IDENTIFICATION OF ENDOPHYTIC BACTERIA FROM Curcuma zedoaria BASED ON PROTEIN PROFILE USING MALDI-TOF MASS SPECTROMETRY
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Valid identification of microorganisms is vital information to establish culture collections. Currently, a molecular approach based on 16S rDNA is widely used for bacterial identification. However, this approach is time-consuming and expensive. Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) allows the identification of microorganisms directly from colonies, and it only takes a few minutes. The aim of this study was to identify endophytic bacteria associated with Curcuma zedoaria based on protein profiles using the MALDI-TOF MS system and to compare the results with 16S rDNA sequencing. Endophytic bacteria were isolated from parts of the medicinal plant C. zedoaria collected from Bogor, West Java, Indonesia. The identification of selected bacteria was performed using protein profiling via MALDI-TOF MS. A total of 66 endophytic bacteria from C. zedoaria were selected for identification. The results of MALDI-TOF MS analysis showed that eleven isolates (16.67%) were correctly identified at the species level, and twenty-three isolates (34.85%) matched the genus level of the molecular approach. These results demonstrate that the MALDI-TOF system is a suitable and feasible approach for bacterial identification, particularly for screening and grouping large numbers of isolates.
Alatoom AA, Cunningham SA, Ihde SM, Mandrekar J, Patel R. 2011. Comparison of direct colony method versus extraction method for identification of gram-positive cocci by use of Bruker Biotyper matrix-assisted laser desorption ionization–time-of-flight mass spectrometry. J Clin Microbiol 49(8):2868–73. doi: 10.1128/JCM.00506-11
Benagli C, Demarta A, Caminada A, Ziegler D, Petrini O, Tonolla M. 2012. A rapid MALDI-TOF MS identification database at genospecies level for clinical and environmental Aeromonas strains. PLoS ONE 7(10):e48441. doi: 10.1371/journal.pone.0048441
Bizzini A, Jaton K, Romo D, Bille J, Prod'hom G, Greub G. 2011. Matrix-assisted laser desorption ionization–time-of-flight mass spectrometry as an alternative to 16S rRNA gene sequencing for identification of difficult-to-identify bacterial strains. J Clin Microbiol 49(2):693–6. doi: 10.1128/JCM.01463-10
Cain TC, Lubman DM, Weber WJ Jr. 1994. Differentiation of bacteria using protein profiles from matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 8:1026–30.
Chiu TC. 2014. Review: Recent advances in bacteria identification by matrix-assisted laser desorption/ionization mass spectrometry using nanomaterials as affinity probes. Int J Mol Sci 15:7266–80. doi: 10.3390/ijms15057266
Demirev PA, Ho YP, Ryzhov V, Fenselau C. 1999. Microorganism identification by mass spectrometry and protein database searches. Anal Chem 71:2732–8.
Eigner U, Holfelder M, Oberdorfer K, Betz-Wild U, Bertsch D, Fahr AM. 2009. Performance of a matrix-assisted laser desorption ionization–time-of-flight mass spectrometry system for the identification of bacterial isolates in the clinical routine laboratory. Clin Lab 55:289–96.
Ferroni A, Suarez S, Beretti JL, Dauphin B, Bille E, Meyer J, ... Nassif X. 2010. Real-time identification of bacteria and species in positive blood culture broths by matrix-assisted laser desorption ionization–time-of-flight mass spectrometry. Am Soc Microbiol 48:1542–8.
Guo L, Ye L, Zhao Q, Ma Y, Yang J, Luo Y. 2014. Comparative study of MALDI-TOF MS and VITEK 2 in bacteria identification. J Thorac Dis 6:534–8. doi: 10.3978/j.issn.2072-1439.2014.02.18
Jamal WY, Ahmad S, Khan ZU, Rotimi VO. 2014. Comparative evaluation of two matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems for the identification of clinically significant yeasts. Int J Infect Dis 26:167–70.
Kudirkiene E, Welker M, Knudsen NR, Bojesen AM. 2015. Rapid and accurate identification of Streptococcus equi subspecies by MALDI-TOF MS. Syst Appl Microbiol 38:315–22.
Lohmann C, Sabou M, Moussaoui W, Prévost G, Delarbre J, Candolfi E, Letscher-Brub V. 2013. Comparison between the Biflex III-Biotyper and the Axima-SARAMIS systems for yeast identification by matrix-assisted laser desorption ionization–time-of-flight mass spectrometry. J Clin Microbiol 51:1231–6.
Martiny D, Busson L, Wybo I, El Haj RA, Dediste A, Vandenberg O. 2012. Comparison of the Microflex LT and Vitek MS systems for routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. J Clin Microbiol 50:1313–25.
Neville SA, Lecordier A, Ziochos H, Chater MJ, Gosbell IB, Maley MW, van Hal SJ. 2011. Utility of matrix-assisted laser desorption ionization time-of-flight mass spectrometry following introduction for routine laboratory bacterial identification. J Clin Microbiol 49:2980–4.
Rajendhran P, Gunasekaran P. 2011. Microbial phylogeny and diversity: small subunit ribosomal RNA sequence analysis and beyond. J Microbiol Res 166:99–110. doi: 10.1016/j.micres.2010.02.003
Reich M, Bosshard PP, Stark M, Beyser K, Borgmann S. 2013. Species identification of bacteria and fungi from solid and liquid culture media by MALDI-TOF mass spectrometry. J Bacteriol Parasitol S5:002:1–8. doi: 10.4172/2155-9597.S5-002
Ryzhov V, Fenselau C. 2001. Characterization of the protein subset desorbed by MALDI from whole bacterial cells. Anal Chem 73:746–50.
Rychert J, Burnham CA, Bythrow M, Garner OB, Ginocchio CC, Jennemann R, ... Branda JA. 2013. Multicenter evaluation of the Vitek MS matrix-assisted laser desorption ionization–time-of-flight mass spectrometry system for identification of gram-positive aerobic bacteria. J Clin Microbiol 51:2225–31. doi: 10.1128/JCM.00682-13
Santos FS, Cayo R, Schandert L, Gales AC. 2013. Evaluation of MALDI-TOF MS in the microbiology laboratory. J Bras Patol Med Lab 49:191–7.
Seng P, Drancourt M, Gouriet F, La Scola B, Fournier P, Rolain JM, Raoult D. 2009. Ongoing revolution in bacteriology: routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis 49:543–51.
Singhal N, Kumar M, Kanaujia PK, Virdi JS. 2015. MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis. Front Microbiol 6:791–806. doi: 10.3389/fmicb.2015.00791
Sulistiyani TR, Lisdiyanti P, Lestari Y. 2014. Population and diversity of endophytic bacteria associated with medicinal plant Curcuma zedoaria. Microbiol Ind 8:65–72. doi: 10.5454/mi.8.2.4
Theel ES, Schmitt BH, Hall L, Cunningham SA, Walchak RC, Patel R, Wengenack NL. 2012. Formic acid-based direct, on-plate testing of yeast and Corynebacterium species by Bruker Biotyper matrix-assisted laser desorption ionization–time-of-flight mass spectrometry. J Clin Microbiol 50:3093–5.
Verroken A, Janssens M, Berhin C, Bogaerts P, Huang TD, Wauters G, Glupczynski Y. 2010. Evaluation of matrix-assisted laser desorption ionization–time-of-flight mass spectrometry for identification of Nocardia species. J Clin Microbiol 48:4015–21.
Woo PCY, Lau SKP, Teng JLL, Tse H, Yuen KY. 2008. Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clin Microbiol Infect 14:908–34.
Wunschel SC, Jarman KH, Petersen CE, Valentine NB, Wahl KL, Schauki D, White VE. 2005. Bacterial analysis by MALDI-TOF mass spectrometry: An inter-laboratory comparison. J Am Soc Mass Spectrom 16(4):456–62. doi: 10.1016/j.jasms.2004.12.004
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