Advances in the uncultured microorganisms in the fermentation system of traditional Chinese fermented food

  • WANG Jiaxuan ,
  • HAO Shuyue ,
  • REN Qing
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  • (School of Light Industry, Beijing Technology and Business University, Beijing 100048, China)

Received date: 2022-07-11

  Revised date: 2022-08-25

  Online published: 2023-06-30

Abstract

Traditional Chinese fermented food has a long history and is loved by people because of its rich nutrition and unique flavor. Microorganisms play an important role in the fermentation of traditional fermented food and have a significant impact on their flavor and quality. However, most of the microorganisms in the traditional Chinese fermented food are still uncultured or difficult to culture. An overview of uncultured microorganisms in nature and in the fermentation system traditional of Chinese fermented food is given, and a summary of the methods used to study uncultured microorganisms is presented, the development and utilization of uncultured microorganisms is also envisaged. The aim is to have a more comprehensive understanding of the microbial diversity and the uncultured microorganisms in traditional Chinese fermented food system, in order to achieve better exploitation and utilization of uncultured microorganisms and promote the development of traditional Chinese fermented food.

Cite this article

WANG Jiaxuan , HAO Shuyue , REN Qing . Advances in the uncultured microorganisms in the fermentation system of traditional Chinese fermented food[J]. Food and Fermentation Industries, 2023 , 49(11) : 306 -314 . DOI: 10.13995/j.cnki.11-1802/ts.032850

References

[1] 夏傲喃, 李建华, 林祥娜, 等.发酵食品微生物多样性分析方法研究进展[J].食品研究与开发, 2021, 42(4):220-224.
XIA A N, LI J H, LIN X N, et al.Research progress on analysis methods of microbial diversity in fermented foods[J].Food Research and Development, 2021, 42(4):220-224.
[2] KÅRLUND A, GÓMEZ-GALLEGO C, KORHONEN J, et al.Harnessing microbes for sustainable development:Food fermentation as a tool for improving the nutritional quality of alternative protein sources[J].Nutrients, 2020, 12(4):1020.
[3] 任聪, 杜海, 徐岩.中国传统发酵食品微生物组研究进展[J].微生物学报, 2017, 57(6):885-898.
REN C, DU H, XU Y.Advances in microbiome study of traditional Chinese fermented foods[J].Acta Microbiologica Sinica, 2017, 57(6):885-898.
[4] 陈镜如, 边鑫, 杨杨, 等.中国传统发酵食品微生物多样性研究进展[J].中国调味品, 2022, 47(2):205-210.
CHEN J R, BIAN X, YANG Y, et al.Research progress on microbial diversity of traditional fermented food in China[J].China Condiment, 2022, 47(2):205-210.
[5] 张春月, 金佳杨, 邱勇隽, 等.传统与未来的碰撞:食品发酵工程技术与应用进展[J].生物技术进展, 2021, 11(4):418-429.
ZHANG C Y, JIN J Y, QIU Y J, et al.Collision between tradition and future:Technology and application progress in food fermentation engineering[J].Current Biotechnology, 2021, 11(4):418-429.
[6] 朱红惠, 黄力, 李文均, 等.未/难培养微生物:风正扬帆再起航,共辉煌[J].微生物学报, 2021, 61(4):777-780.
ZHU H H, HUANG L, LI W J, et al.Uncultivated microorganisms:It is time to refocus and reflourish to the special issue “Uncultivated Microorganisms”[J].Acta Microbiologica Sinica, 2021, 61(4):777-780.
[7] LU X W, WU Q, ZHANG Y, et al.Genomic and transcriptomic analyses of the Chinese Maotai-flavored liquor yeast MT1 revealed its unique multi-carbon co-utilization[J].BMC Genomics, 2015, 16:1064.
[8] HU X L, DU H, XU Y.Identification and quantification of the caproic acid-producing bacterium Clostridium kluyveri in the fermentation of pit mud used for Chinese strong-aroma type liquor production[J].International Journal of Food Microbiology, 2015, 214:116-122.
[9] STALEY J T, KONOPKA A.Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats[J].Annual Review of Microbiology, 1985, 39:321-346.
[10] HE G Q, LIU T J, SADIQ F A, et al.Insights into the microbial diversity and community dynamics of Chinese traditional fermented foods from using high-throughput sequencing approaches[J].Journal of Zhejiang University-SCIENCE B, 2017, 18(4):289-302.
[11] 江汶钰, 张明星, 李洁, 等.豉香型白酒酒丸、酒饼及酒醪中微生物群落多样性研究[J].中国酿造, 2021, 40(7):33-37.
JIANG W Y, ZHANG M X, LI J, et al.Microbial community diversity in Jiuwan, Jiubing and Jiulao of Chi-flavor Baijiu[J].China Brewing, 2021, 40(7):33-37.
[12] MAO P, HU Y L, LIAO T T, et al.Microbial diversity during fermentation of sweet paste, a Chinese traditional seasoning, using PCR-denaturing gradient gel electrophoresis[J].Journal of Microbiology and Biotechnology, 2017, 27(4):678-684.
[13] LEWIS W H, TAHON G, GEESINK P, et al.Innovations to culturing the uncultured microbial majority[J].Nature Reviews Microbiology, 2021, 19(4):225-240.
[14] 张晓华, 钟浩辉, 陈吉祥.细菌活的非可培养状态研究进展[J].中国海洋大学学报(自然科学版), 2020, 50(9):153-160.
ZHANG X H, ZHONG H H, CHEN J X.Research progress on viable but nonculturable state bacteria[J].Periodical of Ocean University of China, 2020, 50(9):153-160.
[15] ARORA D, GUPTA P, JAGLAN S, et al.Expanding the chemical diversity through microorganisms co-culture:Current status and outlook[J].Biotechnology Advances, 2020, 40:107521.
[16] BARTELME R P, CUSTER J M, DUPONT C L, et al.Influence of substrate concentration on the culturability of heterotrophic soil microbes isolated by high-throughput dilution-to-extinction cultivation[J].mSphere, 2020, 5(1):e00024-e00020.
[17] 熊盈盈, 莫祯妮, 邱树毅, 等.未培养环境微生物培养方法的研究进展[J].微生物学通报, 2021, 48(5):1 765-1 779.
XIONG Y Y, MO Z N, QIU S Y, et al.Research progress on culture methods of uncultured environmental microorganisms[J].Microbiology China, 2021, 48(5):1 765-1 779.
[18] 刘飞翔, 董其惠, 吴蓉, 等.不同国家和地区传统发酵食品及其发酵微生物研究进展[J].食品科学, 2020, 41(21):338-350.
LIU F X, DONG Q H, WU R, et al.Recent advances in traditional fermented foods and starter cultures for their production in different countries and regions[J].Food Science, 2020, 41(21):338-350.
[19] 陈坚, 汪超, 朱琪, 等.中国传统发酵食品研究现状及前沿应用技术展望[J].食品科学技术学报, 2021, 39(2):1-7.
CHEN J, WANG C, ZHU Q, et al.Research status and application prospect of frontier technology of traditional fermented food in China[J].Journal of Food Science and Technology, 2021, 39(2):1-7.
[20] SUN Z B, GUO L Y, YAN Y, et al.Sporosarcina beigongshangi sp.nov, isolated from pit mud of Baijiu[J].Archives of Microbiology, 2022, 204(1):10.
[21] WEI Z X, MA S C, CHEN R, et al.Aminipila luticellarii sp.nov., an anaerobic bacterium isolated from the pit mud of strong aromatic Chinese liquor, and emended description of the genus Aminipila[J].International Journal of Systematic and Evolutionary Microbiology, 2021, 71(10).DOI:10.1099/ijsem.0.004710.
[22] ZHANG X F, WANG H H, SUN X Y, et al.Lysobacter zhanggongensis sp.nov.isolated from a pit mud[J].Current Microbiology, 2017, 74(12):1 389-1 393.
[23] MA K D, CHEN X R, GUO X, et al.Bacillus vini sp.nov.isolated from alcohol fermentation pit mud[J].Archives of Microbiology, 2016, 198(6):559-564.
[24] SUN Z B, DAI F, YAN Y, et al.Pseudoxanthomonas beigongshangi sp.nov, a novel bacteria with predicted nitrite and nitrate reduce ability isolated from pit mud of Baijiu[J].Antonie Van Leeuwenhoek, 2021, 114(8):1 307-1 314.
[25] LU L F, YANG Y, CHAI L J, et al.Blautia liquoris sp.nov., isolated from the mud in a fermentation cellar used for the production of Chinese strong-flavour liquor[J].International Journal of Systematic and Evolutionary Microbiology, 2021, 71(10).DOI:10.1099/ijsem.0.005041.
[26] LIU C L, HUANG D, LIU L Y, et al.Clostridium swellfunianum sp.nov., a novel anaerobic bacterium isolated from the pit mud of Chinese Luzhou-flavor liquor production[J].Antonie Van Leeuwenhoek, 2014, 106(4):817-825.
[27] XU P X, CHAI L J, QIU T, et al.Clostridium fermenticellae sp.nov., isolated from the mud in a fermentation cellar for the production of the Chinese liquor, Baijiu[J].International Journal of Systematic and Evolutionary Microbiology, 2019, 69(3):859-865.
[28] CHAI L J, FANG G Y, XU P X, et al.Novisyntrophococcus fermenticellae Gen.nov., sp.nov., isolated from an anaerobic fermentation cellar of Chinese strong-flavour Baijiu[J].International Journal of Systematic and Evolutionary Microbiology, 2021, 71(9).DOI:10.1099/ijsem.0.004991.
[29] GU Y, ZHU X J, LIN F, et al.Caproicibacterium amylolyticum Gen.nov., sp.nov., a novel member of the family Oscillospiraceae isolated from pit clay used for making Chinese strong aroma-type liquor[J].International Journal of Systematic and Evolutionary Microbiology, 2021, 71(4).DOI:10.1099/ijsem.0.004789.
[30] WANG H L, GU Y, ZHAO D, et al.Caproicibacterium lactatifermentans sp.nov., isolated from pit clay used for the production of Chinese strong aroma-type liquor[J].International Journal of Systematic and Evolutionary Microbiology, 2022, 72(1).DOI:10.1099/ijsem.0.005206.
[31] 张应刚, 许涛, 郑蕾, 等.窖泥群落结构及功能微生物研究进展[J].微生物学通报, 2021, 48(11):4 327-4 343.
ZHANG Y G, XU T, ZHENG L, et al.Research progress on community structure and functional microorganisms of pit mud[J].Microbiology China, 2021, 48(11):4 327-4 343.
[32] 孙乐平. 扩增子测序与培养组学联用分析白酒酒糟和窖泥中微生物的多样性[D].北京:北京工商大学, 2020.
SUN L P.Culturing the Baijiu microorganism from fermentation vinasse and pit mud with culturomics and amplicon-based metagenomic approaches[D].Beijing:Beijing Technology and Business University, 2020.
[33] 邓杰, 卫春会, 边名鸿, 等.浓香型白酒不同窖龄窖池窖泥中古菌群落结构分析[J].食品科学, 2017, 38(8):37-42.
DENG J, WEI C H, BIAN M H, et al.Archaeal community analysis of pit mud from cellars of different ages for Luzhou-flavor liquor[J].Food Science, 2017, 38(8):37-42.
[34] CAI W C, XUE Y A, TANG F X, et al.The depth-depended fungal diversity and non-depth-depended aroma profiles of pit mud for strong-flavor Baijiu[J].Frontiers in Microbiology, 2022, 12:789845.
[35] ZHANG H M, MENG Y J, WANG Y L, et al.Prokaryotic communities in multidimensional bottom-pit-mud from old and young pits used for the production of Chinese strong-flavor Baijiu[J].Food Chemistry, 2020, 312:126084.
[36] YAN Y, XING X, SUN Z B, et al.Brevibacterium renqingii sp.nov, isolated from the Daqu of Baijiu[J].Archives of Microbiology, 2021, 203(5):2 291-2 296.
[37] LI D N, HUANG W, QIU S Y.Thermoflavimicrobium daqui sp.nov., a thermophilic microbe isolated from Moutai-flavour Daqu[J].International Journal of Systematic and Evolutionary Microbiology, 2019, 69(9):2 709-2 716.
[38] GAO Z Q, SU C L, YANG X Y, et al.Franconibacter daqui sp.nov., a facultatively alkaliphilic species isolated from a Daqu sample[J].International Journal of Systematic and Evolutionary Microbiology, 2017, 67(12):4 962-4 966.
[39] YAO S, ZHAI L, XIN C H, et al.Scopulibacillus daqui sp.nov., a thermophilic bacterium isolated from high temperature Daqu[J].International Journal of Systematic and Evolutionary Microbiology, 2016, 66(11):4 723-4 728.
[40] GAN S H, YANG F, SAHU S K, et al.Deciphering the composition and functional profile of the microbial communities in Chinese Moutai liquor starters[J].Frontiers in Microbiology, 2019, 10:1540.
[41] YANG Y, WANG S T, LU Z M, et al.Metagenomics unveils microbial roles involved in metabolic network of flavor development in medium-temperature Daqu starter[J].Food Research International, 2021, 140:110037.
[42] CAI W C, WANG Y R, NI H, et al.Diversity of microbiota, microbial functions, and flavor in different types of low-temperature Daqu[J].Food Research International (Ottawa, Ont.), 2021, 150(Pt A):110734.
[43] 熊盈盈. 第三代测序技术和培养法联合使用对酱香大曲细菌多样性及其功能的研究[D].贵阳:贵州大学, 2021.
XIONG Y Y.Study on bacterial diversity and function of Maotai-flavor Daqu by the combination of the third generation sequencing technology and culture method[D].Guiyang:Guizhou University, 2021.
[44] 王柏文, 吴群, 徐岩, 等.中国白酒酒曲微生物组研究进展及趋势[J].微生物学通报, 2021, 48(5):1 737-1 746.
WANG B W, WU Q, XU Y, et al.Recent advances and perspectives in study of microbiome in Chinese Jiuqu starter[J].Microbiology China, 2021, 48(5):1 737-1 746.
[45] NIU L L, XIONG M J, TANG T Y, et al.Aeromicrobium camelliae sp.nov., isolated from Pu’er tea[J].International Journal of Systematic and Evolutionary Microbiology, 2015, 65(12):4 369-4 373.
[46] NIU L L, XIONG M J, ZHU D C, et al.Pullulanibacillus camelliae sp.nov., isolated from Pu’er tea[J].International Journal of Systematic and Evolutionary Microbiology, 2016, 66(11):4 760-4 765.
[47] NIU L L, TANG T Y, MA Z L, et al.Paenibacillus yunnanensis sp.nov., isolated from Pu’er tea[J].International Journal of Systematic and Evolutionary Microbiology, 2015, 65(11):3 806-3 811.
[48] WANG D J, XIANG Y Q, JIANG C Y, et al.Pueribacillus theae Gen.nov., sp.nov., isolated from Pu’er tea[J].International Journal of Systematic and Evolutionary Microbiology, 2018, 68(9):2 878-2 882.
[49] NIU L L, XIONG M J, ZHANG J, et al.Bacillus camelliae sp.nov., isolated from Pu’er tea[J].International Journal of Systematic and Evolutionary Microbiology, 2018, 68(2):564-569.
[50] LI Q, LAI X, TENG C Q.Characterization of key aroma compounds and core functional microorganisms in different aroma types of Liupao tea[J].Food Research International, 2022, 152:110925.
[51] LI M Y, XIAO Y, ZHONG K, et al.Study on taste characteristics and microbial communities in Pingwu Fuzhuan brick tea and the correlation between microbiota composition and chemical metabolites[J].Journal of Food Science and Technology, 2022, 59(1):34-45.
[52] 王桥美, 彭文书, 杨瑞娟, 等.普洱茶发酵过程中可培养微生物的群落结构分析[J].食品与发酵工业, 2020, 46(20):88-93.
WANG Q M, PENG W S, YANG R J, et al.Community structure of culturable microbes during the fermentation of Pu-erh tea[J].Food and Fermentation Industries, 2020, 46(20):88-93.
[53] 黄紫衡, 陈欢, 黄丽, 等.六堡茶渥堆过程中可培养微生物的分离与鉴定[J/OL].食品科学, 2021:1-16.(2021-11-19).https://kns.cnki.net/kcms/detail/11.2206.TS.20211118.1117.018.html.
HUANG Z H, CHEN H, HUANG L, et al.Isolation and identification of culturable microbes during the fermentation of Liupao tea[J/OL].Food Science, 2021:1-16.(2021-11-19).https://kns.cnki.net/kcms/detail/11.2206.TS.20211118.1117.018.html.
[54] LIU X Y, QIAN M, SHEN Y X, et al.An high-throughput sequencing approach to the preliminary analysis of bacterial communities associated with changes in amino acid nitrogen, organic acid and reducing sugar contents during soy sauce fermentation[J].Food Chemistry, 2021, 349:129131.
[55] 赵才贤. 酱香型白酒大曲和酒醅的微物群落结构特征及其变化规律研究[D].贵阳:贵州大学, 2021.
ZHAO C X.Study on the structure characteristics and variation for microbial community in Daqu and fermented grains of Jiang-flavour Chinese spirits production[D].Guiyang:Guizhou University, 2021.
[56] TANG H, MA H M, HOU Q C, et al.Profiling of koumiss microbiota and organic acids and their effects on koumiss taste[J].BMC Microbiology, 2020, 20(1):85.
[57] LIU Z G, LI J Y, ZHOU X W, et al.The lactic acid bacteria and yeast community of home-made sauerkraut from three provinces in Southwest China[J].Archives of Microbiology, 2021, 203(6):3 171-3 182.
[58] ZHI Y, WU Q, XU Y.Genome and transcriptome analysis of surfactin biosynthesis in Bacillus amyloliquefaciens MT45[J].Scientific Reports, 2017, 7(1):1-13.
[59] 魏军林, 聂尧, 杜海, 等.营养相互作用对传统发酵食品微生物群落构建的推动作用研究进展[J].微生物学通报, 2021, 48(11):4 412-4 424.
WEI J L, NIE Y, DU H, et al.How trophic interactions drive the spontaneous construction of microbial community in traditional fermented foods:A review[J].Microbiology China, 2021, 48(11):4 412-4 424.
[60] LIU C L, HUANG D, ZHANG W X.Combining culture-dependent and culture-independent molecular methods for the isolation and purification of a potentially novel anaerobic species from pit mud in a Chinese liquor distillery[J].Journal of the Institute of Brewing, 2016, 122(4):754-762.
[61] MU D S, LIANG Q Y, WANG X M, et al.Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing[J].Microbiome, 2018, 6(1):230.
[62] GAO J J, LIU G Y, LI A J, et al.Domination of pit mud microbes in the formation of diverse flavour compounds during Chinese strong aroma-type Baijiu fermentation[J].LWT, 2021, 137:110442.
[63] 卢萌萌. 浓香型白酒窖泥中未培养厌氧菌的可培养化研究[D].无锡:江南大学, 2020.
LU M M.Cultivating uncultured anaerobes from pit mud of Chinese strong-aroma type liquor[D].Wuxi:Jiangnan University, 2020.
[64] DUSSÉAUX S, CROUX C, SOUCAILLE P, et al.Metabolic engineering of Clostridium acetobutylicum ATCC 824 for the high-yield production of a biofuel composed of an isopropanol/butanol/ethanol mixture[J].Metabolic Engineering, 2013, 18:1-8.
[65] 韩颖. 古井窖泥菌群中厌氧菌的纯化培养与分子鉴定[D].哈尔滨:哈尔滨工业大学, 2017.
HAN Y.Purification and molecular identification of anaerobic bacteria in Gujing tribute pit mud[D].Harbin:Harbin Institute of Technology, 2017.
[66] 高凤. 东北酸菜发酵过程亚硝酸盐微生物酶降解机制及应用[D].镇江:江苏大学, 2019.
GAO F.Mechanism and application of nitrite enzymatic degradation by microorganisms in saukraut in northeast China[D].Zhenjiang:Jiangsu University, 2019.
[67] 刘文容. 黄酒陈酿过程中酸败乳酸菌的分离鉴定及其特性研究[D].无锡:江南大学, 2017.
LIU W R.Studies on the isolation, identification and characteristics of spoilage lactic acid bacteria in storage of Chinese rice wine[D].Wuxi:Jiangnan University, 2017.
[68] LAGIER J C, DUBOURG G, MILLION M, et al.Culturing the human microbiota and culturomics[J].Nature Reviews Microbiology, 2018, 16(9):540-550.
[69] XU J L, SUN L P, XING X, et al.Culturing bacteria from fermentation pit muds of Baijiu with culturomics and amplicon-based metagenomic approaches[J].Frontiers in Microbiology, 2020, 11:1223.
[70] DU R B, LIU J, JIANG J, et al.Construction of a synthetic microbial community for the biosynthesis of volatile sulfur compound by multi-module division of labor[J].Food Chemistry, 2021, 347:129036.
[71] CHANG Y X, HOU F Y, PAN Z Y, et al.Optimization of culturomics strategy in human fecal samples[J].Frontiers in Microbiology, 2019, 10:2891.
[72] XU J L, SUN L P, SUN Z B, et al.Pontibacter beigongshangensis sp.nov, isolated from the mash of wine[J].Current Microbiology, 2019, 76(12):1 525-1 530.
[73] 郝淑月, 任清.北工商海洋杆菌诱导戊糖片球菌产生细菌素及降黄酒生物胺功效研究[J].食品科学技术学报, 2021, 39(1):88-95.
HAO S Y, REN Q.Study on bacteriocin production of Pediococcus pentosaceus induced by Pontibacter beigongshangensis and reduction the biogenic amines content in Huangjiu[J].Journal of Food Science and Technology, 2021, 39(1):88-95.
[74] 李意涵, 任清, 徐嘉良, 等.北工商海洋杆菌色素的提取与稳定性的初步研究[J].食品科技, 2021, 46(7):7-13.
LI Y H, REN Q, XU J L, et al.Extraction and stability of the Pontibacter beigongshangensis pigment[J].Food Science and Technology, 2021, 46(7):7-13.
[75] LI K X, SANG X, ZHU Y L, et al.Lentibacillus panjinensis sp.nov, isolated from shrimp paste, a traditional Chinese fermented seafood[J].Current Microbiology, 2020, 77(9):1 997-2 001.
[76] ZHU X Y, ZHOU Y, WANG Y, et al.Production of high-concentration n-caproic acid from lactate through fermentation using a newly isolated Ruminococcaceae bacterium CPB6[J].Biotechnology for Biofuels, 2017, 10:102.
[77] LI P, TIAN W N, JIANG Z, et al.Genomic characterization and probiotic potency of Bacillus sp.DU-106, a highly effective producer of L-lactic acid isolated from fermented yogurt[J].Frontiers in Microbiology, 2018, 9:2216.
[78] YU P, HUANG X X, REN Q, et al.Purification and characterization of a H2O2-tolerant alkaline protease from Bacillus sp.ZJ1502, a newly isolated strain from fermented bean curd[J].Food Chemistry, 2019, 274:510-517.
[79] WU Q, ZHU Y, FANG C, et al.Can we control microbiota in spontaneous food fermentation? -Chinese liquor as a case example[J].Trends in Food Science & Technology, 2021, 110:321-331.
[80] YU Y J, LI X, ZHANG J H, et al.Lactobacillus jinshani sp.nov, isolated from solid-state vinegar culture of Zhenjiang aromatic vinegar[J].Antonie Van Leeuwenhoek, 2020, 113(1):43-54.
[81] 孙佳. 金山醋酸乳杆菌比较基因组分析与酿醋功能评价[D].无锡:江南大学, 2021.
SUN J.Comparative genome analysis of Acetilactobacillus jinshanensis and its function in vinegar fermentation[D].Wuxi:Jiangnan University, 2021.
[82] PARK B J, PARK S J, YOON D N, et al.Cultivation of autotrophic ammonia-oxidizing Archaea from marine sediments in coculture with sulfur-oxidizing bacteria[J].Applied and Environmental Microbiology, 2010, 76(22):7 575-7 587.
[83] CROSS K L, CAMPBELL J H, BALACHANDRAN M, et al.Targeted isolation and cultivation of uncultivated bacteria by reverse genomics[J].Nature Biotechnology, 2019, 37(11):1 314-1 321.
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