Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore/Experiment 6

From BugSigDB


Reviewed Marked as Reviewed by ChiomaBlessing on 2024-3-18

Curated date: 2024/03/07

Curator: Deacme

Revision editor(s): Deacme, ChiomaBlessing

Subjects

Location of subjects
Singapore
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
Health study participation health questionnaire participation,health survey participation,Health study participation,health study participation
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Indian participants
Group 1 name Corresponds to the case (exposed) group for case-control studies
Malay participants
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Participants who belong to the Malay ethnic group
Group 0 sample size Number of subjects in the control (unexposed) group
10
Group 1 sample size Number of subjects in the case (exposed) group
12
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
1 month

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V4
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).
relative abundances
Statistical test
Kruskall-Wallis
LEfSe
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)?
No
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
2.0

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-3-18

Curated date: 2024/03/07

Curator: Deacme

Revision editor(s): Deacme, ChiomaBlessing

Source: Fig 5b (1st cladogram)

Description: Significant taxa abundance in participants of Malay descent compared to participants of Indian descent

Abundance in Group 1: increased abundance in Malay participants

NCBI Quality ControlLinks
Sutterella stercoricanis
Klebsiella granulomatis

Revision editor(s): Deacme, ChiomaBlessing