Modulating the human gut microbiome and health markers through kombucha consumption: a controlled clinical study

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Reviewed Marked as Reviewed by Svetlana up on 2025-3-20

Curated date: 2025/02/11

Curator: YokoC

Revision editor(s): YokoC, WikiWorks

Subjects

Location of subjects: United States of America

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Response to diet Response to diet,response to diet

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Control T-3 (time point 3)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Kombucha T-3 (time point 3)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Participants on a beige diet, drinking 16 oz of kombucha daily at the end of the treatment, 4 weeks (time point 3).

Group 0 sample size Number of subjects in the control (unexposed) group: 8

Group 1 sample size Number of subjects in the case (exposed) group: 16

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 3 months

Lab analysis

Sequencing type: WMS

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: log transformation

Statistical test: ANCOM-BC

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, body mass index, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-3-20

Curated date: 2025/02/12

Curator: YokoC

Revision editor(s): YokoC, WikiWorks, KateRasheed

Source: Figure 4a

Description: Log-fold-change for differentially abundant features at the species level in gut microbiome samples from control subjects vs kombucha treatment subjects at the end of the experiment (t-3).

Abundance in Group 1: increased abundance in Kombucha T-3 (time point 3)

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Cuneatibacter caecimuris
Fusobacterium nucleatum
Lactobacillus amylovorus
Varibaculum cambriense
Fusobacterium vincentii
Porphyromonas sp001808555Porphyromonas sp001808555
Ezakiella coagulans
Allisonella pneumosintesAllisonella pneumosintes
Peptoniphilus grossensis
Mobiluncus mulieris
Anaerococcus prevotii
Lactobacillus gasseri
Porphyromonas gingivalis
Parabacteroides pacaensis
Acutalibacter sp009936055Acutalibacter sp009936055

Revision editor(s): YokoC, WikiWorks, KateRasheed

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-3-20

Curated date: 2025/02/26

Curator: YokoC

Revision editor(s): YokoC, KateRasheed

Source: Figure 4a

Description: Description: Log-fold-change for differentially abundant features at the species level in gut microbiome samples from control subjects vs kombucha treatment subjects at the end of the experiment (t-3).

Abundance in Group 1: decreased abundance in Kombucha T-3 (time point 3)

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Aggregatibacter actinomycetemcomitans
Allisonella histaminiformans
Bifidobacterium choloepi
Heyndrickxia coagulans CSIL1
Metamycoplasma hominis
Neisseria mucosa C102
Pasteurella multocida
Prevotella sp. CAG:1092
Prevotella sp. CAG:386
Prevotella sp. CAG:732
Rothia aeria
Ruminococcus sp. CAG:177
Streptococcus salivarius
Sutterella wadsworthensis 2_1_59BFAA
Turicibacter sp. H121
Actinobacillus aerogenesActinobacillus aerogenes
Candidatus Saccharimonas
bacterium F082
Cryptobacteroides sp000432655Cryptobacteroides sp000432655
Ellagibacter isourolithinifaciens
Tractidigestivibacter sp000752675Tractidigestivibacter sp000752675
Segatella albensis
Bifidobacterium indicum
Heyndrickxia coagulans
Phocaeicola sp000434735Phocaeicola sp000434735
Clostridium sp. CAG:299
Segatella hominis
Eubacterium sp000433975Eubacterium sp000433975
Gardnerella vaginalis
Rodentibacter pneumotropicus
Clostridium celatum
Leyella stercorea
Gallibacterium anatis
Lautropia mirabilis
Peptidiphaga gingivicola
Gardnerella swidsinskii
Actinobacillus lignieresii

Revision editor(s): YokoC, KateRasheed

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-3-20

Curated date: 2025/02/26

Curator: YokoC

Revision editor(s): YokoC, KateRasheed

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Kombucha T-1 (time point 1)

Group 0 sample size Number of subjects in the control (unexposed) group: 16

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-3-20

Curated date: 2025/02/26

Curator: YokoC

Revision editor(s): YokoC, KateRasheed

Source: Figure 4b

Description: Log-fold-change for differentially abundant features at the species level in gut microbiome samples from kombucha treatment subjects at the end of the experiment (t-3) vs the starting point (t-1).

Abundance in Group 1: increased abundance in Kombucha T-3 (time point 3)

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Weissella soli
Leuconostoc kimchii

Revision editor(s): YokoC, KateRasheed

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-3-20

Curated date: 2025/02/26

Curator: YokoC

Revision editor(s): YokoC, KateRasheed

Source: Figure 4b

Description: Log-fold-change for differentially abundant features at the species level in gut microbiome samples from kombucha treatment subjects at the end of the experiment (t-3) vs the starting point (t-1).

Abundance in Group 1: decreased abundance in Kombucha T-3 (time point 3)

NCBI	Quality Control	Links
Heyndrickxia coagulans CSIL1
Neisseria mucosa C102
TM7 phylum sp. oral taxon 348
Heyndrickxia coagulans

Revision editor(s): YokoC, KateRasheed

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-3-20

Curated date: 2025/02/28

Curator: YokoC

Revision editor(s): YokoC, KateRasheed

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Kombucha T-2 (time point 2)

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-3-20

Curated date: 2025/03/04

Curator: YokoC

Revision editor(s): YokoC, KateRasheed

Source: Figure 4c

Description: Log-fold-change for differentially abundant features at the species level in gut microbiome samples from kombucha treatment subjects at time point 3 vs time point 2.

Abundance in Group 1: increased abundance in Kombucha T-3 (time point 3)

NCBI	Quality Control	Links
Weissella soli
Leuconostoc kimchii

Revision editor(s): YokoC, KateRasheed

Signature 2