Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn's disease
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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
- 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 , Mucosa of descending colon 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,Descending colon mucosa,Descending colon mucosa of organ,Descending colon mucous membrane,Descending colon organ mucosa,Mucosa of organ of descending colon,Mucous membrane of descending colon,Organ mucosa of descending colon,Mucosa of descending colon,mucosa of descending colon
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Crohn's disease Colitis, Granulomatous,CROHN DIS,Crohn Disease,Crohn disease,Crohn's associated gastritis,Crohn's disease,Crohn's disease of colon,Crohn's disease of large bowel,CROHNS DIS,Crohns Disease,Enteritis, Granulomatous,Enteritis, Regional,Gastritis Associated with Crohn Disease,Gastritis Associated with Crohn's Disease,granulomatous colitis,Ileitis, Regional,Ileitis, Terminal,Ileocolitis,pediatric Crohn's disease,regional enteritis,crohn disease,crohn's disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy adults
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pediatric crohn's disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- children (<18 years old) diagnosed with crohn’s disease. The exclusion criteria implemented to further refine the cohort in this study include: presence of diabetes mellitus, presence of infectious gastroenteritis within the past 2 months, and irritable bowel syndrome.
- 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
- 10
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks including probiotics use
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Mass spectrometry
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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Signature 1
Source: Figure 5a
Description: Taxonomic alterations of protein acetylation in the pediatric CD microbiome. LEfSe analysis of lysine acetylome-based taxonomic compositions.
Abundance in Group 1: decreased abundance in pediatric crohn's disease
| NCBI | Quality Control | Links |
|---|---|---|
| Megamonas | ||
| Megamonas funiformis | ||
| Roseburia inulinivorans | ||
| Selenomonadaceae | ||
| Selenomonadales | ||
| Lachnospira eligens ATCC 27750 |
Signature 2
Source: Figure 5a
Description: Taxonomic alterations of protein acetylation in the pediatric CD microbiome. acetylome-based. LEfSe analysis of lysine acetylome-based taxonomic compositions.
Abundance in Group 1: increased abundance in pediatric crohn's disease
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli |
Revision editor(s): Sophy
Experiment 2
Subjects
Lab analysis
Statistical Analysis
Signature 1
Source: figure 5b
Description: Taxonomic alterations of protein acetylation in the pediatric CD microbiome. LEfSe analysis of metaproteome-based taxonomic compositions.
Abundance in Group 1: increased abundance in pediatric crohn's disease
| NCBI | Quality Control | Links |
|---|---|---|
| Gammaproteobacteria | ||
| Fungi | ||
| Spirochaetia | ||
| Saccharomycetes | ||
| Saccharomycetales | ||
| Viruses | ||
| Spirochaeta | ||
| Ascomycota | ||
| Anaerotruncus | ||
| Caudoviricetes |
Revision editor(s): Folakunmi
Signature 2
Source: figure 5b
Description: Taxonomic alterations of protein acetylation in the pediatric CD microbiome. LEfSe analysis of metaproteome-based taxonomic compositions.
Abundance in Group 1: decreased abundance in pediatric crohn's disease
Revision editor(s): Folakunmi
Experiment 3
Subjects
Lab analysis
Statistical Analysis
Signature 1
Source: figure 5e
Description: Taxonomic alterations of protein acetylation in the pediatric CD microbiome. LEfSe analysis of the acetylome-to-metaproteome ratios of all quantified taxa in the lysine acetylome data set.
Abundance in Group 1: increased abundance in pediatric crohn's disease
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Ruminococcus |
Revision editor(s): Folakunmi
Experiment 4
Subjects
- 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
- Gut microbiome measurement Gut microbiome measurement,gut microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Metaproteome aliquot of human gut
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Lysine acetylome aliquot of human gut
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- relative abundance of kac levels (for each taxon listed in supplementary data 3) in human fecal microbiome samples lysine acetylome aliquot
- Group 0 sample size Number of subjects in the control (unexposed) group
- 209
- Group 1 sample size Number of subjects in the case (exposed) group
- 209
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Signature 1
Source: figure 2b
Description: Lysine acetylome-to-metaproteome ratios of quantified phyla and genera in human gut microbiome. Comparisons of the percentage of acetylation in lysine acetylomic aliquot with that in metaproteomic aliquot.
Abundance in Group 1: increased abundance in Lysine acetylome aliquot of human gut
| NCBI | Quality Control | Links |
|---|---|---|
| Fusicatenibacter | ||
| Odoribacter | ||
| Lachnoclostridium | ||
| Butyricicoccus | ||
| Bacillota |
Revision editor(s): Folakunmi
Signature 2
Source: figure 2b
Description: Lysine acetylome-to-metaproteome ratios of quantified phyla and genera in human gut microbiome. Comparisons of the percentage of acetylation in lysine acetylomic aliquot with that in metaproteomic aliquot.
Abundance in Group 1: decreased abundance in Lysine acetylome aliquot of human gut
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Butyrivibrio | ||
| Actinomycetota | ||
| Pseudomonadota | ||
| Parasutterella | ||
| Collinsella | ||
| Chordata | ||
| Gemmiger | ||
| Homo |
Revision editor(s): Folakunmi
