Evolution of bacterial consortia in spontaneously started rye sourdoughs during two months of daily propagation

PLoS ONE

Volumn 9, Issue 4, 2014, Pages

  Bessmeltseva, Marianna ^a,b   Viiard, Ene ^a,b   Simm, Jaak ^b   Paalme, Toomas ^a,b   Sarand, Inga ^a,b  

^a Competence Center of Food and Fermentation Technologies ^*  (Estonia)

^b TALLINN UNIVERSITY OF TECHNOLOGY   (Estonia)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

AMPLICON; ARTICLE; BACTERIAL STRAIN; BACTERIUM DETECTION; CANDIDA GLABRATA; CANDIDA KRUSEI; CONTROLLED STUDY; DNA BARCODING; DOUGH; FUNGAL STRAIN; FUNGUS IDENTIFICATION; GENE SEQUENCE; INOCULATION; KAZACHSTANIA UNISPORA; LACTIC ACID BACTERIUM; LACTOBACILLUS; LACTOBACILLUS BREVIS; LACTOBACILLUS CRUSTORUM; LACTOBACILLUS PARALIMENTARIUS; LACTOBACILLUS PLANTARUM; MICROBIAL COMMUNITY; MICROBIAL CONSORTIUM; MICROBIAL DIVERSITY; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PYROSEQUENCING; REPRODUCIBILITY; RYE; SACCHAROMYCES CEREVISIAE; SOLID STATE FERMENTATION; SPECIES COMPOSITION; TEMPERATURE SENSITIVITY; BACTERIAL COUNT; BACTERIAL PHENOMENA AND FUNCTIONS; CARBOHYDRATE METABOLISM; CLASSIFICATION; FERMENTATION; GENETICS; PH; TEMPERATURE; TIME; YEAST;

BACTERIAL PHYSIOLOGICAL PHENOMENA; CARBOHYDRATE METABOLISM; COLONY COUNT, MICROBIAL; DNA BARCODING, TAXONOMIC; FERMENTATION; HYDROGEN-ION CONCENTRATION; LACTOBACILLUS; MICROBIAL CONSORTIA; RNA, RIBOSOMAL, 16S; SECALE CEREALE; TEMPERATURE; TIME FACTORS; YEASTS;

EID: 84899695744     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0095449     Document Type: Article

References (49)

1. Gobbetti M, Simonetti MS, Corsetti A, Santinelli F, Rossi, P at al. (1995) Volatile compound and organic acid production by mixed wheat sour dough starters: influence of fermentation parameters and dynamics during baking. Food Microbiology 12: 497-507.
2. De Vuyst L, Neysens P (2005) The sourdough microflora: biodiversity and metabolic interactions. Trends Food Sci Technol 16: 43-56. (Pubitemid 40984903)
3. Diowksz A, Ambroziak W (2006) Sourdough. In: Hui YH, Corke H, De Leyn I, Nip WK, Cross NA, editors. Bakery Products: Science and Technology. Oxford: Blackwell Publishing Ltd. 365-380.
4. Rosenquist H, Hansen A (2000) The microbial stability of two bakery sourdoughs made from conventionally and organically grown rye. Food Microbiol 17: 241-250.
5. Hansen AS (2004) Sourdough bread. In: Hui YH, Meunier-Goddik L, Hansen AS, Josephsen J, Nip WK et al., editors. Handbook of Food and Beverage Fermentation Technology. New York: Marcel Dekker, Inc. 840-870.
6. Müller MRA, Wolfrum G, Stolz P, Ehrmann MA, Vogel RF (2001) Monitoring the growth of Lactobacillus species during a rye flour fermentation. Food Microbiol. 18: 217-227. (Pubitemid 32566598)
7. Vogelmann SA, Seitter M, Singer U, Brandt MJ, Hertel C (2009) Adaptability of lactic acid bacteria and yeasts to sourdoughs prepared from cereals, pseudocereals and cassava and use of competitive strains as starters. Int J Food Microbiol 130: 205-212.
8. Weckx S, Van der Meulen R, Maes D, Scheirlinck I, Huys G, et al. (2010) Lactic acid bacterial community dynamics and metabolite production of rye sourdough fermentations share characteristics of wheat and spelt sourdough fermentations. Food Microbiol 27: 1000-1008.
9. Viiard E, Mihhalevski A, Rühka T, Paalme T, Sarand I (2013) Evaluation of the microbial community in industrial rye sourdough upon continuous back-slopping propagation revealed Lactobacillus helveticus as the dominant species. J Appl Microbiol 114: 404-12.
10. Van der Meulen R, Scheirlinck I, Van Schoor A, Huys G, Vancanneyt M, et al. (2007) Population dynamics and metabolite target analysis of lactic acid bacteria during laboratory fermentations of wheat and spelt sourdoughs. Appl Environ Microbiol 73: 4741-4750. (Pubitemid 47237221)
11. Ercolini D, Pontonio E, De Filippis F, Minervini F, La Storia A, et al. (2013) Microbial ecology dynamics during rye and wheat sourdough preparation. Applied and Environmental Microbiology 79(24): 7827-36.
12. Hammes WP, Stolz P, Gänzle M (1996) Metabolism of lactobacilli in traditional sourdoughs. Adv Food Sci 18: 176-184. (Pubitemid 127033635)
13. Hammes WP, Gänzle MG (1998) Sourdough breads and related products. In: Woods BJB, editor. Microbiology of Fermented Foods, vol 1. London: Blackie Academic. 199-216.
14. Gobbetti M (1998) The sourdough microflora: interactions of lactic acid bacteria and yeasts. Trends food Sci Technol 9: 267.
15. Meroth CB, Walter J, Hertel C, Brandt MJ, Hammes WP (2003) Monitoring the bacterial population dynamics in sourdough fermentation processes by using PCR-denaturing gradient gel electrophoresis. Appl Environ Microbiol 69: 474-482.
16. Wick M, Stolz P, Böcker G, Lebault JM (2003) Influence of several process parameters on sourdough fermentation. Acta Biotechnol 23: 51-61. (Pubitemid 36192898)
17. McKenna P, Hoffmann C, Minkah N, Aye PP, Lackner A, et al. (2008) The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis. PLoS Pathog 4(2): 20.
18. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-41.
19. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, et al. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196.
20. Andrighetto C, Psomas E, Tzanetakis N, Suzzi G, Lombardi A (2000) Randomly amplified polymorphic DNA (RAPD) PCR for the identification of yeasts isolated from dairy products. Letters in Applied Microbiology 30(1): 5-9. (Pubitemid 30128894)
21. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA, et al. (2008) Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 74: 2461-2470. (Pubitemid 351555459)
22. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) Ribosomal DNA amplification for phylogenetic study. J Bacteriol 173: 697-703.
23. Siti Hajar MD, Noorhisham TK, Nurina A (2012) Short Technical Communication Yeast identification from domestic ragi for food fermentation by PCR method. International Food Research Journal 19(2): 775-777.
24. Balcazar JL, de Blas I, Ruiz-Zarzuela I, Vendrell D, Girones O, et al. (2007) Sequencing of variable regions of lactic acid bacteria isolated from the intestinal microbiota of healthy salmonids. Comparative Immunology, Microbiology and Infectious Diseases 30: 111-118. (Pubitemid 46158259)
25. Huse SM, Ye Y, Zhou Y, Fodor A. (2012) A core human microbiome as viewed through 16S rRNA sequence clusters. PloS One 7(6): e34242. doi:10.1371/journal. pone.0034242.
26. Delgado S, Rachid CT, Fernandez E, Rychlik T, Alegria A, et al. (2013) Diversity of thermophilic bacteria in raw, pasteurized and selectively-cultured milk, as assessed by culturing, PCR-DGGE and pyrosequencing. Food Microbiol 36: 103-111.
27. Pang H, Kitahara M, Tan Z, Wang Y, Qin G, et al. (2012) Reclassification of Lactobacillus kimchii and Lactobacillus bobalius as later subjective synonyms of Lactobacillus paralimentarius. Int J Syst Evol Microbiol 62: 2383-2387.
28. Moroni AV, Arendt EK, Dal Bello F (2011) Biodiversity of lactic acid bacteria and yeasts in spontaneously-fermented buckwheat and teff sourdoughs. Food Microbiol 28: 497-502.
29. Lonner C (1988) Starter Cultures for Rye Sour Dough, Ph.D. Dissertation. Lund University, Sweden.
30. Minervini F, De Angelis M, Di Cagno R, Gobbetti M (2014) Ecological parameters influencing microbial diversity and stability of traditional sourdough. International Journal of Food Microbiology 171: 136-146.
31. Minervini F, Lattanzi A, De Angelis M, Di Cagno R, Gobbetti M (2012) Influence of Artisan Bakery- or Laboratory-Propagated Sourdoughs on the Diversity of Lactic Acid Bacterium and Yeast Microbiotas. Applied and Environmental Microbiology 78(15): 5328-5340.
32. Vrancken G, Rimaux T, Weckx S, Leroy F, De Vuyst L (2011) Influence of temperature and backslopping time on the microbiota of a type I propagated laboratory wheat sourdough fermentation. Applied and Environmental Microbiology 77(8): 2716-26.
33. Vrancken G, De Vuyst L, Rimaux T, Allemeersch J, Weckx S (2011) Adaptation of Lactobacillus plantarum IMDO 130201, a wheat sourdoughisolate, to growth in wheat sourdough simulation medium at different pH values through differential gene expression. Appl Environ Microbiol 77: 3406-12.
34. Boekhorst J, Siezen RJ, Zwahlen MC, Vilanova D, Pridmore RD, et al. (2009) The complete genomes of Lactobacillus plantarum and Lactobacillus johnsonii reveal extensive differences in chromosome organization and gene content. Microbiology 150: 3601-3611. (Pubitemid 39545309)
35. Plumed-Ferrer C, Koistinen KM, Tolonen TL, Lehesranta SJ, Kärenlampi SO, et al. (2008) Comparative study of sugar fermentation and protein expression patterns of two Lactobacillus plantarum strains grown in three different media. Appl Environ Microbiol 74: 5349-5358.
36. Minervini F, De Angelis M, Di Cagno R, Pinto D, Siragusa S, et al. (2010) Robustness of Lactobacillus plantarum starters during daily propagation of wheat flour sourdough type I. Food Microbiol 27: 897-908.
37. Huys G, Daniel HM, De Vuyst L (2013) Taxonomy and Biodiversity of Sourdough Yeasts and Lactic Acid Bacteria. In: Gobbetti M, Gänzle M, editors. Handbook on Sourdough Technology. New York: Springer Science+ Business Media. 107.
38. Vrancken G, De Vuyst L, Van der Meulen R, Huys G, Vandamme P, et al. (2010) Yeast species composition differs between artisan bakery and spontaneous laboratory sourdoughs. FEMS Yeast Res 10(4): 471-81.
39. Salovaara H, Savolainen J (1984) Yeast types isolated from Finnish sourdough starters. Acta Alimentaria Polonica 10: 242-246.
40. Bhattacharya I, Yan S, Yadav JSS, Tyagi RD, Surampalli RY (2013) Saccharomyces unisporus: Biotechnological Potential and Present Status. Comprehensive Reviews in Food Science and Food Safety 12(4): 353-363.
41. Savard T, Beaulieu C, Boucher I, Champagne CP (2002) Antimicrobial action of hydrolyzed chitosan against spoilage yeasts and lactic acid bacteria of fermented vegetables. Journal of Food Protection 65(5): 828-33. (Pubitemid 34494834)
42. Callon C, Delbès C, Duthoit F, Montel MC (2006) Application of SSCP-PCR fingerprinting to profile the yeast community in raw milk Salers cheeses. Systematic and Applied Microbiology 29(2): 172-80. (Pubitemid 43197815)
43. Londero A, Hamet MF, De Antoni GL, Garrote GL, Abraham AG. (2012) Kefir grains as a starter for whey fermentation at different temperatures: chemical and microbiological characterisation. Journal of Dairy Research 79(3): 262-71.
44. Mu Z, Yang X, Yuan H (2012) Detection and identification of wild yeast in Koumiss. Food Microbiology 31: 301-308.
45. Daniel HM, Moons MC, Huret S, Vrancken G, De Vuyst L (2011) Wickerhamomyces anomalus in the sourdough microbial ecosystem. Antonie Van Leeuwenhoek 99(1): 63-73.
46. Temmerman R, Huys G, Swings J (2004) Identification of lactic acid bacteria: culture-dependent and culture -independent methods. Trends Food Sci Technol 15: 348-359. (Pubitemid 38583550)
47. Cocolin L, Alessandria V, Dolci P, Gorra R, Rantsiou K (2013) Culture independent methods to assess the diversity and dynamics of microbiota during food fermentation. Int J Food Microbiol, http://dx.doi.org/10.1016/j. ijfoodmicro.2013.05.008.
48. Vera A, Rigobello V, Demarigny Y (2009) Comparative study of culture media used for sourdough lactobacilli. Food Microbiology 26(7): 728-33.
49. Ercolini D (2013) High-throughput sequencing and metagenomics: moving forward in the culture-independent analysis of food microbial ecology. Applied and Environmental Microbiology 79(10): 3148-55.