Pyrosequencing vs. culture-dependent approaches to analyze lactic acid bacteria associated to chicha, a traditional maize-based fermented beverage from Northwestern Argentina

International Journal of Food Microbiology

Volumn 198, Issue , 2015, Pages 9-18

  Elizaquível, Patricia ^a   Pérez Cataluña, Alba ^a   Yépez, Alba ^a   Aristimuño, Cecilia ^b   Jiménez, Eugenia ^b   Cocconcelli, Pier Sandro ^d   Vignolo, Graciela ^b   Aznar, Rosa ^a,c  

^a UNIVERSITY OF VALENCIA   (Spain)

^b CENTRO DE REFERENCIA PARA LACTOBACILOS CERELA CONICET   (Argentina)

^c INSTITUTO DE AGROQUÍMICA Y TECNOLOGÍA DE ALIMENTOS CSIC   (Spain)

^d UNIVERSITÀ CATTOLICA DEL SACRO CUORE   (Italy)

Author keywords

Chicha; Diversity; Identification by molecular techniques high throughput sequencing (HTS); Lactic acid bacteria

Indexed keywords

ALCOHOL; GLUCOSE; LACTIC ACID; MALTOSE; RNA 16S; STARCH; SUCROSE;

ALCOHOLIC BEVERAGE; ARGENTINA; ARTICLE; BACTERIAL GENETICS; BACTERIUM CULTURE; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATE; CHICHA; ENTEROCOCCUS DURANS; ENTEROCOCCUS FAECALIS; ENTEROCOCCUS FAECIUM; ENTEROCOCCUS GALLINARUM; ENTEROCOCCUS HIRAE; FERMENTATION; FERMENTED PRODUCT; GENE SEQUENCE; LACTIC ACID BACTERIUM; LACTOBACILLUS PENTOSUS; LACTOBACILLUS PLANTARUM; LEUCONOSTOC; LEUCONOSTOC MESENTEROIDES; MAIZE; MICROBIAL COMMUNITY; NONHUMAN; PEDIOCOCCUS; PEDIOCOCCUS ACIDILACTICI; PYROSEQUENCING; RANDOM AMPLIFIED POLYMORPHIC DNA; SPECIES DIVERSITY; WEISSELLA; WEISSELLA VIRIDESCENS; BACTERIAL COUNT; BEVERAGE; BIODIVERSITY; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; LACTOBACILLALES; METABOLISM; MICROBIOLOGY; PHYSIOLOGY; POLYMERASE CHAIN REACTION; PROCEDURES;

ENTEROCOCCUS; ENTEROCOCCUS FAECIUM; ENTEROCOCCUS HIRAE; LACTOBACILLUS; LACTOBACILLUS PLANTARUM; LACTOBACILLUS ROSSIAE; LACTOCOCCUS; LEUCONOSTOC; LEUCONOSTOC LACTIS; LEUCONOSTOC MESENTEROIDES; OTUS; PEDIOCOCCUS; STREPTOCOCCUS; WEISSELLA; WEISSELLA CONFUSA; WEISSELLA VIRIDESCENS; ZEA MAYS;

ARGENTINA; BACTERIAL TYPING TECHNIQUES; BEVERAGES; BIODIVERSITY; COLONY COUNT, MICROBIAL; FERMENTATION; LACTOBACILLALES; POLYMERASE CHAIN REACTION; RANDOM AMPLIFIED POLYMORPHIC DNA TECHNIQUE; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; ZEA MAYS;

EID: 84920903482     PISSN: 01681605     EISSN: 18793460     Source Type: Journal    
DOI: 10.1016/j.ijfoodmicro.2014.12.027     Document Type: Article

References (49)

1. Abriouel H., Omar N.B., López R.L., Martínez-Cañamero M., Keleke S., Gálvez A. Culture-independent analysis of the microbial composition of the African traditional fermented foods poto poto and dégué by using three different DNA extraction methods. Int. J. Food Microbiol. 2006, 111:228-233.
2. Abriouel H., Omar N.B., Cobo Molinos A., Lucas López R., Grande M.J., Martínez-Viedma P., Ortega E., Martínez Cañamero M., Gálvez A. Comparative analysis of genetic diversity and incidence of virulence factors and antibiotic resistance among enterococcal populations from raw fruit and vegetable foods, water and soil, and clinical samples. Int. J. Food Microbiol. 2008, 123:38-49.
3. Amoa-Awua W.K.A., Owusu M., Feglo P. Utilization of unfermented cassava flour for the production of an indigenous African fermented food, agbelima. World J. Microbiol. Biotechnol. 2005, 21:1201-1207.
4. Arokiyaraj S., Hairul Islam V.I., Bharanidharan R., Raveendar S., Lee J., Kim D.H., Oh Y.K., Kim E.-K., Kim K.H. Antibacterial, anti-inflammatory and probiotic potential of Enterococcus hirae isolated from the rumen of Bos primigenius. World J. Microbiol. Biotechnol. 2014, 30:2111-2118.
5. Aznar R., Chenoll E. Intraspecific diversity of Lactobacillus curvatus, Lactobacillus plantarum, Lactobacillus sakei, and Leuconostoc mesenteroides associated with vacuum-packed meat product spoilage analyzed by randomly amplified polymorphic DNA PCR. J. Food Prot. 2006, 69:2403-2410.
6. Botes A., Todorov S.D., von Mollendorff J.W., Botha A., Dicks L.M. Identification of lactic acid bacteria and yeast from boza. Process Biochem. 2007, 42:267-270.
7. Capozzi V., Ladero V., Beneduce L., Fernández M., Alvarez M.A., Benoit B., Laurent B., Grieco F., Spano G. Isolation and characterization of tyramine-producing Enterococcus faecium strains from red wine. Food Microbiol. 2011, 28:434-439.
8. Chen Y.S., Yanagida F., Hsu J.S. Isolation and characterization of lactic acid bacteria from dochi (fermented black beans), a traditional fermented food in Taiwan. Lett. Appl. Microbiol. 2006, 43:229-235.
9. Chenoll E., Macian M.C., Aznar R. Identification of Carnobacterium, Lactobacillus, Leuconostoc and Pediococcus by rRNA-based techniques. Syst. Appl. Microbiol. 2003, 26:546-556.
10. Chenoll E., Macián M.C., Elizaquivel P., Aznar R. Lactic acid bacteria associated with vacuum-packed cooked meat product spoilage: population analysis by rRNA-based methods. J. Appl. Microbiol. 2007, 102:498-508.
11. Cole J.R., Wang Q., Fish J.A., Chai B., McGarrell D.M., Sun Y., Brown C.T., Porras-Alfaro A., Kuske C.R., Tiedje J.M. Ribosomal Database Project: data and tools for high throughput rRNA analysis Nucl. Acids Res. 2014, 41(Database issue):D633-D642. 10.1093/nar/gkt1244.
12. Cruciata M., Sannino C., Ercolini D., Scatassa M.L., De Filippis F., Mancuso I., La Storia A., Moschetti G., Settannia L. Animal rennets as sources of dairy lactic acid bacteria. Appl. Environ. Microbiol. 2014, 80:2050-2061.
13. De Vuyst L., Neysens P. The sourdough microflora: biodiversity and metabolic interactions. Trends Food Sci. Technol. 2005, 16:43-56.
14. De Vuyst L., Van Kerrebroeck S., Harth H., Huys G., Daniel H.-M., Weckx S. Microbial ecology of sourdough fermentations: diverse or uniform?. Food Microbiol. 2014, 37:11-29.
15. Delibes Mateos R., Barragan Villena A. El Consumo ritual de Chicha en San José de Moro. Arqueología Mochica: Nuevos enfoques. Actas del Primer Congreso Internacional de Jóvenes Investigadores de la Cultura Mochica, Lima, 4-5 de agosto de 2004 2008, 105-117. Institut Français d'études Andines (IFEA); Pontificia Universidad Católica del Perú (PUCP), Lima. L.J. Castillo Butters, H. Bernier, G. Lockard, J. Rucabado Yong (Eds.).
16. Devriese L., Baele M., Butaye P. The genus Enterococcus: taxonomy. Prokaryotes 2006, Vol. 4:163-174. Springer, New York. 3th edition. M. Dworkin, S. Falkow, E. Rosenberg, K.H. Schleifer, E. Stackebrandt (Eds.).
17. Díaz-Ruiz G., Guyot J.P., Ruiz-Teran F., Morlon-Guyot J., Wacher C. Microbial and physiological characterization of weakly amylolytic but fast-growing lactic acid bacteria: a functional role in supporting microbial diversity in Pozol, a Mexican fermented maize beverage. Appl. Environ. Microbiol. 2003, 69:4367-4374.
18. Dutka-Malen S., Evers S., Courvalin P. Detection of glycopeptide resistance genotypes and identification to the species level of clinically relevant Enterococci by PCR. J. Clin. Microbiol. 1995, 33:24-27.
19. Edgar R.C. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011, 27:2194-2200.
20. Elizaquível P., Chenoll E., Aznar R. A TaqMan-based real-time PCR assay for the specific detection and quantification of Leuconostoc mesenteroides in meat products. FEMS Microbiol. Lett. 2008, 278:62-71.
21. Ercolini D. High-throughput sequencing and metagenomics: moving forward in the culture-independent analysis of food microbial ecology. Appl. Environ. Microbiol. 2013, 79:3148-3155.
22. Escalante A., Giles-Gómez M., Hernández G., Córdova-Aguilar M.S., López-Munguía A., Gosset G., Bolívar F. Analysis of bacterial community during the fermentation of pulque, a traditional Mexican alcoholic beverage, using a polyphasic approach. Int. J. Food Microbiol. 2008, 124:126-134.
23. FAO Maize in human nutrition #Gross chemical composition (last accessed 20/10/2014). http://www.fao.org/docrep/t0395e/T0395E03.htm.
24. Goecks J., Nekrutenko A., Taylor J.The, Team Galaxy Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010, 11:R86.
25. Gregersen T. Rapid method for distinction of gram-negative from gram-positive bacteria. Eur. J. Appl. Microbiol. Biotechnol. 1978, 5:123-127.
26. Guarneri T., Rossetti L., Giraffa G. Rapid identification of Lactobacillus brevis using the polymerase chain reaction. Lett. Appl. Microbiol. 2001, 33:377-381.
27. Gulitz A., Stadie J., Ehrmann M.A., Ludwig W., Vogel R.F. Comparative phylobiomic analysis of the bacterial community of water kefir by 16S rRNA gene amplicon sequencing and ARDRA analysis. J. Appl. Microbiol. 2013, 114:1082-1091.
28. Jung J.Y., Lee S.H., Kim J.M., Park M.S., Bae J.W., Hahn Y., Madsen E.L., Jeon C.O. Metagenomic analysis of kimchi, a traditional Korean fermented food. Appl. Environ. Microbiol. 2011, 77:2264-2274.
29. Justé A., Malfliet S., Waud M., Crauwels S., De Cooman L., Aerts G., Marsh T.L., Ruyters S., Willems K., Busschaert P., Lievens B. Bacterial community dynamics during industrial malting, with an emphasis on lactic acid bacteria. Food Microbiol. 2014, 39:39-46.
30. Kleerebezem M., Boekhorst J., van Kranenburg R., Molenaar D., Kuipers O.P., Leer R., Tarchini R., Peters S.A., Sandbrink H.M., Fiers M.W., Stiekema W., Klein Lankhorst R., Bron P.A., Hoffer S.M., Nierop Groot M.N., Kerkhoven R., de Vries M., Ursing B., de Vos W.M., Siezen R.J. Complete genome sequence of Lactobacillus plantarum WCFS1. Proc. Natl. Acad. Sci. U.S.A. PNAS 2003, 100:1990-1995.
31. Koort J., Coenye T., Santos E.M., Molinero C., Jaime I., Rovira J., Vandamme P., Björkroth J. Diversity of Weissella viridescens strains associated with "Morcilla de Burgos". Int. J. Food Microbiol. 2006, 109:164-168.
32. Lacerda Ramos C., Gonzaga de Almaeida E., de Melo Vinícius, Pereira G., Gomes Cardoso P., Souza Dias E., Freitas Schwan R. Determination of dynamic characteristics of microbiota in a fermented beverage produced by Brazilian Amerindians using culture-dependent and culture-independent methods. Int. J. Food Microbiol. 2010, 140:225-231.
33. Layton B.A., Walters S.P., Lam L.H., Boehm A.B. Enterococcus species distribution among human and animal hosts using multiplex PCR. J. Appl. Microbiol. 2010, 109:539-547.
34. Lei V., Jakobsen M. Microbiological characterization and probiotic potential of koko and koko sour water, African spontaneously fermented millet porridge and drink. J. Appl. Microbiol. 2004, 96:384-397.
35. Lorence-Quiñones A., Wacher-Rodarte C., Quintero-Ramírez R. Cereal fermentations in Latin American countries. FAO Agricultural Services Bulletin 1999, 138:99-114. FAO, Rome.
36. Magnusson J., Jonsson H., Schnürer J., Roos S. Weissella soli sp. nov., a lactic acid bacterium isolated from soil. Int. J. Syst. Evol. Microbiol. 2002, 52:831-834.
37. Molenaar D., Bringel F., Schuren F.H., de Vos W.M., Siezen R.J., Kleerebezem M. Exploring Lactobacillus plantarum genome diversity by using microarrays. J. Bacteriol. 2005, 187:6119-6127.
38. Petrosino J.F., Highlander S., Luna R.A., Gibbs R.A., Versalovic J. Metagenomic pyrosequencing and microbial identification. Clin. Chem. 2009, 55:856-866.
39. Pitcher D.G., Saunders N.A., Owen R.J. Rapid extraction of bacterial genomic DNA with guanidinium thiocyanate. Lett. Appl. Microbiol. 1989, 8:151-156.
40. Quillama E., Liendo N. Aislamiento e identificación de bacterias lácticas asociadas a Chicha de Jora. Boletín de Lima N° 100 1995, XVII:171-180.
41. Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., Hollister E.B., Lesniewski R.A., Oakley B.B., Parks D.H., Robinson C.J., Sahl J.W., Stres B., Thallinger G.G., Van Horn D.J., Weber C.F. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 2009, 75:7537-7541.
42. Schoustra S.E., Kasase C., Toarta C., Kassen R., Poulain A.J. Microbial community structure of three traditional Zambian fermented products: Mabisi, Chibwantu and Munkoyo. PLoS ONE 2013, 8:e63948.
43. Sim K., Cox M.J., Wopereis H., Martin R., Knol J., Li M.S., Cookson W.O.C.M., Moffatt M.F., Kroll J.S. Improved detection of Bifidobacteria with optimised 16S rRNA-gene based pyrosequencing. PLoS ONE 2012, 7:e32543.
44. Steinkraus K.H. Fermentations in world food processing. Compre. Rev. in Food Sci. Food Saf. 2002, 1:23-32.
45. Torriani S., Felis G.E., Dellaglio F. Differentiation of Lactobacillus plantarum, L. pentosus, and L. paraplantarum by recA gene sequence analysis and multiplex PCR assay with recA gene-derived primers. Appl. Environ. Microbiol. 2001, 67:3450-3454.
46. Tovar J., Björk I., Asp N.G. Starch content and amylolysis rate in precooked legume flours. J. Agric. Food Chem. 1990, 38:1818-1823.
47. Van der Meulen R., Scheirlinck I., Van Schoor A., Huys G., Vancanneyt M., Vandamme P., De Vuyst L. Population dynamics and metabolite target analysis of lactic acid bacteria during laboratory fermentations of wheat and spelt sourdoughs. Appl. Environ. Microbiol. 2007, 73:4741-4750.
48. Vieira-Dalodé G., Jespersen J., Hounhouigan J., Moller P.L., Nago C.M., Jakobsen M. Lactic acid bacteria and yeasts associated with gowe production from sorghum in Bénin. J. Appl. Microbiol. 2007, 103:342-349.
49. Yousif N.M.K., Huch M., Schuster T., Cho G.-S., Dirar H.A., Holapfel W.H., Franz C.M.A.P. Diversity of lactic acid bacteria from Hussuwa, a traditional African fermented sorghum food. Food Microbiol. 2010, 27:757-768.