Modulating the human gut microbiome and health markers through kombucha consumption: a controlled clinical study/Experiment 1

From BugSigDB


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)

NCBI Quality ControlLinks
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)

NCBI Quality ControlLinks
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