Widespread protein lysine acetylation in gut microbiome and its alterations in patients with Crohn's disease

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Needs review

Curated date: 2023/03/11

Curator: Sophy

Revision editor(s): Sophy

Subjects

Location of subjects: Canada

Host species Species from which microbiome was sampled (if applicable): 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

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

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
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

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

Mann-Whitney (Wilcoxon)

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

Needs review

Curated date: 2023/03/11

Curator: Sophy

Revision editor(s): Sophy, Chloe

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	Links
Megamonas
Megamonas funiformis
Roseburia inulinivorans
Selenomonadaceae
Selenomonadales
[Eubacterium] eligens ATCC 27750

Revision editor(s): Sophy, Chloe

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Reviewed Marked as Reviewed by Chloe on 2023-3-20

Curated date: 2023/03/11

Curator: Sophy

Revision editor(s): Sophy

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	Links
Bacilli

Revision editor(s): Sophy

Signature 3

Needs review

Curated date: 2023/03/11

Curator: Sophy

Revision editor(s): Sophy, Chloe

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

NCBI	Links
Bacteroides uniformis
Dorea
Prevotella micans
Streptococcus
Thomasclavelia spiroformis ⚠
Blautia hansenii
Streptococcaceae
Bacilli
Roseburia faecis
Lactobacillales
Roseburia intestinalis
Thomasclavelia ⚠

Revision editor(s): Sophy, Chloe

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Reviewed Marked as Reviewed by Chloe on 2023-3-20

Curated date: 2023/03/11

Curator: Sophy

Revision editor(s): Sophy, Chloe

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	Links
Bacilli
Ruminococcus

Revision editor(s): Sophy, Chloe

Signature 5

Flag for review

Reviewed Marked as Reviewed by Chloe on 2023-3-20

Curated date: 2023/03/11

Curator: Sophy

Revision editor(s): Sophy

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: decreased abundance in pediatric crohn's disease

NCBI	Links
Megamonas
Megamonas funiformis
Roseburia inulinivorans
Selenomonadaceae
Selenomonadales
[Eubacterium] eligens ATCC 27750

Revision editor(s): Sophy

Signature 6