Development of Genome-Probing Microarrays for Monitoring Lactic Acid Bacteria during Kimchi Fermentation
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1 Development of Genome-Probing Microarray for Monitoring Lactic Acid Bacteria during Kimchi Fermentation Yong-Ha PARK Department of Applied Microbiology Yeungnam Univerity Republic of Korea
2 Variou type of microbial diagnotic microarray Probe Size Senitivity Fabrication method Advantage Diadvantage Oligomer chip 20-70bp 25ng in ilico deign & Oligomer yntheizer Detect not-iolated train & low cot for probe deign Low enitivity & pecificity cdna microarray Kbp 2.5ng in ilico primer deign & PCR Detect not-iolated train & high enitivity Extremely low pecificity Genome probing 3-5 Mbp 0.25ng Culture & Genome extraction High enitivity & pecificity Low throughput obtaining of genome & only detect iolate
3 Bif. angulatu m Bif. bifidum Bif. corynef orme Bif. minimu m Bif. aecular e Car. diverge n Car. picicol a cecorum duran faecium flavece n haemop eroxidu hirae malodor atu moravie ni mundtii phoenic ulicola acchar olyticu olitariu villorum acidophi lu agili alimenta riu amyloph ilu amylovo ru animali brevi caei corynifo rmi ub. corynifo rmi corynifo rmi ub. torquen cripatu curvatu cyprica ei delbruec kii ub. bulgaric u delbruec kii ub. delbruec kii delbruec kii ub. lacti diolivor an equi farcimin i ferment um fructivo ran fuchuen i gramini helvetic u ingluvie i jenenii johnoni i kefiri kimchi malefer mentan mali maltaro micu murinu ori parabuc hneri paracae i ub. paracae i paracae i ub. toleran pentou plantaru m reuteri rhamno u rumini akei ub. carnou akei ub. akei alivariu ub. aliciniu anfranc iceni harpea e uebicu vaccino tercu vaginali vitulinu zeae Lcc. garvieae Lcc. lacti ub. hordnia e Lcc. lacti ub. lacti Lcc. picium Lcc. plantaru m Lcc. raffinola cti argentin um carnou m citreum citreum fallax fructou m gelidum inhae lacti meente roide ub. cremori meente roide ub. dextrani cum meente roide ub. meente roide peudo meente roide Oenoc occu oeni acidilact ici clauen ii damno u dextrini cu inopinat u parvulu pentoa ceu urinaeeq ui alactolyt icu angino u autrali criceti downei entericu equi ub. zooepid emicu feru gordonii hyointe tinali iniae miti mutan pyogene ratti anguini obrinu ui thermop hilu vetibul ari cibaria confua halotole ran hanii hellenic a kandleri kimchii minor parame enteroid e oli thailand eni viridec en MR2 MR5 MR6 KM1 KM4 KM6 Negative Control Target Microorganim : Lactic Acid Bacteria Negative Control
4 Monitoring Population Dynamic of Lactic Acid Bacteria during Fermentation of Kimchi uing Genome-Probing Microarray K1 K2 K3 K4 K5 K6 K7 K8 K9 K10 Appl. Environ. Microbiol (12):
5 mali lacti peudomeenteroide meenteroide B. ubtili W. kimchii W. koreeni W. hanii E. coli W. confua akei caei citreum malefermentan
6 Population Dynamic of Lactic Acid Bacteria during Fermentation of Kimchi 5 Normalized SNR with 10ng of E.coli genome Weiella kandleri Pediococcu acidilactici Leuconotoc lacti Leuconotoc meenteroide Weiella koreeni K1 K2 K3 K4 K5 K6 K7 K8 K9 K10
7
8 Microarray profiling of tarter cultured kimchii Weiella cibaria Weiella confua Leuconotoc lacti Leuconotoc meenteroide ubp. Meenteroide Lactobacillu akei ubp. akei Lactobacillu malefermentan Lactobacillu delbrueckii ubp. bulgari Carnobacterium divergen
9 Subtracted Genome Microarray (SGM) Fabrication of microarray with train (or ubpecie) - level reolution Printing the train-pecific genome uing PCR-baed uppreion ubtractive hybridization Akopyant et al., PNAS,1998
10 Salmonella choleraeui ubp. indica Salmonella choleraeui ubp. alamae Salmonella choleraeui ubp. choleraeui Salmonella typhimurium Salmonella bongori Salmonella enteritidi Salmonella choleraeui ubp. arizonae Salmonella choleraeui ubp. diarizonae Salmonella choleraeui ubp. hountenae 3 mix Nucleic Acid Re (13):e113
11 (A) Relative SNR (%) S. indica S. choleraeui S. bongori S. arizonae S. hountenae S. alamae S. typhimurium S. enteritidi S. diarizonae 80 (B) S. indica S. choleraeui S. bongori S. arizonae S. hountenae S. alamae S. typhimurium S. enteritidi S. diarizonae
12
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