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Abstract: chinese traditional fermented foods have a very long history dating back thousands of years and have become an indispensable part of Chinese dietary culture. A plethora of research has been conducted to unravel the composition and dynamics of microbial consortia associated with chinese traditional fermented foods using culture-dependent as well as culture-independent methods, like different high-throughput sequencing (HTS) techniques. These HTS techniques enable us to understand the relationship between a food product and its microbes to a greater extent than ever before. Considering the importance of Chinese traditional fermented products, the objective of this paper is to review the diversity and dynamics of microbiota in chinese traditional fermented foods revealed by HTS approaches.

高通量测序在探究中国传统发酵食品菌群多样性及动态变化中的应用

[1]Abram, F., 2015. Systems-based approaches to unravel multi-species microbial community functioning. Comput. Struct. Biotechnol. J., 13:24-32.

[2]Alain, K., Querellou, J., 2009. Cultivating the uncultured: limits, advances and future challenges. Extremophiles, 13(4):583-594.

[3]Amann, J., 1911. Die direkte zählung der wasserbakterien mittels des ultramikroskops. Centralbl. Bakteriol., 29: 381-384 (in German).

[4]Ayrapetyan, M., Williams, T.C., Oliver, J.D., 2015. Bridging the gap between viable but non-culturable and antibiotic persistent bacteria. Trends Microbiol., 23(1):7-13.

[5]Azat, R., Liu, Y., Li, W., et al., 2016. Probiotic properties of lactic acid bacteria isolated from traditionally fermented Xinjiang cheese. J. Zhejiang Univ.-Sci. B (Biomed. & Biotechnol.), 17(8):597-609.

[6]Bokulich, N.A., Mills, D.A., 2012. Next-generation approaches to the microbial ecology of food fermentations. BMB Rep., 45(7):377-389.

[7]Cao, Z.H., Gu, D.H., Lin, Q.Y., et al., 2011. Effect of pu-erh tea on body fat and lipid profiles in rats with diet-induced obesity. Phytother. Res., 25(2):234-238.

[8]Centers for Disease Control and Prevention, 2001. Botulism outbreak associated with eating fermented food—Alaska, 2001. MMWR Morb. Mortal. Wkly. Rep., 50(32):680-682.

[9]Chao, S.H., Huang, H.Y., Chang, C.H., et al., 2013. Microbial diversity analysis of fermented mung beans (Lu-Doh-Huang) by using pyrosequencing and culture methods. PLoS ONE, 8(5):e63816. http://doi.org/10.1371/journal.pone.0063816

[10]de Vuyst, L., Schrijvers, V., Paramithiotis, S., et al., 2002. The biodiversity of lactic acid bacteria in greek traditional wheat sourdoughs is reflected in both composition and metabolite formation. Appl. Environ. Microbiol., 68(12): 6059-6069.

[11]de Vuyst, L., van Kerrebroeck, S., Harth, H., et al., 2014. Microbial ecology of sourdough fermentations: diverse or uniform? Food Microbiol., 37:11-29.

[12]Du, M., Chen, J., Zhang, X., et al., 2007. Retention of virulence in a viable but nonculturable Edwardsiella tarda isolate. Appl. Environ. Microbiol., 73(4):1349-1354.

[13]Elizaquivel, P., Pérez-Cataluña, A., Yépez, A., et al., 2015. Pyrosequencing vs. culture-dependent approaches to analyze lactic acid bacteria associated to chicha, a traditional maize-based fermented beverage from Northwestern Argentina. Int. J. Food Microbiol., 198:9-18.

[14]Ercolini, D., de Filippis, F., la Storia, A., et al., 2012. “Remake” by high-throughput sequencing of the microbiota involved in the production of water buffalo mozzarella cheese. Appl. Environ. Microbiol., 78(22):8142-8145.

[15]Ercolini, D., Pontonio, E., de Filippis, F., et al., 2013. Microbial ecology dynamics during rye and wheat sourdough preparation. Appl. Environ. Microbiol., 79(24): 7827-7836.

[16]Escobar-Zepeda, A., Sanchez-Flores, A., Baruch, M.Q., 2016. Metagenomic analysis of a Mexican ripened cheese reveals a unique complex microbiota. Food Microbiol., 57:116-127.

[17]Fakruddin, M., Mannan, K.S.B., Andrews, S., 2013. Viable but nonculturable bacteria: food safety and public health perspective. ISRN Microbiol., 2013(8113):703813.

[18]Fang, R.S., Dong, Y.C., Chen, F., et al., 2015. Bacterial diversity analysis during the fermentation processing of traditional Chinese yellow rice wine revealed by 16S rDNA 454 pyrosequencing. J. Food Sci., 80(10):M2265-M2271.

[19]Gao, J., Gu, F., He, J., et al., 2013. Metagenome analysis of bacterial diversity in Tibetan kefir grains. Eur. Food Res. Technol., 236(3):549-556.

[20]Gobbetti, M., Corsetti, A., 1997. Lactobacillus sanfrancisco a key sourdough lactic acid bacterium: a review. Food Microbiol., 14(2):175-187.

[21]Guan, Z.B., Zhang, Z.H., Cao, Y., et al., 2012. Analysis and comparison of bacterial communities in two types of ‘wheat Qu’, the starter culture of Shaoxing rice wine, using nested PCR-DGGE. J. Inst. Brew., 118(1):127-132.

[22]Hammes, W.P., Gänzle, M.G., 1997. Sourdough breads and related products. In: Wood, B.J.B. (Ed.), Microbiology of Fermented Foods. Springer US, p.199-216.

[23]Hayashi, K., 1991. PCR-SSCP: a simple and sensitive method for detection of mutations in the genomic DNA. PCR Methods Appl., (1):34-38.

[24]Hou, Y., Shao, W., Xiao, R., et al., 2009. Pu-erh tea aqueous extracts lower atherosclerotic risk factors in a rat hyperlipidemia model. Exp. Gerontol., 44(6-7):434-439.

[25]Hu, H., Xu, Y., Lu, H.P., et al., 2015. Evaluation of yeasts from Tibetan fermented products as agents for biocontrol of blue mold of Nashi pear fruits. J. Zhejiang Univ.-Sci. B (Biomed. & Biotechnol.), 16(4):275-285.

[26]Hugenholtz, P., 2002. Exploring prokaryotic diversity in the genomic era. Genome Biol., 3:reviews0003.1.

[27]Jiang, S., Lu, J., Li, H., 2012. Comparative metatranscriptomic analysis of microbial communities at two different stages during the pile-fermentation of Puer tea. J. Beijing Univ. Chem. Technol. (Nat. Sci. Ed.), 39(6):84-89 (in Chinese).

[28]Jung, J.Y., Lee, S.H., Kim, J.M., et al., 2011. Metagenomic analysis of kimchi, a traditional Korean fermented food. Appl. Environ. Microbiol., 77(7):2264-2274.

[29]Jung, J.Y., Lee, S.H., Jin, H.M., et al., 2013. Metatranscriptomic analysis of lactic acid bacterial gene expression during kimchi fermentation. Int. J. Food Microbiol., 163(2-3):171-179.

[30]Kaeberlein, T., Lewis, K., Epstein, S.S., 2002. Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science, 296(5570): 1127-1129.

[31]Kergourlay, G., Taminiau, B., Daube, G., et al., 2015. Metagenomic insights into the dynamics of microbial communities in food. Int. J. Food Microbiol., 213(20): 31-39.

[32]Kline, L., Sugihara, T., 1971. Microorganisms of the San Francisco sour dough bread process II. Isolation and characterization of undescribed bacterial species responsible for the souring activity. Appl. Environ. Microbiol., 21(3): 459-465.

[33]Ktenioudaki, A., Alvarez-Jubete, L., Smyth, T.J., et al., 2015. Application of bioprocessing techniques (sourdough fermentation and technological aids) for brewer’s spent grain breads. Food Res. Int., 73:107-116.

[34]Lewis, K., Epstein, S., D'Onofrio, A., et al., 2010. Uncultured microorganisms as a source of secondary metabolites. J. Antibiotics, 63(8):468-476.

[35]Li, P., Liang, H., Lin, W.T., et al., 2015. Microbiota dynamics associated with environmental conditions and potential roles of cellulolytic communities in traditional Chinese cereal starter solid-state fermentation. Appl. Environ. Microbiol., 81(15):5144-5156.

[36]Li, X.R., Ma, E.B., Yan, L.Z., et al., 2011. Bacterial and fungal diversity in the traditional Chinese liquor fermentation process. Int. J. Food Microbiol., 146(1):31-37.

[37]Li, X.R., Ma, E.B., Yan, L.Z., et al., 2013. Bacterial and fungal diversity in the starter production process of Fen liquor, a traditional Chinese liquor. J. Microbiol., 51(4):430-438.

[38]Li, Z., Li, H., Deng, C., et al., 2014. Effect of Lactobacillus plantarum DM616 on dough fermentation and Chinese steamed bread quality. J. Food Process Pres., 39(1):30-37.

[39]Ling, Z., Kong, J., Jia, P., et al., 2010. Analysis of oral microbiota in children with dental caries by PCR-DGGE and barcoded pyrosequencing. Microb. Ecol., 60(3): 677-690.

[40]Liu, S.N., Han, Y., Zhou, Z.J., 2011. Lactic acid bacteria in traditional fermented Chinese foods. Food Res. Int., 44(3): 643-651.

[41]Liu, S.P., Mao, J., Liu, Y.Y., et al., 2015. Bacterial succession and the dynamics of volatile compounds during the fermentation of Chinese rice wine from Shaoxing region. World J. Microbiol. Biotechnol., 31(12):1907-1921.

[42]Liu, T., Li, Y., Chen, J., et al., 2016. Prevalence and diversity of lactic acid bacteria in Chinese traditional sourdough revealed by culture dependent and pyrosequencing approaches. LWT-Food Sci. Technol., 68:91-97.

[43]Liu, W., Zheng, Y., Kwok, L.Y., et al., 2015. High-throughput sequencing for the detection of the bacterial and fungal diversity in Mongolian naturally fermented cow’s milk in Russia. BMC Microbiol., 15:45.

[44]Lyu, C., Chen, C., Ge, F., et al., 2013. A preliminary metagenomic study of puer tea during pile fermentation. J. Sci. Food Agric., 93(13):3165-3174.

[45]Mardis, E.R., 2008. Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet., 9:387-402.

[46]Marsh, A.J., O'Sullivan, O., Hill, C., et al., 2013. Sequencing-based analysis of the bacterial and fungal composition of kefir grains and milks from multiple sources. PLoS ONE, 8(7):e69371.

[47]Marsh, T.L., 1999. Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products. Curr. Opin. Microbiol., 2(3): 323-327.

[48]Mayo, B., Rachid, C.T., Alegría, Á., et al., 2014. Impact of next generation sequencing techniques in food microbiology. Curr. Genomics, 15(4):293-309.

[49]Muyzer, G., 1999. DGGE/TGGE a method for identifying genes from natural ecosystems. Curr. Opin. Microbiol., 2(3):317-322.

[50]Nalbantoglu, U., Cakar, A., Dogan, H., et al., 2014. Metagenomic analysis of the microbial community in kefir grains. Food Microbiol., 41:42-51.

[51]Nie, Z., Zheng, Y., Wang, M., et al., 2013. Exploring microbial succession and diversity during solid-state fermentation of Tianjin duliu mature vinegar. Bioresour. Technol., 148:325-333.

[52]Oliver, J.D., 2005. The viable but nonculturable state in bacteria. J. Microbiol., 43(1):93-100.

[53]Park, E.J., Kim, K.H., Abell, G.C., et al., 2011. Metagenomic analysis of the viral communities in fermented foods. Appl. Environ. Microb., 77(4):1284-1291.

[54]Peng, Q., Yang, Y., Guo, Y., et al., 2015. Analysis of bacterial diversity during acetic acid fermentation of Tianjin duliu aged vinegar by 454 pyrosequencing. Curr. Microbiol., 71(2):195-203.

[55]Piao, H., Hawley, E., Kopf, S., et al., 2015. Insights into the bacterial community and its temporal succession during the fermentation of wine grapes. Front. Microbiol., 6:809.

[56]Prakash, O., Shouche, Y., Jangid, K., et al., 2013. Microbial cultivation and the role of microbial resource centers in the omics era. Appl. Microbiol. Biotechnol., 97(1):51-62.

[57]Quigley, L., O'Sullivan, O., Beresford, T.P., et al., 2012. High-throughput sequencing for detection of subpopulations of bacteria not previously associated with artisanal cheeses. Appl. Environ. Microbiol., 78(16):5717-5723.

[58]Riesenfeld, C.S., Schloss, P.D., Handelsman, J., 2004. Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet., 38:525-552.

[59]Shaffer, N., Wainwright, R.B., Middaugh, J.P., et al., 1990. Botulism among alaska natives. The role of changing food preparation and consumption practices. West J. Med., 153(4):390-393.

[60]Shi, G., 1999. Talk about Chinese vinegar. China Brew., 6:39-40 (in Chinese).

[61]Simonen, M., Palva, I., 1993. Protein secretion in Bacillus species. Microbiol. Mol. Biol. Rev., 57(1):109-137.

[62]Smit, G., Smit, B.A., Engels, W.J., 2005. Flavour formation by lactic acid bacteria and biochemical flavour profiling of cheese products. FEMS Microbiol. Rev., 29(3):591-610.

[63]Stewart, E.J., 2012. Growing unculturable bacteria. J. Bacteriol., 194(16):4151-4160.

[64]Sun, Z., Liu, W., Bao, Q., et al., 2014. Investigation of bacterial and fungal diversity in tarag using high-throughput sequencing. J. Dairy Sci., 97(10):6085-6096.

[65]Tesfaye, W., Morales, M.L., García-Parrilla, M., et al., 2002. Wine vinegar: technology, authenticity and quality evaluation. Trends Food Sci. Technol., 13(1):12-21.

[66]Tian, J., Zhu, Z., Wu, B., et al., 2013. Bacterial and fungal communities in Pu’er tea samples of different ages. J. Food Sci., 78(8):M1249-M1256.

[67]Venter, J.C., Remington, K., Heidelberg, J.F., et al., 2004. Environmental genome shotgun sequencing of the Sargasso sea. Science, 304(5667):66-74.

[68]Wang, C.D., Chen, Q., Wang, Q., et al., 2014. Long-term batch brewing accumulates adaptive microbes, which comprehensively produce more flavorful Chinese liquors. Food Res. Int., 62:894-901.

[69]Wang, P., Mao, J., Meng, X., et al., 2014. Changes in flavour characteristics and bacterial diversity during the traditional fermentation of Chinese rice wines from Shaoxing region. Food Control, 44:58-63.

[70]Wang, Z.M., Lu, Z.M., Yu, Y.J., et al., 2015. Batch-to-batch uniformity of bacterial community succession and flavor formation in the fermentation of Zhenjiang aromatic vinegar. Food Microbiol., 50:64-69.

[71]Weckx, S., van der Meulen, R., Allemeersch, J., et al., 2010. Community dynamics of bacteria in sourdough fermentations as revealed by their metatranscriptome. Appl. Environ. Microbiol., 76(16):5402-5408.

[72]Weckx, S., Allemeersch, J., van der Meulen, R., et al., 2011. Metatranscriptome analysis for insight into whole-ecosystem gene expression during spontaneous wheat and spelt sourdough fermentations. Appl. Environ. Microbiol., 77(2):618-626.

[73]Wei, C.L., Chao, S.H., Tsai, W.B., et al., 2013. Analysis of bacterial diversity during the fermentation of inyu, a high-temperature fermented soy sauce, using nested PCR-denaturing gradient gel electrophoresis and the plate count method. Food Microbiol., 33(2):252-261.

[74]Winterberg, H., 1898. Zur methodik der bakterienzählung. Zeitschr. f. Hygiene, 29(1):75-93 (in German).

[75]Xie, G., Wang, L., Gao, Q., et al., 2013. Microbial community structure in fermentation process of Shaoxing rice wine by illumina-based metagenomic sequencing. J. Sci. Food Agric., 93(12):3121-3125.

[76]Xu, H., Liu, W., Gesudu, Q., et al., 2015. Assessment of the bacterial and fungal diversity in home-made yoghurts of Xinjiang, China by pyrosequencing. J. Sci. Food Agric., 95(10):2007-2015.

[77]Xu, W., Huang, Z., Zhang, X., et al., 2011. Monitoring the microbial community during solid-state acetic acid fermentation of Zhenjiang aromatic vinegar. Food Microbiol., 28(6):1175-1181.

[78]Yang, X.P., Luo, J.F., Xin, L., et al., 2013. Microbial community structure and change during solid fermentation of Pu-erh tea. Food Sci., 34(19):142-147 (in Chinese).

[79]Zhang, G., He, G., 2013. Predominant bacteria diversity in Chinese traditional sourdough. J. Food Sci., 78(8): M1218-M1223.

[80]Zhang, G., Sadiq, F.A., Zhu, L., et al., 2015. Investigation of microbial communities of Chinese sourdoughs using culture-dependent and DGGE approaches. J. Food Sci., 80(11):M2535-M2542.

[81]Zhang, G.H., Wu, T., Sadiq, F.A., et al., 2016. A study revealing the key aroma compounds of steamed bread made by Chinese traditional sourdough. J. Zhejiang Univ.-Sci. B (Biomed. & Biotechnol.), 17(10):787-797.

[82]Zhang, J.C., Liu, W.J., Sun, Z.H., et al., 2011. Diversity of lactic acid bacteria and yeasts in traditional sourdoughs collected from western region in Inner Mongolia of China. Food Control, 22(5):767-774.

[83]Zhang, X., Zhao, J., Du, X., 2014. Barcoded pyrosequencing analysis of the bacterial community of Daqu for light-flavour Chinese liquor. Lett. Appl. Microbiol., 58(6):549-555.

[84]Zhang, Z., Guan, Z., Liang, X., et al., 2012. Establishment of PCR-DGGE for analysing the bacterial community of Shaoxing rice wine wheat Qu. Sci. Technol. Food Ind., 33(14):206-209, 213 (in Chinese).

[85]Zhao, M., Zhang, D.L., Su, X.Q., et al., 2015. An integrated metagenomics/metaproteomics investigation of the microbial communities and enzymes in solid-state fermentation of Pu-erh tea. Sci. Rep., 5:10117.

[86]Zheng, Q., Lin, B., Wang, Y., et al., 2015. Proteomic and high-throughput analysis of protein expression and microbial diversity of microbes from 30- and 300-year pit muds of Chinese Luzhou-flavor liquor. Food Res. Int., 75:305-314.