Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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
- Day 1 participants
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Day 7 participants
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The day participants stopped the course of Omeprazole at therapeutic dose (20mg daily)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 34
- Group 1 sample size Number of subjects in the case (exposed) group
- 34
- 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
- Richness Number of species
- increased
Signature 1
Source: Fig 5a (3rd Cladogram)
Description: Significant taxa abundance in participants at Day 7 after a course of Omeprazole (20 mg) compared to Day 1
Abundance in Group 1: increased abundance in Day 7 participants
Revision editor(s): Deacme, ChiomaBlessing
Signature 2
Source: Fig 5a (3rd Cladogram)
Description: Significant taxa abundance in participants at Day 7 after a course of Omeprazole (20 mg) compared to Day 1
Abundance in Group 1: decreased abundance in Day 7 participants
| NCBI | Quality Control | Links |
|---|---|---|
| Collinsella tanakaei | ||
| Thermoanaerobacterales | ||
| Enterobacteriaceae | ||
| Enterobacterales | ||
| Gammaproteobacteria |
Revision editor(s): Deacme, ChiomaBlessing
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Day 7
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Day 14
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The day that marked the 7th day after participants stopped the course of Omeprazole at therapeutic dose (20mg daily)
Lab analysis
Statistical Analysis
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
Source: Fig 5a (2nd Cladogram)
Description: Significant taxa abundance in participants at Day 14 after they stopped the course of Omeprazole (20 mg) compared to Day 7
Abundance in Group 1: increased abundance in Day 14
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes | ||
| Anaerotruncus | ||
| Anaerotruncus colihominis | ||
| Bacteroidales | ||
| Bacteroidia | ||
| Turicibacter | ||
| Turicibacteraceae | ||
| TuricibacteralesTuricibacterales |
Revision editor(s): Deacme, ChiomaBlessing
Signature 2
Source: Fig 5a (2nd cladogram)
Description: Significant taxa abundance in participants at Day 14 after they stopped the course of Omeprazole (20 mg) compared to Day 7
Abundance in Group 1: decreased abundance in Day 14
Revision editor(s): Deacme, ChiomaBlessing
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Chinese participants
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Indian participants
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who belong to the Indian ethnic group
- Group 0 sample size Number of subjects in the control (unexposed) group
- 12
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
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
Source: Fig 5b (1st cladogram)
Description: Significant taxa abundance in participants of Indian descent compared to participants of Chinese descent
Abundance in Group 1: increased abundance in Indian participants
| NCBI | Quality Control | Links |
|---|---|---|
| Erysipelothrix |
Revision editor(s): Deacme, ChiomaBlessing
Signature 2
Source: Fig 5b (1st cladogram)
Description: Significant taxa abundance in participants of Indian descent compared to participants of Chinese descent
Abundance in Group 1: decreased abundance in Indian participants
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus colihominis | ||
| Verrucomicrobiaceae | ||
| Akkermansia muciniphila | ||
| Verrucomicrobiales | ||
| Fusobacterium naviforme |
Revision editor(s): Deacme, ChiomaBlessing
Experiment 6
Subjects
- 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
Lab analysis
Statistical Analysis
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
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 Control | Links |
|---|---|---|
| Sutterella stercoricanis | ||
| Klebsiella granulomatis |
Revision editor(s): Deacme, ChiomaBlessing
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Male participants
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Female participants
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants who identify with the female gender
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
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
Source: Fig 5c
Description: Significant taxa abundance in Female participants compared to Male participants
Abundance in Group 1: increased abundance in Female participants
Revision editor(s): Deacme, ChiomaBlessing
Signature 2
Source: Fig 5c
Description: Significant taxa abundance in Female participants compared to Male participants
Abundance in Group 1: decreased abundance in Female participants
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerolineae | ||
| Caldilinea | ||
| Caldilinea tarbellica | ||
| Caldilineaceae | ||
| Caldilineales | ||
| Lactobacillaceae | ||
| Lactobacillus | ||
| Oribacterium | ||
| Oribacterium sinus | ||
| Fusobacterium naviforme |
Revision editor(s): Deacme, ChiomaBlessing
The taxa of Proteobacteria phylum, Gammaproteobacteria class, Enterobacteriales order and Enterobacteriaceae family were only associated with the Day 7 group when it was compared to the Day 14 group, but not when the Day 7 group was compared to that from Day 1 (data not shown).
There was a significant increase in the relative abundance of the Bacilli class, Lactobacillales order, Streptococcaceae family, Streptococcus and Veillonella genera and Streptococcus vestibularis and Veillonella dispar species immediately after PPI use (Day 7), which diminished seven days after stopping omeprazole on Day 14.
Bacteroidetes phylum was associated with the Day 14 group when findings from that day were compared to those from Day 1 and Day 7 (data not shown).
