Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics
Open accessAbstract
Kombucha, a fermented tea generated from the co-culture of yeasts and bacteria, has gained worldwide popularity in recent years due to its potential benefits to human health. As a result, many studies have attempted to characterize both its biochemical properties and microbial composition. Here, we have applied a combination of whole metagenome sequencing (WMS) and amplicon (16S rRNA and Internal Transcribed Spacer 1 [ITS1]) sequencing to investigate the microbial communities of homemade Kombucha fermentations from day 3 to day 15. We identified the dominant bacterial genus as Komagataeibacter and dominant fungal genus as Zygosaccharomyces in all samples at all time points. Furthermore, we recovered three near complete Komagataeibacter genomes and one Zygosaccharomyces bailii genome and then predicted their functional properties. Also, we determined the broad taxonomic and functional profile of plasmids found within the Kombucha microbial communities. Overall, this study provides a detailed description of the taxonomic and functional systems of the Kombucha microbial community. Based on this, we conject that the functional complementarity enables metabolic cross talks between Komagataeibacter species and Z. bailii, which helps establish the sustained a relatively low diversity ecosystem in Kombucha.
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Metagenomic studies have been mainly conducted on single food types and on limited sample sizes, hindering inter-study integrative analyses currently available only for other environments such as the human gut.
“Nevertheless, metagenomic studies have been mainly conducted on single food types 18-24 and on limited sample sizes, 25,26 hindering inter-study integrative analyses currently available only for other environments such as the human gut. 27-31”
From Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. (2024) · cites this paper as [24]
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- Authors
- Arıkan, M., Mitchell, A. L., Finn, R. D., & Gürel, F.
- Affiliations
- Istanbul Medipol University (TR)
- European Bioinformatics Institute (GB)
- Istanbul University (TR)
- Corresponding author
- Arıkan, Muzaffer
- Gürel, Filiz
- Venue
- Journal of Food Science
- Publisher
- Wiley
- Published
- 2020-01-20
- Volume
- 85
- Issue
- 2
- Pages
- 455-464
- ISSN
- 0022-1147 (ISSN-L)
- 1750-3841
- PMC
- PMC7027524
- OpenAlex
- W3001198075
- Cited by
- 123
- References
- 75
- Citations by year
- 2026: 15 · 2025: 12 · 2024: 28 · 2023: 20 · 2022: 26 · 2021: 22
- FWCI
- 11.02
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Food Science (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Türkiye Bilimsel ve Teknolojik Araştirma Kurumu (215Z672)
- Bilimsel Araştirma Projeleri Birimi, Istanbul Üniversitesi (20138)
- Biotechnology and Biological Sciences Research Council (BB/M011755/1, BB/R015228/1)
- European Molecular Biology Laboratory
- Topics
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Agricultural and Biological Sciences › Food Science › Fermentation and Sensory Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- kombucha, microbial community composition, Komagataeibacter, Zygosaccharomyces bailii, yeast-bacteria co-culture, fermented tea, plasmids, functional metagenomics, metabolic crosstalk, 16S rRNA, ITS1
- MeSH terms
- Fermented Foods, Bacteria, Beverages, Fermentation, Yeasts, Sequence Analysis, DNA, Metagenome, Metagenomics, Microbiota
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