The gut microbiota in conventional and serrated precursors of colorectal cancer
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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
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): LGeistlinger, WikiWorks, ChiomaBlessing
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
- Colorectal adenoma adenoma of large bowel,adenoma of large intestine,adenoma of the large bowel,adenoma of the large intestine,colorectal adenoma,colorectum adenoma,large bowel adenoma,large intestine adenoma,Colorectal adenoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- conventional adenoma cases
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- conventional adenoma cases; those with at least one tubular or tubulovillous adenoma and no other polyps of hyperplastic, SSA, or unclassified histology. HP cases; having at least one HP, with no other polyps of tubular, tubulovillous, SSA, or unclassified histology. SSA cases; having at least one SSA, with or without HP(s), and with no other polyps of tubular, tubulovillous, or unclassified histology. Proximal polyps; polyps located in the cecum, ascending colon, hepatic flexure, transverse colon, or splenic flexure. Distal polyps; polyps located in the descending colon, sigmoid colon, or rectum.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 323
- Group 1 sample size Number of subjects in the case (exposed) group
- 144
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- NYU included who had not been on long-term antibiotic treatment
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).
- raw counts
- Statistical test
- DESeq2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- 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
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Table 2 + Supplemental Table S5 + S3+ S4
Description: Differential abundance was detected by the “DESeq” function in the DESeq2 package. All classes and genera with an FDR-adjusted q < 0.10 are included in the table. Models were adjusted for sex, age, study, and categorical BMI. See Additional file 1: Table S5 for comparisons at the phylum, order, and family level
Abundance in Group 1: increased abundance in conventional adenoma cases
Revision editor(s): WikiWorks
Signature 2
Source: Table 2 + Supplemental Table S5 + S3+ S4
Description: Differential abundance was detected by the “DESeq” function in the DESeq2 package. All classes and genera with an FDR-adjusted q < 0.10 are included in the table. Models were adjusted for sex, age, study, and categorical BMI. See Additional file 1: Table S5 for comparisons at the phylum, order, and family level
Abundance in Group 1: decreased abundance in conventional adenoma cases
| NCBI | Quality Control | Links |
|---|---|---|
| Coprobacillus | ||
| Cyanobacteriota |
Revision editor(s): WikiWorks
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Hyperplastic Polyp Hp,hyperplastic polyp,metaplastic polyp,MP,Hyperplastic Polyp,hyperplastic Polyp
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- hyperplastic polyp cases
- Group 1 sample size Number of subjects in the case (exposed) group
- 40
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table 2 + Supplemental Table S5 + S3+ S4
Description: Differential abundance was detected by the “DESeq” function in the DESeq2 package. All classes and genera with an FDR-adjusted q < 0.10 are included in the table. Models were adjusted for sex, age, study, and categorical BMI. See Additional file 1: Table S5 for comparisons at the phylum, order, and family level
Abundance in Group 1: increased abundance in hyperplastic polyp cases
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes | ||
| Lacticaseibacillus zeae |
Revision editor(s): WikiWorks
Signature 2
Source: Table 2 + Supplemental Table S5 + S3+ S4
Description: Differential abundance was detected by the “DESeq” function in the DESeq2 package. All classes and genera with an FDR-adjusted q < 0.10 are included in the table. Models were adjusted for sex, age, study, and categorical BMI. See Additional file 1: Table S5 for comparisons at the phylum, order, and family level
Abundance in Group 1: decreased abundance in hyperplastic polyp cases
| NCBI | Quality Control | Links |
|---|---|---|
| Gammaproteobacteria | ||
| Coprobacillus | ||
| Enterobacterales |
Revision editor(s): WikiWorks
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Colon Sessile Serrated Adenoma/Polyp colon sessile serrated adenoma,colon sessile serrated adenoma/polyp,colon sessile serrated polyp,colon SSA,colon SSA/P,colon SSP,sessile serrated adenoma,Colon Sessile Serrated Adenoma/Polyp,colon Sessile Serrated Adenoma/Polyp
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Sessile serrated adenoma cases
- Group 1 sample size Number of subjects in the case (exposed) group
- 33
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table 2 + Supplemental Table S5 + S3+ S4
Description: Differential abundance was detected by the “DESeq” function in the DESeq2 package. All classes and genera with an FDR-adjusted q < 0.10 are included in the table. Models were adjusted for sex, age, study, and categorical BMI. See Additional file 1: Table S5 for comparisons at the phylum, order, and family level
Abundance in Group 1: decreased abundance in Sessile serrated adenoma cases
| NCBI | Quality Control | Links |
|---|---|---|
| Erysipelotrichia | ||
| Gammaproteobacteria |
Revision editor(s): WikiWorks
Experiment 4
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): LGeistlinger, WikiWorks, ChiomaBlessing
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Colorectal adenoma adenoma of large bowel,adenoma of large intestine,adenoma of the large bowel,adenoma of the large intestine,colorectal adenoma,colorectum adenoma,large bowel adenoma,large intestine adenoma,Colorectal adenoma
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Proximal conventional adenoma cases
- Group 1 sample size Number of subjects in the case (exposed) group
- 87
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Supplemental Table S6 + S3
Description: Differentially abundant taxa (phylum‐OTU level) between controls and proximal or distal conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10 are included in the table.
Abundance in Group 1: increased abundance in Proximal conventional adenoma cases
Revision editor(s): WikiWorks
Signature 2
Source: Supplemental Table S6 + S3
Description: Differentially abundant taxa (phylum‐OTU level) between controls and proximal or distal conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10 are included in the table.
Abundance in Group 1: decreased abundance in Proximal conventional adenoma cases
| NCBI | Quality Control | Links |
|---|---|---|
| Coprobacillus |
Revision editor(s): WikiWorks
Experiment 5
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): LGeistlinger, WikiWorks, ChiomaBlessing
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Distal conventional adenoma cases
- Group 1 sample size Number of subjects in the case (exposed) group
- 55
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Supplemental Table S6 + S3
Description: Differentially abundant taxa (phylum‐OTU level) between controls and proximal or distal conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10, are included in the table.
Abundance in Group 1: decreased abundance in Distal conventional adenoma cases
| NCBI | Quality Control | Links |
|---|---|---|
| Christensenellaceae | ||
| Clostridia | ||
| Clostridiaceae | ||
| Clostridium | ||
| Enterococcaceae | ||
| Enterococcus | ||
| Mollicutes | ||
| Synergistota | ||
Revision editor(s): WikiWorks, Lwaldron, Fatima, Merit, Davvve
Experiment 6
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): LGeistlinger, WikiWorks, ChiomaBlessing
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non-advanced conventional adenoma cases
- Group 1 sample size Number of subjects in the case (exposed) group
- 121
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Supplemental Table S6 + S3
Description: Differentially abundant taxa (phylum‐OTU level) between controls and non‐advanced or advanced conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10 are included in the table.
Abundance in Group 1: increased abundance in Non-advanced conventional adenoma cases
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Odoribacter | ||
| Bacilli | ||
| Lactobacillales | ||
| Lacticaseibacillus zeae | ||
| Streptococcaceae | ||
| Streptococcus | ||
| Dorea | ||
| Veillonellaceae | ||
| Sutterella | ||
| Alcaligenaceae | ||
| Phascolarctobacterium |
Revision editor(s): WikiWorks
Experiment 7
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): LGeistlinger, WikiWorks, ChiomaBlessing
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- advanced conventional adenoma cases
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Supplemental Table S7 + S3
Description: Differentially abundant taxa (phylum‐OTU level) between controls and non‐advanced or advanced conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10 are included in the table.
Abundance in Group 1: increased abundance in advanced conventional adenoma cases
Revision editor(s): WikiWorks
Signature 2
Source: Supplemental Table S7 + S3
Description: Differentially abundant taxa (phylum‐OTU level) between controls and non‐advanced or advanced conventional adenoma cases, as detected by the DESeq function in the DESeq2 package. Models were adjusted for age, sex, categorical BMI, and study. All taxa with an FDR‐adjusted q<0.10 are included in the table.
Abundance in Group 1: decreased abundance in advanced conventional adenoma cases
| NCBI | Quality Control | Links |
|---|---|---|
| Barnesiellaceae | ||
| Cyanobacteriota | ||
| Christensenellaceae | ||
| Lachnobacterium | ||
| Lachnospira | ||
| Alphaproteobacteria |
Revision editor(s): WikiWorks
