Microbial Composition of SCOBY Starter Cultures Used by Commercial Kombucha Brewers in North America
Abstract
:1. Introduction
2. Materials and Methods
2.1. Chemicals, Reagents and Microbiological Media
2.2. Microbial Media and Cultures
2.3. Kombucha SCOBY Starter Culture Sampling and Processing
2.3.1. Sectioning of Commercial Kombucha SCOBY (Spatial Analysis Study)
2.3.2. Collection of Representative Commercial Kombucha SCOBY (Taxonomic Diversity Study)
2.3.3. Sample Homogenization and DNA Extraction
2.4. Quantitive PCR Estimation of Kombucha SCOBY Microbial Population Size
2.5. Metabarcoding Analyses of Kombucha SCOBY Bacterial and Fungal Communities
2.5.1. Metabarcoding Library Preparation and Sequencing
2.5.2. Metabarcoding Sequence Processing and Analyses
2.6. Shotgun Metagenomic Sequencing Analysis of Composite ‘Meta-’SCOBY DNA Sample
2.6.1. Meta-SCOBY Library Preparation and Sequencing
2.6.2. Sequence Pre-Processing
2.6.3. Kmer Analysis of Meta-SCOBY Community Composition
2.6.4. Mapping of Meta-SCOBY Reads against a Komagataeibacter Composite Reference Genome
2.7. Statistical Analyses
2.8. Sequence Data Availability
3. Results
3.1. Spatial Distribution of Fungi and Bacteria within a Single Kombucha SCOBY
3.2. Fungal and Bacterial Communities Associated with 103 Commercial Kombucha SCOBY
3.3. Defining Kombucha SCOBY Archetypes Based upon Microbial Community Composition
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Taxa (ASV) | Metabarcoding | Shotgun Sequencing | |
---|---|---|---|
Relative Abundance | Prevalence 1 | Proportion of Kmers 2 | |
Fungi | |||
g__Brettanomyces | 0.813 ± 0.259 | 0.990 | 0.8884 |
g__Zygosaccharomyces | 0.068 ± 0.170 | 0.625 | 0.0173 |
s__Starmerella davenportii | 0.047 ± 0.124 | 0.481 | 0.016 |
s__Lachancea fermentati | 0.038 ± 0.141 | 0.385 | 0.0086 |
k__Fungi | 0.012 ± 0.050 | 0.183 | NA |
f__Saccharomycetales_unidentified | 0.008 ± 0.072 | 0.019 | NA |
g__Candida | 0.007 ± 0.062 | 0.019 | 0.0005 |
g__Hanseniaspora | 0.004 ± 0.021 | 0.125 | 0.0038 |
g__Pichia | 0.001 ± 0.011 | 0.010 | 0.0043 |
p__Ascomycota | 0.001 ± 0.005 | 0.058 | NA |
g__Kregervanrija | 0.001 ± 0.004 | 0.019 | 0.0076 |
Bacteria | |||
g__Komagataeibacter | 0.809 ± 0.299 | 0.971 | 0.7088 |
Lactobacillales total | 0.129 | 0.0589 | |
f__Lactobacillaceae | 0.072 ± 0.167 | 0.394 | NA |
o__Lactobacillales_unidentified | 0.050 ± 0.117 | 0.327 | NA |
g__Oenococcus | 0.007 ± 0.061 | 0.077 | 0.019 |
g__Tanticharoenia | 0.039 ± 0.130 | 0.462 | 0.0003 |
g__Acetobacter | 0.012 ± 0.055 | 0.173 | 0.117 |
f__Acetobacteraceae | 0.006 ± 0.030 | 0.144 | NA |
f__Bacillaceae_unidentified | 0.005 ± 0.040 | 0.029 | 0.0112 |
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Harrison, K.; Curtin, C. Microbial Composition of SCOBY Starter Cultures Used by Commercial Kombucha Brewers in North America. Microorganisms 2021, 9, 1060. https://doi.org/10.3390/microorganisms9051060
Harrison K, Curtin C. Microbial Composition of SCOBY Starter Cultures Used by Commercial Kombucha Brewers in North America. Microorganisms. 2021; 9(5):1060. https://doi.org/10.3390/microorganisms9051060
Chicago/Turabian StyleHarrison, Keisha, and Chris Curtin. 2021. "Microbial Composition of SCOBY Starter Cultures Used by Commercial Kombucha Brewers in North America" Microorganisms 9, no. 5: 1060. https://doi.org/10.3390/microorganisms9051060