Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics

Arıkan, Muzaffer; Mitchell, Alex L.; Finn, Robert D.; Gürel, Filiz

doi:10.1111/1750-3841.14992

Cited by 94 publications

(76 citation statements)

References 77 publications

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“…Prior to this study, Starmerella , one of the major fungi replacing Brettanomyces in Cluster II, had not been described in molecular ecology studies of the solid-phase Kombucha SCOBY. Starmerella is a relatively new genus into which several Candida species have been reclassified [ 72 ], thus earlier Kombucha studies reporting Candida at genus level may have observed species currently classified as Starmerella . Starmerella davenportii , detected in the ‘meta’-SCOBY, was recently isolated from Kombucha and shown to generate volatile aroma compounds and organic acids during a black tea fermentation [ 73 ].…”

Section: Discussionmentioning

confidence: 99%

Microbial Composition of SCOBY Starter Cultures Used by Commercial Kombucha Brewers in North America

Harrison

Curtin

2021

Microorganisms

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Kombucha fermentation is initiated by transferring a solid-phase cellulosic pellicle into sweetened tea and allowing the microbes that it contains to initiate the fermentation. This pellicle, commonly referred to as a symbiotic culture of bacteria and yeast (SCOBY), floats to the surface of the fermenting tea and represents an interphase environment, where embedded microbes gain access to oxygen as well as nutrients in the tea. To date, various yeast and bacteria have been reported to exist within the SCOBY, with little consensus as to which species are essential and which are incidental to Kombucha production. In this study, we used high-throughput sequencing approaches to evaluate spatial homogeneity within a single commercial SCOBY and taxonomic diversity across a large number (n = 103) of SCOBY used by Kombucha brewers, predominantly in North America. Our results show that the most prevalent and abundant SCOBY taxa were the yeast genus Brettanomyces and the bacterial genus Komagataeibacter, through careful sampling of upper and lower SCOBY layers. This sampling procedure is critical to avoid over-representation of lactic acid bacteria. K-means clustering was used on metabarcoding data of all 103 SCOBY, delineating four SCOBY archetypes based upon differences in their microbial community structures. Fungal genera Zygosaccharomyces, Lachancea and Starmerella were identified as the major compensatory taxa for SCOBY with lower relative abundance of Brettanomyces. Interestingly, while Lactobacillacae was the major compensatory taxa where Komagataeibacter abundance was lower, phylogenic heat-tree analysis infers a possible antagonistic relationship between Starmerella and the acetic acid bacterium. Our results provide the basis for further investigation of how SCOBY archetype affects Kombucha fermentation, and fundamental studies of microbial community assembly in an interphase environment.

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Section: Discussionmentioning

confidence: 99%

Microbial Composition of SCOBY Starter Cultures Used by Commercial Kombucha Brewers in North America

Harrison

Curtin

2021

Microorganisms

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“…Shotgun metagenomics allows to overcome the challenges that affect both assembly based and mapping‐based metagenomic profiling (Laudadio et al ., 2019), particularly, of high‐complexity samples (Walsh et al ., 2016; Seol et al ., 2019; Sirén et al ., 2019), including KMC (Arıkan et al ., 2020; Villarreal‐Soto et al ., 2020). Hence, we have implemented a shotgun metagenomic approach to gather an unbiased snapshot of the community structure and potential functionality in KMC that were previously exposed to space and different levels of Mars‐like conditions, simulated on low Earth orbit outside the International Space Station (ISS), within the BIOMEX project (de Vera et al ., 2019; Podolich et al ., 2019).…”

Section: Introductionmentioning

confidence: 99%

Shotgun metagenomic analysis of kombucha mutualistic community exposed to Mars‐like environment outside the International Space Station

Goés-Neto

Kukharenko

Orlovska

et al. 2021

Environmental Microbiology

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Kombucha is a multispecies microbial ecosystem mainly composed of acetic acid bacteria and osmophilic acid-tolerant yeasts, which is used to produce a probiotic drink. Furthermore, Kombucha Mutualistic Community (KMC) has been recently proposed to be used during long space missions as both a living functional fermented product to improve astronauts' health and an efficient source of bacterial nanocellulose. In this study, we compared KMC structure and functions before and after samples were exposed to the space/Mars-like environment outside the International Space Station in order to investigate the changes related to their re-adaptation to Earth-like conditions by shotgun metagenomics, using both diversity and functional analyses of Community Ecology and Complex Networks approach. Our study revealed that the long-term exposure to space/Mars-like conditions on low Earth orbit may disorganize the KMC to such extent that it will not restore the initial community structure; however, KMC core microorganisms of the community were maintained. Nonetheless, there were no significant differences in the community functions, meaning that the KMC communities are ecologically resilient. Therefore, despite the extremely harsh conditions, key KMC species revived and provided the community with the genetic background needed to survive long periods of time under extraterrestrial conditions.

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“…The study proved that shotgun sequencing technology could be used to evaluate the microbial community composition during beef production, as well as pathogen population shifts ( Yang et al, 2016 ). Several studies have shown that shotgun sequencing technology is also applicable to the study of microbial communities in food or beverages that require fermentation ( Ferrocino et al, 2018 ; Arikan et al, 2020 ), as well as human microbes found in the skin ( Oh et al, 2014 ), saliva ( Hasan et al, 2014 ), and gastrointestinal tract ( Vangay et al, 2018 ; Zhao et al, 2018 ). In addition to research in the field of microbiology, shotgun sequencing technology has also been successfully used in animal diet analysis ( Srivathsan et al, 2015 ), animal diversity ( Zhou et al, 2013 ), and ingredient identification in food ( Haiminen et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

The Species Identification in Traditional Herbal Patent Medicine, Wuhu San, Based on Shotgun Metabarcoding

Liu

Shi

et al. 2021

Front. Pharmacol.

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Traditional herbal patent medicine typically consists of multiple ingredients, making it challenging to supervise contamination by impurities and the improper use of raw materials. This study employed shotgun metabarcoding for the species identification of biological ingredients in traditional herbal patent medicine, Wuhu San. The five prescribed herbal materials found in Wuhu San were collected, and their reference sequences were obtained by traditional DNA barcoding using Sanger sequencing. Two lab-made and three commercial Wuhu San samples were collected, and a total of 37.14 Gb of shotgun sequencing data was obtained for these five samples using the Illumina sequencing platform. A total of 1,421,013 paired-end reads were enriched for the Internal Transcribed Spacer 2 (ITS2), psbA and trnH intergenic spacer region (psbA-trnH), maturase k (matK), and ribulose-1, 5-bisphosphate carboxylase (rbcL) regions. Furthermore, 80, 11, 9, and 8 operational taxonomic units were obtained for the ITS2, psbA-trnH, matK, and rbcL regions, respectively, after metagenomic assembly, annotation, and chimeric detection. In the two lab-made mock samples, all labeled ingredients in the Wuhu San prescription were successfully detected, and the positive control, Panax quinquefolius L., was detected in the HSZY172 mock sample. Three species, namely Angelica sinensis (Oliv.) Diels, Saposhnikovia divaricata (Turcz. ex Ledeb.) Schischk., and Carthamus tinctorius L., belonging to three labeled ingredients, Angelicae Sinensis Radix (Danggui), Saposhnikoviae Radix (Fangfeng), and Carthami Flos (Honghua), were detected in the three commercial samples. Angelica dahurica (Hoffm.) Benth. & Hook. f. ex Franch. & Sav., the original Angelicae Dahuricae Radix (Baizhi) species, was only detected in WHS003. Arisaema erubescens (Wall.) Schott, Arisaema heterophyllum Blume, or Arisaema amurense Maxim., the original Arisaematis Rhizoma (Tiannanxing) species, were not detected in any of the commercial samples, which could be attributed to the fact that this medicinal material underwent extensive processing. In addition, the Saposhnikovia divaricata adulterant was detected in all the commercial samples, while 24 fungal genera, including Aspergillus, were identified in both the lab-made and commercial samples. This study showed that shotgun metabarcoding provided alternative strategy and technical means for identifying prescribed ingredients in traditional herbal patent medicine and displayed the potential to effectively complement traditional methods.

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Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics

Cited by 94 publications

References 77 publications

Microbial Composition of SCOBY Starter Cultures Used by Commercial Kombucha Brewers in North America

Microbial Composition of SCOBY Starter Cultures Used by Commercial Kombucha Brewers in North America

Shotgun metagenomic analysis of kombucha mutualistic community exposed to Mars‐like environment outside the International Space Station

The Species Identification in Traditional Herbal Patent Medicine, Wuhu San, Based on Shotgun Metabarcoding

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