Rapid identification of acetic acid bacteria using MALDI-TOF mass spectrometry fingerprinting

Systematic and Applied Microbiology

Volumn 36, Issue 2, 2013, Pages 75-81

  Andrés Barrao, Cristina ^a   Benagli, Cinzia ^b   Chappuis, Malou ^a   Ortega Pérez, Ruben ^a   Tonolla, Mauro ^a,b   Barja, François ^a  

^a UNIVERSITY OF GENEVA   (Switzerland)

^b Cantonal Institute of Microbiology   (Switzerland)

Author keywords

Acetic acid bacteria; MALDI TOF MS; Vinegar; Whole cell identification

Indexed keywords

BACTERIAL RNA; RNA 16S; VINEGAR;

ACETIC ACID BACTERIUM; ACETOBACTER; ARTICLE; BACTERIAL STRAIN; BACTERIUM; BACTERIUM COLONY; BACTERIUM CULTURE; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; GENE SEQUENCE; GLUCONACETOBACTER; GLUCONOBACTER; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NEIGHBOR JOINING METHOD; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RNA FINGERPRINTING; SEQUENCE ANALYSIS;

ACETIC ACID; ACETOBACTERACEAE; ALCOHOLS; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

ACETOBACTER; BACTERIA (MICROORGANISMS); GLUCONACETOBACTER; GLUCONOBACTER;

EID: 84875379879     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2012.09.002     Document Type: Article

References (38)

1. Alauzet C., Teyssier C., Jumas-Bilak E., Gouby A., Chiron R., Rabaud C., Counil F., Lozniewski A., Marchandin H. Gluconobacter as well as Asaia species, newly emerging opportunistic human pathogens among acetic acid bacteria. J. Clin. Microbiol. 2010, 48:3935-3942.
2. Asai T. Taxonomic studies on acetic acid bacteria and allied oxidative bacteria isolated from fruits: a new classification of the oxidative bacteria. J. Agric. Chem. Soc. Jpn. 1935, 11:674-708. (in Japanese).
3. Benagli C., Rossi V., Dolina M., Tonolla M., Petrini O. Matrix-assisted laser desorption ionization-time of flight mass spectrometry for the identification of clinically relevant bacteria. PLoS ONE 2011, 6(1):e16424.
4. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Sayers E.W. GenBank. Nucl. Acids Res. 2011, 39(Database issue):D32-D37.
5. Bizzini A., Greub G. MALDI-TOF MS, a revolution in clinical microbial identification. Clin. Microbiol. Infect. 2010, 16:1614-1619.
6. Cleenwerck I., De Vos P. Polyphasic taxonomy of acetic acid bacteria: an overview of the currently applied methodology. Int. J. Food Microbiol. 2008, 125(1):2-14.
7. Cleenwerck I., De Vos P., De Vuyst L. Phylogeny and differentiation of species of the genus Gluconacetobacter and related taxa based on multilocus sequence analyses of housekeeping genes and reclassification of Acetobacter xylinus subsp. sucrofermentans as Gluconacetobacter sucrofermentans (Toyosaki et al., 1996) sp. nov., comb. nov. Int. J. Syst. Evol. Microbiol. 2010, 60(10):2277-2283.
8. Crotti E., Rizzi A., Chouaia B., Ricci I., Favia G., Alma A., Sacchi L., Bourtzis K., Mandrioli M., Cherif A., Bandi C., Daffonchio D. Acetic acid bacteria, newly emerging symbionts of insects. Appl. Environ. Microbiol. 2010, 76:6963-6970.
9. De Ley J., Gillis M., Swings J. Acetobacteraceae. Bergey's Manual of Systematic Bacteriology 1984, vol. 1:267-278. Williams & Wilkins, Baltimore, USA.
10. De Vero L., Gala E., Gullo M., Solieri L., Landi S., Giudici P. Application of denaturing gradient gel electrophoresis (DGGE) analysis to evaluate acetic acid bacteria in traditional balsamic vinegar. Food Microbiol. 2006, 23:809-813.
11. De Vuyst L., Camu N., De Winter T., Vandemeulebroecke K., Van de Perre V., Vancanneyt M., De Vos P., Cleenwerck I. Validation of the (GTG)5-rep-PCR fingerprinting technique for rapid classification and identification of acetic acid bacteria, with a focus on isolates from Ghanaian fermented cocoa beans. Int. J. Food Microbiol. 2008, 125:79-90.
12. Drancourt M., Raoult D. Sequence-based identification of new bacteria: a proposition for creation of an orphan bacterium repository. J. Clin. Microbiol. 2005, 43:4311-4315.
13. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl. Acids Res. 2004, 32:1792-1797.
14. Edgar R.C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004, 5:113-131.
15. Fernández-Pérez R., Torres C., Sanz S., Ruiz-Larrea F. Strain typing of acetic acid bacteria responsible for vinegar production by the submerged elaboration method. Food Microbiol. 2010, 27:973-978.
16. Fernández-Pérez R., Torres C., Sanz S., Ruiz-Larrea F. Rapid molecular methods for enumeration and taxonomical identification of acetic acid bacteria responsible for submerged vinegar production. Eur. Food Res. Technol. 2010, 231:813-819.
17. González A., Mas A. Differentiation of acetic acid bacteria based on sequence analysis of 16S-23S rRNA gene internal transcribed spacer sequences. Int. J. Food Microbiol. 2011, 147:217-222.
18. González A., Hierro N., Poblet M., Mas A., Guillamón J.M. Application of molecular methods to demonstrate species and strain evolution of acetic acid bacteria population during wine production. Int. J. Food Microbiol. 2005, 102:295-304.
19. González A., Guillamón J.M., Mas A., Poblet M. Application of molecular methods for routine identification of acetic acid bacteria. Int. J. Food Microbiol. 2006, 108:141-146.
20. Kallow W., Erhanrd M., Shah H.N., Raptakis E., Welker M. MALDI-TOF MS for microbial identification: years of experimental development to an established protocol. Mass Spectrometry from Microbial Proteomics 2010, 255-277. Wiley and Sons, Chichester, UK. H.N. Shah, S.E. Gharbia (Eds.).
21. Kimura M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 1980, 16:111-120.
22. Kumar S., Nei M., Dudley J., Tamura K. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief. Bioinform. 2008, 9:299-306.
23. Ludwig W. Nucleic acid techniques in bacterial systematics and identification. Int. J. Food Microbiol. 2007, 120:225-236.
24. Pedraza R.O. Recent advances in nitrogen-fixing acetic acid bacteria. Int. J. Food Microbiol. 2008, 125:25-35.
25. Raspor P., Goranovic D. Biotechnological applications of acetic acid bacteria. Crit. Rev. Biotechnol. 2008, 28:101-124.
26. Ruiz A., Poblet M., Mas A., Guillamón J.M. Identification of acetic acid bacteria by RFLP of PCR-amplified 16S and 16S-23S rDNA intergenic spacer. Int. J. Syst. Evol. Microbiol. 2000, 50:1981-1987.
27. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4:406-425.
28. Sauer S., Kliem M. Mass spectrometry tools for the classification and identification of bacteria. Nat. Rev. Microbiol. 2010, 8:74-82.
29. Sievers M., Swings J. Family Acetobacteraceae. Bergey's Manual of Systematic Bacteriology 2005, vol. 2:41-81. Springer, New York. second ed.
30. Sievers M., Sellmer S., Teuber M. Acetobacter europaeus sp. nov., a main component of industrial vinegar fermenters in Central Europe. Syst. Appl. Microbiol. 1992, 15:386-392.
31. Sokollek S.J., Hertel C., Hammes W.P. Cultivation and preservation of vinegar bacteria. J. Biotechnol. 1998, 60:195-206.
32. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28:2731-2739.
33. Torija J.M., Mateo E., Guillamón J.M., Mas A. Design and optimisation of TaqMan-MGB probes for the identification and quantification of acetic acid bacteria. Food Microbiol. 2010, 27:257-265.
34. Trček J. Quick identification of acetic acid bacteria based on nucleotide sequences of the 16S-23S rDNA internal transcribed spacer region and of the PQQ-dependent alcohol dehydrogenase gene. Syst. Appl. Microbiol. 2005, 28:735-745.
35. Yamada Y., Kondo K. Gluconoacetobacter, a new subgenus comprising the acetate-oxidizing acetic acid bacteria with ubiquinone-10 in the genus Acetobacter. J. Gen. Appl. Microbiol. 1984, 30:297-303.
36. Yamada Y., Yukphan P. Genera and species in acetic acid bacteria. Int. J. Food Microbiol. 2008, 125:15-24.
37. Yamada Y., Hoshino K., Ishikawa T. The phylogeny of acetic acid bacteria based on the partial sequences of 16S ribosomal RNA: the elevation of the subgenus Gluconoacetobacter to the generic level. Biosci. Biotechnol. Biochem. 1997, 61:1244-1251.
38. Yukphan P., Malimas T., Potacharoen W., Tanasupawat S., Tanticharoen M., Yamada Y. Neoasaia chiangmaiensis gen. nov., sp. nov., a novel osmotolerant acetic acid bacterium in the α-Proteobacteria. J. Gen. Appl. Microbiol. 2005, 51:301-311.