Gut microbiome and serum metabolome alterations associated with lactose intolerance (LI): a case‒control study and paired-sample study based on the American Gut Project (AGP)
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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
- Canada
- United Kingdom
- 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
- Lactose intolerance lactase persistence,lactose intolerance,lactose intolerance (disease),LM - lactose malabsorption,Lactose intolerance
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Participants without Lactose Intolerance(Non-LI)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Participants with Lactose Intolerance(LI)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with condition, Lactose intolerance (LI) which is a prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 562
- Group 1 sample size Number of subjects in the case (exposed) group
- 562
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, alcohol consumption measurement, body mass index, diet, geographic area, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Fig 1c
Description: Characteristics and functional alterations in the gut microbiota in AGP.
Abundance in Group 1: increased abundance in Participants with Lactose Intolerance(LI)
Revision editor(s): Nathcynthia, Rahila, Tosin
Signature 2
Source: Fig 1c
Description: Characteristics and functional alterations in the gut microbiota in AGP.
Abundance in Group 1: decreased abundance in Participants with Lactose Intolerance(LI)
Revision editor(s): Nathcynthia, Rahila, Tosin
Experiment 2
Subjects
- Location of subjects
- China
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls (HC)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 41
- Group 1 sample size Number of subjects in the case (exposed) group
- 41
- 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
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Fig 3b
Description: LeFSe analysis reveals significant taxonomic differences between LI Patients and HCs.
Abundance in Group 1: increased abundance in Participants with Lactose Intolerance(LI)
Revision editor(s): Nathcynthia, Rahila, Tosin
Signature 2
Source: Fig 3b
Description: LeFSe analysis reveals significant taxonomic differences between LI Patients and HCs.
Abundance in Group 1: decreased abundance in Participants with Lactose Intolerance(LI)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium sp. AF36-18BH | ||
| Eubacterium sp. | ||
| Faecalibacterium sp. CAG:82 | ||
| Lachnospira eligens | ||
| unclassified Faecalibacterium | ||
| uncultured Ruminococcus sp. |
Revision editor(s): Nathcynthia, Rahila, Tosin
Experiment 3
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Rattus norvegicus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- FMT-Healthy Controls group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FMT-Lactose Intolerance group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats receiving gut microbiota from LI patients .
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not specified
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
Statistical Analysis
- Statistical test
- Spearman Correlation
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- Not specified
- 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
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Text: FMT ANIMAL STUDY- The abundances of the microbial genera such as Escherichia, Shigella, Dielma, Sutterella, and Coprobacillus, were more abundant in the FMT-LI group than in the FMT-HC group
Description: Heatmap based on the relative abundance of the genera between the two groups.
Abundance in Group 1: increased abundance in FMT-Lactose Intolerance group
| NCBI | Quality Control | Links |
|---|---|---|
| Coprobacillus | ||
| Dielma | ||
| Sutterella | ||
| Escherichia/Shigella sp. |
Revision editor(s): Nathcynthia, Tosin
Signature 2
Source: Text: FMT ANIMAL STUDY- The abundances of the microbial genera Faecalibacterium, Fusicatenibacter, and Eubacterium hallii were significantly decreased, in the FMT-LI group than in the FMT-HC group.
Description: Heatmap based on the relative abundance of the genera between the two groups.
Abundance in Group 1: decreased abundance in FMT-Lactose Intolerance group
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerobutyricum hallii | ||
| Faecalibacterium | ||
| Fusicatenibacter |
Revision editor(s): Nathcynthia, Tosin
Experiment 4
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Participants with Lactose intolerance (LI)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with condition, Lactose intolerance (LI) which is a prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 41
- Group 1 sample size Number of subjects in the case (exposed) group
- 41
- 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
Statistical Analysis
- Statistical test
- T-Test
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 3d-I.
Description: Comparison of the relative abundances at the species level according to metagenomic sequencing between the two groups.
Abundance in Group 1: increased abundance in Participants with Lactose intolerance (LI)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides fragilis | ||
| Dialister massiliensis | ||
| Escherichia coli | ||
| Shigella flexneri | ||
| Streptococcus salivarius |
Revision editor(s): Tosin, Nathcynthia
Signature 2
Source: Figure 3d-I
Description: Comparison of the relative abundances at the species level according to metagenomic sequencing between the two groups.
Abundance in Group 1: decreased abundance in Participants with Lactose intolerance (LI)
| NCBI | Quality Control | Links |
|---|---|---|
| Eubacterium sp. |
Revision editor(s): Tosin, Nathcynthia
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Participants with Lactose Intolerance
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with condition, Lactose intolerance (LI) which is prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption.
Lab analysis
Statistical Analysis
- Statistical test
- Spearman Correlation
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- Not specified
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Text: Comparison of metagenomic and metabolomic signatures between LI patients and HCs in China- Compositional analysis revealed significant alterations in microbial abundance at the genus and species levels between LI patients and HCs. At the genus level, there was a greater abundance of Escherichia and Haemophilus in LI patients than in controls
Description: Heatmap based on the relative abundance of the genera between the two groups.
Abundance in Group 1: increased abundance in Participants with Lactose Intolerance
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia |
Revision editor(s): Tosin, Nathcynthia
Signature 2
Source: Text: Comparison of metagenomic and metabolomic signatures between LI patients and HCs in China - Compositional analysis revealed significant alterations in microbial abundance at the genus and species levels between LI patients and HCs. At the genus level, LI patients showed a reduced abundance of Veilonella, Enterococcus, and Erysipelatoclostridium in LI patients than in controls.
Description: Heatmap based on the relative abundance of the genera between the two groups.
Abundance in Group 1: decreased abundance in Participants with Lactose Intolerance
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus | ||
| Thomasclavelia | ||
| Veillonella |
Revision editor(s): Tosin, Nathcynthia
