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http://dx.doi.org/10.5478/MSL.2022.13.4.106

High-Throughput Screening Technique for Microbiome using MALDI-TOF Mass Spectrometry: A Review  

Mojumdar, Abhik (Biochemical analysis team, center for research equipment, Korea Basic Science Institute (KBSI), Ochang Center)
Yoo, Hee-Jin (Biochemical analysis team, center for research equipment, Korea Basic Science Institute (KBSI), Ochang Center)
Kim, Duck-Hyun (Biochemical analysis team, center for research equipment, Korea Basic Science Institute (KBSI), Ochang Center)
Cho, Kun (Biochemical analysis team, center for research equipment, Korea Basic Science Institute (KBSI), Ochang Center)
Publication Information
Mass Spectrometry Letters / v.13, no.4, 2022 , pp. 106-114 More about this Journal
Abstract
A rapid and reliable approach to the identification of microorganisms is a critical requirement for large-scale culturomics analysis. MALDI-TOF MS is a suitable technique that can be a better alternative to conventional biochemical and gene sequencing methods as it is economical both in terms of cost and labor. In this review, the applications of MALDI-TOF MS for the comprehensive identification of microorganisms and bacterial strain typing for culturomics-based approaches for various environmental studies including bioremediation, plant sciences, agriculture and food microbiology have been widely explored. However, the restriction of this technique is attributed to insufficient coverage of the mass spectral database. To improve the applications of this technique for the identification of novel isolates, the spectral database should be updated with the peptide mass fingerprint (PMF) of type strains with not only microbes with clinical relevance but also from various environmental sources. Further, the development of enhanced sample processing methods and new algorithms for automation and de-replication of isolates will increase its application in microbial ecology studies.
Keywords
MALDI-TOF; mass spectrometry; microbiome; environment;
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1 Nosalova, L.; Malinicova, L.; Kiskova, J.; Timkova, I.; Sedlakova-Kadukova, J.; Pristas, P. Geomicrobiology Journal 2021, 38, 415. DOI: 10.1080/01490451.2021.1871685   DOI
2 Garcia Lara, B.; Wrobel, K.; Corrales Escobosa, A.R.; Serrano Torres, O.; Enciso Donis, I.; Wrobel, K. Folia Microbiologica 2021, 66, 355. DOI: 10.1007/s12223-020-00848-8   DOI
3 Silva-Jimenez, H.; Araujo-Palomares, C.L.; MaciasZamora, J.V.; Ramirez-Alvarez, N.; Garcia-Lara, B.; Corrales-Escobosa, A.R. Journal of the Mexican Chemical Society 2018, 62, 214. DOI: 10.29356/jmcs.v62i2.411   DOI
4 Furlan, J.P.R.; Pitondo-Silva, A.; Braz, V.S.; Gallo, I.F.L.; Stehling, E.G. World Journal of Microbiology and Biotechnology 2019, 35, 1. DOI: 10.1007/s11274-019-2614-0   DOI
5 Junior, P.S.P.C.; Cardoso, F.P.; Martins, A.D.; Buttros, V.H.T.; Pasqual, M.; Dias, D.R.; Schwan, R.F.; Doria, J. Microbiological research 2020, 241, 126585. DOI: 10.1016/j.micres.2020.126585   DOI
6 Franco-Duarte, R., Cernakova, L., Kadam, S., S. Kaushik, K., Salehi, B., Bevilacqua, A., Corbo, M.R., Antolak, H., Dybka-Stepien, K., Leszczewicz, M., Relison Tintino, S. Microorganisms 2019, 7, 130. DOI: 10.3390/microorganisms7050130   DOI
7 Sauer, S., Kliem, M. Nature Reviews Microbiology, 2010, 8, 74. DOI: 10.1038/nrmicro2243   DOI
8 Everley, R.A.; Mott, T.M.; Wyatt, S.A.; Toney, D.M.; Croley, T.R. Journal of the American Society for Mass Spectrometry 2008, 19, 1621. DOI: 10.1016/j.jasms.2008.07.003   DOI
9 Wang, Y.; Zhou, Q.; Li, B.; Liu, B.; Wu, G.; Ibrahim, M.; Xie, G.; Li, H.; Sun, G. BMC microbiology 2012, 12, 1. DOI: 10.1186/1471-2180-12-182   DOI
10 Ekstrom, S.; Onnerfjord, P.; Nilsson, J.; Bengtsson, M.; Laurell, T.; Marko-Varga, G. Analytical chemistry 2000, 72, 286. DOI: 10.1021/ac990731l   DOI
11 Sawada, H.; Horita, H.; Misawa, T.; Takikawa, Y. Journal of general plant pathology 2019, 85, 413. DOI: 10.1007/s10327-019-00869-3   DOI
12 Pinar-Mendez, A.; Fernandez, S.; Baquero, D.; Vilaro, C.; Galofre, B.; Gonzalez, S.; Rodrigo-Torres, L.; Arahal, D.R.; Macian, M.C.; Ruvira, M.A. Water Research 2021, 203, 117543. DOI: 10.1016/j.watres.2021.117543   DOI
13 Fenselau, C.C. Journal of the American Society for Mass Spectrometry 2013, 24, 1161. DOI: 10.1007/s13361-013-0660-7   DOI
14 Biswas, S.; Rolain, J.-M. Journal of microbiological methods 2013, 92, 14. DOI: 10.1016/j.mimet.2012.10.014   DOI
15 Singhal, N.; Kumar, M.; Kanaujia, P.K.; Virdi, J.S. Frontiers in microbiology 2015, 6, 791. DOI: 10.3389/fmicb.2015.00791   DOI
16 Muthuri, C.; Nyambura, N.; Njeri, V.; Tani, A.; Wangari, M. Afr. J. Microbiol. Res 2012, 6, 6414. DOI: 10.5897/AJMR12.1112   DOI
17 Pramanik, K.; Mitra, S.; Sarkar, A.; Soren, T.; Maiti, T.K. Environmental Science and Pollution Research 2017, 24, 24419. DOI: 10.1007/s11356-017-0033-z   DOI
18 Costerousse, B.; Schonholzer-Mauclaire, L.; Frossard, E.; Thonar, C. Applied and environmental microbiology 2018, 84, e01715. DOI: 10.1128/AEM.01715-17   DOI
19 Sarkar, A.; Pramanik, K.; Mitra, S.; Soren, T.; Maiti, T.K. Journal of plant physiology 2018, 231, 434. DOI: 10.1016/j.jplph.2018.10.010   DOI
20 Kajiwara, H. Journal of microbiological methods 2016, 120, 1. DOI: 10.1016/j.mimet.2015.08.014   DOI
21 Wang, Z.; Russon, L.; Li, L.; Roser, D.C.; Long, S.R. Rapid Communications in Mass Spectrometry 1998, 12, 456. DOI: 10.1002/(SICI)1097-0231(19980430)12:8<456::AID-RCM177>3.0.CO;2-U   DOI
22 Ruelle, V.; Moualij, B.E.; Zorzi, W.; Ledent, P.; Pauw, E.D. Rapid Communications in Mass Spectrometry 2004, 18, 2013. DOI: 10.1002/rcm.1584   DOI
23 Ashfaq, M.Y.; Da'na, D.A.; Al-Ghouti, M.A. Journal of Environmental Management 2022, 305, 114359. DOI: 10.1016/j.jenvman.2021.114359   DOI
24 Havlicek, V.; Lemr, K.; Schug, K.A. Analytical chemistry 2013, 85, 790. DOI: 10.1021/ac3031866   DOI
25 Dingle, T.C.; Butler-Wu, S.M. Clinics in laboratory medicine 2013, 33, 589. DOI: 10.1016/j.cll.2013.03.001   DOI
26 De Carolis, E.; Vella, A.; Vaccaro, L.; Torelli, R.; Spanu, T.; Fiori, B.; Posteraro, B.; Sanguinetti, M. The Journal of Infection in Developing Countries 2014, 8, 1081. DOI: 10.3855/jidc.3623   DOI
27 Zeng, Y.; Wu, N.; Madsen, A.M.; Chen, X.; Gardiner, A.T.; Koblizek, M. Frontiers in microbiology 2021, 11, 606612. DOI: 10.3389/fmicb.2020.606612   DOI
28 Zhang, D.; Palmer, J.; Teh, K.H.; Flint, S. Lwt 2020, 134, 110165. DOI: 10.1016/j.lwt.2020.110165   DOI
29 Ge, M.; Li, B.; Wang, L.; Tao, Z.; Mao, S.; Wang, Y.; Xie, G.; Sun, G. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 2014, 133, 730. DOI: 10.1016/j.saa.2014.06.056   DOI
30 Illikoud, N.; Rossero, A.; Chauvet, R.; Courcoux, P.; Pilet, M.-F.; Charrier, T.; Jaffres, E.; Zagorec, M. Food microbiology 2019, 81, 22. DOI: 10.1016/j.fm.2018.01.015   DOI
31 Niestepski, S.; Harnisz, M.; Korzeniewska, E.; Osinska, A. 2019. Isolation of anaerobic bacteria of the Bacteroides fragilis group from environmental samples. In E3S Web of Conferences: EDP Sciences. 00058. DOI: 10.1051/e3sconf/201910000058   DOI
32 Vicenzi, F.J.; Pillonetto, M.; Souza, H.A.P.H.d.M.d.; Palmeiro, J.K.; Riedi, C.A.; Rosario-Filho, N.A.; DallaCosta, L.M. Memorias do Instituto Oswaldo Cruz 2016, 111, 37. DOI: 10.1590/0074-02760150314   DOI
33 Fehlberg, L.C.C.; Andrade, L.H.S.; Assis, D.M.; Pereira, R.H.V.; Gales, A.C.; Marques, E.A. Diagnostic microbiology and infectious disease 2013, 77, 126. DOI: 10.1016/j.diagmicrobio.2013.06.011   DOI
34 Alsayegh, S.Y.; Al Disi, Z.; Al-Ghouti, M.A.; Zouari, N. Biotechnology Reports 2021, 31, e00660. DOI: 10.1016/j.btre.2021.e00660   DOI
35 Sandrin, T.R.; Goldstein, J.E.; Schumaker, S. Mass spectrometry reviews 2013, 32, 188. DOI: 10.1002/mas.21359   DOI
36 Sala-Comorera, L.; Caudet-Segarra, L.; Galofre, B.; Lucena, F.; Blanch, A.R.; Garcia-Aljaro, C. International Journal of Food Microbiology 2020, 334, 108850. DOI: 10.1016/j.ijfoodmicro.2020.108850   DOI
37 Holland, R.; Wilkes, J.; Rafii, F.; Sutherland, J.; Persons, C.; Voorhees, K.; Lay Jr, J. Rapid Communications in Mass Spectrometry 1996, 10, 1227. DOI: 10.1002/(SICI)1097-0231(19960731)10:10<1227::AID-RCM659>3.0.CO;2-6   DOI
38 Kostrzewa, M.; Sparbier, K.; Maier, T.; Schubert, S. PROTEOMICS-Clinical Applications 2013, 7, 767. DOI: 10.1002/prca.201300042   DOI
39 Krishnamurthy, T.; Rajamani, U.; Ross, P. Rapid Communications in Mass Spectrometry 1996, 10, 883. DOI: 10.1002/(SICI)1097-0231(19960610)10:8<883::AID-RCM594>3.0.CO;2-V   DOI
40 Martiny, D.; Busson, L.; Wybo, I.; El Haj, R.A.; Dediste, A.; Vandenberg, O. Journal of clinical microbiology 2012, 50, 1313. DOI: 10.1128/JCM.05971-11   DOI
41 Dieckmann, R.; Graeber, I.; Kaesler, I.; Szewzyk, U.; Von Dohren, H. Applied microbiology and biotechnology 2005, 67, 539. DOI: 10.1007/s00253-004-1812-2   DOI
42 Powthong, P.; Suntornthiticharoen, P. Bulgarian Journal of Agricultural Science 2018, 24, 623.
43 Donohue, M.J.; Best, J.M.; Smallwood, A.W.; Kostich, M.; Rodgers, M.; Shoemaker, J.A. Analytical chemistry 2007, 79, 1939. DOI: 10.1021/ac0611420   DOI
44 Malinicova, L.; Nosal'ova, L.; Timkova, I.; Pristas, P.; Sedlakova-Kadukova, J. Inzynieria Mineralna 2020. . DOI: 10.29227/IM-2020-01-47   DOI
45 Vidali, M. Pure and applied chemistry 2001, 73, 1163. DOI: 10.1351/pac200173071163   DOI
46 Silva, N.M.; de Oliveira, A.M.S.A.; Pegorin, S.; Giusti, C.E.; Ferrari, V.B.; Barbosa, D.; Martins, L.F.; Morais, C.; Setubal, J.C.; Vasconcellos, S.P. PLoS One 2019, 14, e0215396. DOI: 10.1371/journal.pone.0215396   DOI
47 Lovecka, P.; Pacovska, I.; Stursa, P.; Vrchotova, B.; Kochankova, L.; Demnerova, K. New biotechnology 2015, 32, 26. DOI: 10.1016/j.nbt.2014.07.003   DOI