Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia
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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
- Liberia
- 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
- Helminthiasis helminth infection,helminthiasis,helminthosis,parasitic helminthiasis infectious disease,worm infection,Helminthiasis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Zero Soil Transmitted Helminth infection (Zero STH infection)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Soil Transmitted Helminth infection (High STH infection)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Soil Transmitted Helminth infection (High STH infection) refers to individuals found with eggs from Ascaris helminth; when their feces was measured by the Kato-Katz smear in eggs per gram (EPG).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
- Group 1 sample size Number of subjects in the case (exposed) group
- 26
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- 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
- 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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Table S5
Description: Differential abundance in the gut microbiota between infected and uninfected groups in Liberia (based on the presence of eggs in feces for Ascaris helminth).
Abundance in Group 1: decreased abundance in High Soil Transmitted Helminth infection (High STH infection)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteria | ||
| Cellulosilyticum | ||
| Eubacteriales | ||
| Clostridium_XIXClostridium_XIX | ||
| Odoribacter | ||
| Lachnospiraceae incertae sedis | ||
| Burkholderiales | ||
| Betaproteobacteria | ||
| Faecalibacterium |
Revision editor(s): KateRasheed, WikiWorks
Signature 2
Source: Table S5
Description: Differential abundance in the gut microbiota between infected and uninfected groups in Liberia (based on the presence of eggs in feces for Ascaris helminth).
Abundance in Group 1: increased abundance in High Soil Transmitted Helminth infection (High STH infection)
Revision editor(s): KateRasheed, WikiWorks
Experiment 2
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Soil Transmitted Helminth infection (High STH infection) refers to individuals found with eggs from any helminth; when their feces was measured by the Kato-Katz smear in eggs per gram (EPG).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Table S5
Description: Differential abundance in the gut microbiota between infected and uninfected groups in Liberia (based on the presence of any helminth eggs in feces).
Abundance in Group 1: increased abundance in High Soil Transmitted Helminth infection (High STH infection)
Revision editor(s): KateRasheed, WikiWorks
Signature 2
Source: Table S5
Description: Differential abundance in the gut microbiota between infected and uninfected groups in Liberia (based on the presence of any helminth eggs in feces).
Abundance in Group 1: decreased abundance in High Soil Transmitted Helminth infection (High STH infection)
Revision editor(s): KateRasheed, WikiWorks
Experiment 3
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Soil Transmitted Helminth infection (High STH infection) refers to individuals with CT≤ 28, when Ascaris qPCR was carried out.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Table S5
Description: Differential abundance in the gut microbiota between infected and uninfected groups in Liberia (based on the CT value when Ascaris qPCR was carried out).
Abundance in Group 1: increased abundance in High Soil Transmitted Helminth infection (High STH infection)
Revision editor(s): KateRasheed, WikiWorks
Signature 2
Source: Table S5
Description: Differential abundance in the gut microbiota between infected and uninfected groups in Liberia (based on the CT value when Ascaris qPCR was carried out).
Abundance in Group 1: decreased abundance in High Soil Transmitted Helminth infection (High STH infection)
Revision editor(s): KateRasheed, WikiWorks
Experiment 4
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Soil Transmitted Helminth infection (High STH infection) refers to individuals with CT≤ 28, when Necator qPCR was carried out.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Table S5
Description: Differential abundance in the gut microbiota between infected and uninfected groups in Liberia (based on the CT value when Necator qPCR was carried out).
Abundance in Group 1: increased abundance in High Soil Transmitted Helminth infection (High STH infection)
Revision editor(s): KateRasheed, WikiWorks
Signature 2
Source: Table S5
Description: Differential abundance in the gut microbiota between infected and uninfected groups in Liberia (based on the CT value when Necator qPCR was carried out).
Abundance in Group 1: decreased abundance in High Soil Transmitted Helminth infection (High STH infection)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteria | ||
| Prevotella | ||
| Prevotellaceae | ||
| Bacteroidota | ||
| Bacteroidia | ||
| Bacteroidales | ||
| Lachnospiraceae incertae sedis | ||
| Pasteurellales | ||
| Pasteurellaceae | ||
| Haemophilus | ||
| Lachnospiraceae |
Revision editor(s): KateRasheed, WikiWorks
Experiment 5
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Soil Transmitted Helminth infection (High STH infection) refers to individuals with CT≤ 28, when any helminth qPCR(quantitative real-time PCR) was carried out.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Table S5
Description: Differential abundance in the gut microbiota between infected and uninfected groups in Liberia (based on the CT value when any helminth qPCR was carried out).
Abundance in Group 1: increased abundance in High Soil Transmitted Helminth infection (High STH infection)
Revision editor(s): KateRasheed, WikiWorks
Signature 2
Source: Table S5
Description: Differential abundance in the gut microbiota between infected and uninfected groups in Liberia (based on the CT value when any helminth qPCR was carried out).
Abundance in Group 1: decreased abundance in High Soil Transmitted Helminth infection (High STH infection)
Revision editor(s): KateRasheed, WikiWorks
Experiment 6
Subjects
- Location of subjects
- Indonesia
- Group 0 sample size Number of subjects in the control (unexposed) group
- 43
- Group 1 sample size Number of subjects in the case (exposed) group
- 78
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Table S5
Description: Differential abundance in the gut microbiota between infected and uninfected groups in Indonesia (based on the CT value when any helminth qPCR was carried out).
Abundance in Group 1: increased abundance in High Soil Transmitted Helminth infection (High STH infection)
Revision editor(s): KateRasheed, WikiWorks
Signature 2
Source: Table S5
Description: Differential abundance in the gut microbiota between infected and uninfected groups in Indonesia (based on the CT value when any helminth qPCR was carried out).
Abundance in Group 1: decreased abundance in High Soil Transmitted Helminth infection (High STH infection)
Revision editor(s): KateRasheed, WikiWorks
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 2008 - Uninfected
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 2010 - Uninfected
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 2010 refers to individuals that were treated with anthelmintics or placebo in 2010, although they were not infected.
- Group 1 sample size Number of subjects in the case (exposed) group
- 32
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Differential abundance in the gut microbiota between uninfected individuals in Indonesia (2008-2010), treated with anthelmintics or placebo in 2010.
Abundance in Group 1: increased abundance in 2010 - Uninfected
| NCBI | Quality Control | Links |
|---|---|---|
| Betaproteobacteria | ||
| Burkholderiales | ||
| Comamonadaceae |
Revision editor(s): KateRasheed, WikiWorks
Signature 2
Source: Table S5
Description: Differential abundance in the gut microbiota between uninfected individuals in Indonesia (2008-2010), treated with anthelmintics or placebo in 2010.
Abundance in Group 1: decreased abundance in 2010 - Uninfected
Revision editor(s): KateRasheed, WikiWorks
Experiment 8
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 2010 refers to individuals that were treated with placebo in 2010, although they were not infected.
- Group 1 sample size Number of subjects in the case (exposed) group
- 16
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Differential abundance in the gut microbiota between uninfected individuals in Indonesia (2008-2010), treated with placebo in 2010.
Abundance in Group 1: increased abundance in 2010 - Uninfected
| NCBI | Quality Control | Links |
|---|---|---|
| Betaproteobacteria | ||
| Burkholderiales | ||
| Comamonadaceae | ||
| unclassified Bacteroidales |
Revision editor(s): KateRasheed, WikiWorks
Signature 2
Source: Table S5
Description: Differential abundance in the gut microbiota between uninfected individuals in Indonesia (2008-2010), treated with placebo in 2010.
Abundance in Group 1: decreased abundance in 2010 - Uninfected
Revision editor(s): KateRasheed, WikiWorks
Experiment 9
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 2010 refers to individuals that were untreated and uninfected in year 2010 (time effect).
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Differential abundance in the gut microbiota between untreated uninfected individuals in Indonesia in the year 2008-2010 (time effect).
Abundance in Group 1: increased abundance in 2010 - Uninfected
| NCBI | Quality Control | Links |
|---|---|---|
| Comamonadaceae | ||
| Betaproteobacteria | ||
| Burkholderiales |
Revision editor(s): KateRasheed, WikiWorks
Signature 2
Source: Table S5
Description: Differential abundance in the gut microbiota between untreated uninfected individuals in Indonesia in the year 2008-2010 (time effect).
Abundance in Group 1: decreased abundance in 2010 - Uninfected
Revision editor(s): KateRasheed, WikiWorks
Experiment 10
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 2010 refers to individuals that were treated with anthelmintics although they were not infected with STH species (treatment effect).
Lab analysis
Statistical Analysis
Signature 1
Source: Table S5
Description: Differential abundance in the gut microbiota between uninfected individuals in Indonesia (2008-2010 ), treated with anthelmintics in 2010 (treatment effect).
Abundance in Group 1: increased abundance in 2010 - Uninfected
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus | ||
| Flavobacteriaceae | ||
| Flavobacteriales | ||
| Flavobacteriia | ||
| Pseudomonadales | ||
| Sphingobacteriaceae | ||
| Sphingobacteriales | ||
| Sphingobacteriia |
Revision editor(s): KateRasheed, WikiWorks
Signature 2
Source: Table S5
Description: Differential abundance in the gut microbiota between uninfected individuals in Indonesia (2008-2010), treated with anthelmintics in 2010 (treatment effect).
Abundance in Group 1: decreased abundance in 2010 - Uninfected
| NCBI | Quality Control | Links |
|---|---|---|
| Brucellaceae | ||
| Ochrobactrum |
Revision editor(s): KateRasheed, WikiWorks
Experiment 11
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 2010 - Treated with albendazole
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 2008 - Infected
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 2008 refers to the STH-infected individuals.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 27
- Group 1 sample size Number of subjects in the case (exposed) group
- 78
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- increased
Signature 2
Source: Table S5
Description: Differential abundance in the gut microbiota between infected and uninfected individuals after treatment with albendazole.
Abundance in Group 1: decreased abundance in 2008 - Infected
Revision editor(s): KateRasheed, WikiWorks
Experiment 12
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 2010 - Treated with albendazole and dewormed
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Table S5
Description: Differential abundance in the gut microbiota between infected and uninfected individuals after treatment with albendazole and deworming (deworming effect)
Abundance in Group 1: decreased abundance in 2008 - Infected
| NCBI | Quality Control | Links |
|---|---|---|
| Sphingobacterium | ||
| unclassified Deltaproteobacteria | ||
| Clostridium_XVIIIClostridium_XVIII | ||
| Butyricimonas | ||
| Xylanibacter | ||
| unclassified Sutterellaceae | ||
| Leuconostoc |
Revision editor(s): KateRasheed, WikiWorks
Experiment 13
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 2010 - Self cleared individuals
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 2008 refers to individuals with STH infection.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Table S5
Description: Differentially abundant taxa among self-cleared individuals and uninfected individuals.
Abundance in Group 1: decreased abundance in 2008 - Infected
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bacteroides | ||
| Parabacteroides | ||
| Porphyromonadaceae | ||
| Synergistales | ||
| Synergistia | ||
| Synergistota | ||
| Olsenella |
Revision editor(s): KateRasheed, WikiWorks
Experiment 14
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Uninfected (Zero STH infection)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Heavy Infected (Ascaris)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Heavy Infected (Ascaris) refers to individuals heavily infected with Ascaris helminth infection in 2008.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 43
- 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
- Richness Number of species
- increased
Signature 1
Source: Table S5
Description: Differentially abundant taxa among uninfected individuals and individuals heavily infected with Ascaris helminth.
Abundance in Group 1: increased abundance in Heavy Infected (Ascaris)
Revision editor(s): KateRasheed, WikiWorks
Signature 2
Source: Table S5
Description: Differentially abundant taxa among uninfected individuals and individuals heavily infected with Ascaris helminth.
Abundance in Group 1: decreased abundance in Heavy Infected (Ascaris)
Revision editor(s): KateRasheed, WikiWorks
Experiment 15
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Heavy Infected (Necator)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Heavy Infected (Necator) refers to individuals heavily infected with Necator helminth infection in 2008.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Table S5
Description: Differentially abundant taxa among Indonesia uninfected individuals and individuals heavily infected with Necator helminth in 2008.
Abundance in Group 1: increased abundance in Heavy Infected (Necator)
Revision editor(s): KateRasheed, WikiWorks
Signature 2
Source: Table S5
Description: Differentially abundant taxa among Indonesia uninfected individuals and individuals heavily infected with Necator helminth in 2008.
Abundance in Group 1: decreased abundance in Heavy Infected (Necator)
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadales | ||
| Lachnospiraceae | ||
| Actinomyces | ||
| Actinomycetales | ||
| Actinomycetaceae | ||
| Tissierellia | ||
| unclassified Bacteroidales |
Revision editor(s): KateRasheed, WikiWorks
Experiment 16
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Heavy Infected (Trichuris)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Heavy Infected (Trichuris) refers to individuals heavily infected with Trichuris helminth infection in 2008.
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Table S5
Description: Differentially abundant taxa among Indonesia uninfected individuals and individuals heavily infected with Trichuris helminth in 2008.
Abundance in Group 1: increased abundance in Heavy Infected (Trichuris)
Revision editor(s): KateRasheed, WikiWorks
Signature 2
Source: Table S5
Description: Differentially abundant taxa among Indonesia uninfected individuals and individuals heavily infected with Trichuris helminth in 2008.
Abundance in Group 1: decreased abundance in Heavy Infected (Trichuris)
| NCBI | Quality Control | Links |
|---|---|---|
| Klebsiella | ||
| Lachnospiraceae incertae sedis | ||
| Rhodococcus | ||
| Sphingobacteriaceae | ||
| Escherichia/Shigella sp. |
Revision editor(s): KateRasheed, WikiWorks
Experiment 17
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Self-cleared
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Still-Infected
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Still-infected refers to baseline (2008) untreated, infected individuals who remained infected in 2010.
- 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
- 26
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Table S5
Description: Differentially abundant taxa between baseline (2008) untreated, infected individuals who remained infected in 2010, and those who were free from the infection in 2010 without anthelmintic treatment (“self-cleared”).
Abundance in Group 1: increased abundance in Still-Infected
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister | ||
| Clostridium XIVaClostridium XIVa |
Revision editor(s): KateRasheed, WikiWorks
Signature 2
Source: Table S5
Description: Differentially abundant taxa between baseline (2008) untreated, infected individuals who remained infected in 2010, and those who were free from the infection in 2010 without anthelmintic treatment (“self-cleared”).
Abundance in Group 1: decreased abundance in Still-Infected
Revision editor(s): KateRasheed, WikiWorks
