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Article

Sea Grape (Caulerpa racemosa) Kombucha: A Comprehensive Study of Metagenomic and Metabolomic Profiling, Its Molecular Mechanism of Action as an Antioxidative Agent, and the Impact of Fermentation Time

by
Dian Aruni Kumalawati
1,
Reza Sukma Dewi
2,
Noor Rezky Fitriani
3,
Scheirana Zahira Muchtar
2,
Juan Leonardo
4,
Nurpudji Astuti Taslim
5,
Raffaele Romano
6,*,
Antonello Santini
7,* and
Fahrul Nurkolis
8,9,10
1
Biomedical Science Department, Faculty of Science and Technology, State Islamic University of Sunan Kalijaga (UIN Sunan Kalijaga), Yogyakarta 55281, Indonesia
2
Biology Department, Faculty of Science and Technology, State Islamic University of Sunan Kalijaga (UIN Sunan Kalijaga), Yogyakarta 55281, Indonesia
3
Chemistry Department, Faculty of Mathematics and Natural Sciences, IPB University, Bogor 16680, Indonesia
4
Citra Deli Kreasitama Ltd., Banten 15124, Indonesia
5
Division of Clinical Nutrition, Department of Nutrition, Faculty of Medicine, Hasanuddin University, Makassar 90245, Indonesia
6
Department of Agricultural Sciences, University of Napoli Federico II, Via Università, 100-80055 Portici, Italy
7
Department of Pharmacy, University of Napoli Federico II, Via Domenico Montesano, 49-80131 Napoli, Italy
8
Master of Basic Medical Science, Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
9
Institute for Research and Community Service, State Islamic University of Sunan Kalijaga (UIN Sunan Kalijaga), Yogyakarta 55281, Indonesia
10
Medical Research Center of Indonesia, Surabaya 60286, Indonesia
*
Authors to whom correspondence should be addressed.
Beverages 2025, 11(5), 134; https://doi.org/10.3390/beverages11050134
Submission received: 13 July 2025 / Revised: 21 August 2025 / Accepted: 1 September 2025 / Published: 5 September 2025

Abstract

Sea grape kombucha has been known to exhibit high antioxidant activity due to its elevated total polyphenol content. This study aims to identify and characterize the active microbial community involved in the fermentation of kombucha using sea grapes (C. racemosa) as the primary substrate. Furthermore, it evaluates the effects of different Symbiotic Culture of Bacteria and Yeast (SCOBY) starter concentrations on the physicochemical properties and antioxidant activity of sea grape kombucha. Our results showed that the pH of the kombucha was higher after 7 days of fermentation compared to later time points. The microbial community was composed of 97.08% bacteria and 2.92% eukaryotes, divided into 10 phyla and 69 genera. The dominant genus in all samples was Komagataeibacter. Functional profiling based on 16S rRNA data revealed that metabolic functions accounted for 77.04% of predicted microbial activities during fermentation. The most enriched functional categories were carbohydrate metabolism (15.70%), cofactor and vitamin metabolism (15.54%), and amino acid metabolism (14.24%). At KEGG Level 3, amino acid-associated pathways, particularly alanine, aspartate, and glutamate metabolism (4.24%), were predominant. The fermentation process in sea grape kombucha is primarily driven by carbohydrate and amino acid metabolism, supported by energy-generating and cofactor biosynthesis pathways. Our findings indicate that different metabolic pathways lead to variations in kombucha components, and distinct fermentation stages result in different metabolic reactions. For instance, early fermentation stages (Day 7) are dominated by amino acid metabolism, whereas the late stages (Day 21) show increased activity in carbohydrate and sulfur metabolism. Metabolomic analysis revealed that increasing the SCOBY starter concentration significantly influenced pH, soluble solid content, vitamin C, tannin, and flavonoid content. These variations suggest that fermentation duration and microbial composition significantly influence the spectrum of bioactive metabolites, which synergistically provide functional benefits such as antimicrobial, antioxidant, and metabolic health-promoting activities. For example, sample K1 produced more fatty acids and simple sugar alcohols, sample K2 enriched complex lipid compounds and phytosterols, while sample K3 dominated the production of polyols and terpenoid compounds.
Keywords: Caulerpa racemosa; kombucha; metagenomic; metabolomic; antioxidant; Komagataeibacter; functional food Caulerpa racemosa; kombucha; metagenomic; metabolomic; antioxidant; Komagataeibacter; functional food

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MDPI and ACS Style

Kumalawati, D.A.; Dewi, R.S.; Fitriani, N.R.; Muchtar, S.Z.; Leonardo, J.; Astuti Taslim, N.; Romano, R.; Santini, A.; Nurkolis, F. Sea Grape (Caulerpa racemosa) Kombucha: A Comprehensive Study of Metagenomic and Metabolomic Profiling, Its Molecular Mechanism of Action as an Antioxidative Agent, and the Impact of Fermentation Time. Beverages 2025, 11, 134. https://doi.org/10.3390/beverages11050134

AMA Style

Kumalawati DA, Dewi RS, Fitriani NR, Muchtar SZ, Leonardo J, Astuti Taslim N, Romano R, Santini A, Nurkolis F. Sea Grape (Caulerpa racemosa) Kombucha: A Comprehensive Study of Metagenomic and Metabolomic Profiling, Its Molecular Mechanism of Action as an Antioxidative Agent, and the Impact of Fermentation Time. Beverages. 2025; 11(5):134. https://doi.org/10.3390/beverages11050134

Chicago/Turabian Style

Kumalawati, Dian Aruni, Reza Sukma Dewi, Noor Rezky Fitriani, Scheirana Zahira Muchtar, Juan Leonardo, Nurpudji Astuti Taslim, Raffaele Romano, Antonello Santini, and Fahrul Nurkolis. 2025. "Sea Grape (Caulerpa racemosa) Kombucha: A Comprehensive Study of Metagenomic and Metabolomic Profiling, Its Molecular Mechanism of Action as an Antioxidative Agent, and the Impact of Fermentation Time" Beverages 11, no. 5: 134. https://doi.org/10.3390/beverages11050134

APA Style

Kumalawati, D. A., Dewi, R. S., Fitriani, N. R., Muchtar, S. Z., Leonardo, J., Astuti Taslim, N., Romano, R., Santini, A., & Nurkolis, F. (2025). Sea Grape (Caulerpa racemosa) Kombucha: A Comprehensive Study of Metagenomic and Metabolomic Profiling, Its Molecular Mechanism of Action as an Antioxidative Agent, and the Impact of Fermentation Time. Beverages, 11(5), 134. https://doi.org/10.3390/beverages11050134

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