biochemical Engineering Lab for 3 years. o Engineered D-amino acid oxidase and glutaryl-7ACA acylase.