Metagenomic analysis reveals microbial community and functional capacity in Kombucha

Main Article Content

Lei Yuan
Luyao Fan
Jie Hou
Rong Luo
Shuo Wang
Wenyuan Zhou
Zhenquan Yang


fermentation, Kombucha, metagenomics, microbial community


Kombucha is a traditional beverage obtained from fermented sugar-tea by a community of bacteria and yeasts. Understanding the microbial composition and their functions in Kombucha fermentation is of significance, but most of the studies have relied on the culture-dependent method. In this study, a metagenomic analysis was conducted to obtain a more comprehensive insight into Kombucha fermentation. Results showed that the bacteria of Kombucha were dominated by Komagataeibacter (36.24 to 63.35%), Gluconacetobacter (10.39 to 26.21%), Gluconobacter (6.62 to 27.10%), Acetobacter (0.3 to 6.64%), and the fungus Kluyveromyces (0.63 to 36.98%) was also identified. Taxonomic composition and abundance of the microbial community were distinct with each Kombucha sample. The carbohydrate active enzyme functions of the communities primarily comprised glycosyltransferase (GT) families (40.6%), glycoside hydrolase (GH) families (32.0%), and carbohydrate-binding module (CBM) families (12.9%). Moreover, functional genes and their KEGG pathways were predicted, which demonstrated that the functional genes present in the bacterial community were enriched in pathways for neurodegenerative disease, amino acid metabolism, metabolism of cofactors and vitamins, carbohydrate metabolism, folding, sorting and degradation, and translation. The results of this study would provide a better understanding of the microbiota and metabolites as well as health-promoting potential of Kombucha, and may facilitate the optimization of the process to produce Kombucha products with desirable qualities.

Abstract 859 | PDF Downloads 683 HTML Downloads 339 XML Downloads 132


Amiri, S., Moghanjougi, Z.M., Bari, M.R. and Khaneghah, A.M., 2021. Natural protective agents and their applications as bio-preservatives in the food industry: an overview of current and future applications. Italian Journal of Food Science 33: 55–68. 10.15586/ijfs.v33iSP1.2045

Chakravorty, S., Bhattacharya, S., Chatzinotas, A., Chakraborty, W., Bhattacharya, D. and Gachhui, R., 2016. Kombucha tea fermentation: microbial and biochemical dynamics. International Journal of Food Microbiology 220: 63–72. 10.1016/j.ijfoodmicro.2015.12.015

Chen, C., Liu, Y., Tian, H., Ai, L. and Yu, H., 2020. Metagenomic analysis reveals the impact of JIUYAO microbial diversity on fermentation and the volatile profile of Shaoxing-jiu. Food Micro-biology 86: 103326. 10.1016/

de Miranda, J.F., Ruiz, L.F., Silva, C.B., Uekane, T.M., Silva, K.A., Gonzalez, A.G.M., Fernandes, F.F. and Lima, A.R., 2022. Kombucha: a review of substrates, regulations, composition, and biological properties. Journal of Food Science 87: 503–527. 10.1111/1750-3841.16029

Diguta, C.F., Nitoi, G.D., Matei, F., Luta, G. and Cornea, C.P., 2020. The biotechnological potential of Pediococcus spp. isolated from Kombucha microbial consortium. Foods 9: 1780. 10.3390/foods9121780

Doyle, C.J., Gleeson, D., Toole, P.W.O. and Cotter, P.D., 2017. High-throughput metataxonomic characterization of the raw milk microbiota identifies changes reflecting lactation stage and storage conditions. International Journal of Food Microbiology 255: 1–6. 10.1016/j.ijfoodmicro.2017.05.019

Duze, S.T., Marimani, M. and Patel, M., 2021. Tolerance of Listeria monocytogenes to biocides used in food processing environments. Food Microbiology 97: 103758. 10.1016/

Fabricio, M.F., Mann, M.B., Kothe, C.I., Frazzon, J., Tischer, B., Flores, S.H. and Ayub, M.A.Z., 2022. Effect of freeze-dried kombucha culture on microbial composition and assessment of metabolic dynamics during fermentation. Food Microbiology 101: 103889. 10.1016/

Filippis, F.D., Valentino, V., Alvarez-Ordóñez, A., Cotter, P.D. and Ercolini, D., 2021. Environmental microbiome mapping as a strategy to improve quality and safety in the food industry. Current Opinion in Food Science 38: 168–176. 10.1016/j.cofs.2020.11.012

Fu, C., Yan, F., Cao, Z., Xie, F. and Lin, J., 2014. Antioxidant activities of kombucha prepared from three different substrates and changes in content of probiotics during storage. Food Science and Technology 34: 123–126. 10.1590/S0101-20612014005000012

Hou, J., Luo, R., Ni, H., Li, K., Mgomi, F.C., Fan, L. and Yuan, L., 2021. Antimicrobial potential of kombucha against foodborne pathogens: a review. Quality Assurance and Safety of Crops & Foods 13: 53–61. 10.15586/qas.v13i3.920

Jafari, R., Naghavi, NS., Khosravi-Darani, K., Doudi, M. and Shahanipour, K., 2022. Isolation, molecular and phylogenetic identification of microorganisms from Kombucha solution and evaluation of their viability using flow cytometery. Food Science and Technology 42: e63220. 10.1590/fst.63220

Jayabalan, R., Malbasa, R.V., Loncar, E.S., Vitas, J.S. and Sathish Kumar, M., 2014. A review on kombucha tea—micro-biology, composition, fermentation, beneficial effects, toxicity, and tea fungus. Comprehensive Reviews in Food Science and Food Safety 13: 538–550. 10.1111/1541–4337.12073

Leal, J.M., Suárez, L.V., Jayabalan, R., Oros, J.H. and Escalante-Aburto, A., 2018. A review on health benefits of kombucha nutritional compounds and metabolites. CyTA–Journal of Food 16: 390–399. 10.1080/19476337.2017.1410499

Lee, K.R., Jo, K., Ra, K.S., Suh, H.J., and Hong, K.B., 2022. Kombucha fermentation using commercial kombucha pellicle and culture broth as starter. Food Science and Technology 42: e70020. 10.1590/fst.70020

Li, R., Xu, Y., Chen, J., Wang, F., Zou, C. and Yin, J., 2022. Enhancing the proportion of gluconic acid with a microbial community reconstruction method to improve the taste quality of Kombucha. LWT–Food Science and Technology 155: 112937. 10.1016/j.lwt.2021.112937

Marsh, A.J., O’Sullivan, O., Hill, C., Ross, R.P. and Cotter, P.D., 2014. Sequence-based analysis of the bacterial and fungal compositions of multiple kombucha (tea fungus) samples. Food Microbiology 38: 171–178. 10.1016/

Milićević, B., Tomović, V., Danilović, B. and Savić, D., 2021. The influence of starter cultures on the lactic acid bacteria microbiota of Petrovac sausage. Italian Journal of Food Science 33: 24–34. 10.15586/ijfs.v33i2.1918

Morales, D., 2020. Biological activities of kombucha beverages: the need of clinical evidence. Trends in Food Science & Technology 105: 323–333. 10.1016/j.tifs.2020.09.025

Noronha, M.C.D., Cardoso, R.R., D’Almeida, C.T.D.S., Carmo, M.A.V.D., Azevedo, L., Maltarollo, V.G., Junior, J.I.R., Eller, M.R., Cameron, L.C., Ferreira, M.S.L. and de Barros, F.A.R., 2022. Black tea kombucha: physicochemical, microbiological and comprehensive phenolic profile changes during fermentation, and antimalarial activity. Food Chemistry 384: 132515. 10.1016/j.foodchem.2022.132515

Song, Q., Zhao, F., Wang, B., Han, Y. and Zhou, Z., 2021. Metagenomic insights into Chinese northeast suancai: predominance and diversity of genes associated with nitrogen metabolism in traditional household suancai fermentation. Food Research International 139: 109924. 10.1016/j.foodres.2020.109924

Subbiahdoss, G., Osmen, S. and Reimhult, E., 2022. Cellulosic biofilm formation of Komagataeibacter in kombucha at oil-water interfaces. Biofilm 4: 100071. 10.1016/j.bioflm.2022.100071

Torán-Pereg, P., Noval, B.D., Valenzuela, S., Martinez, J., Prado, D.P., Perise, R. and Arboleya, J.C., 2021. Microbiological and sensory characterization of kombucha SCOBY for culinary applications. International Journal of Gastronomy and Food Science 23: 100314. 10.1016/j.ijgfs.2021.100314

Villarreal-Soto, S.A., Bouajila, J., Pace, M., Leech, J., Cotter, P.D., Souchard, J.P., Taillandier, P. and Beaufort, S., 2020. Metabolome-microbiome signatures in the fermented beverage, Kombucha. International Journal of Food Microbiology 333: 108778. 10.1016/j.ijfoodmicro.2020.108778

Wang, J.L., Zhao, F., Cairang, Z.M., Li, X.Y., Kong, J., Zeng, S.Y., Zhang, M.Y., Zhao, Z.X. and Zhang, X.P., 2021. Correlation between the bacterial community and flavour of fermented fish. Quality Assurance and Safety of Crops & Foods 13(3): 82–91. 10.15586/qas.v13i3.908

Yang, J., Lagishetty, V., Kurnia, P., Henning, S.M., Ahdoot, A.I. and Jacobs, J.P., 2022. Microbial and chemical profiles of commercial Kombucha products. Nutrients 14: 670. 10.3390/nu14030670

Zhang, J., Liu, S., Sun, H., Jiang, Z., Xu, Y., Mao, J., Qian, B., Wang, L. and Mao, J., 2022. Metagenomics-based insights into the microbial community profiling and flavor development potentiality of baijiu Daqu and huangjiu wheat Qu. Food Research International 152: 110707. 10.1016/j.foodres.2021.110707

Zhuang, S., Tan, Y., Hong, H., Li, D., Zhang, L. and Luo, Y., 2022. Exploration of the roles of spoilage bacteria in degrading grass carp proteins during chilled storage: a combined metagenomic and metabolomic approach. Food Research International 152: 110926. 10.1016/j.foodres.2021.110926