Metagenomic sequencing reveals altered gut microbial compositions and gene functions in patients with non-segmental vitiligo/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by Chloe on 2023-10-30

Curated date: 2023/10/16

Curator: Deacme

Revision editor(s): Chloe, Deacme

Subjects

Location of subjects
China
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
Vitiligo VAMAS6,vitiligo,vitiligo-associated multiple autoimmune disease susceptibility 6,Vitiligo
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
Non-segmental Vitiligo patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Individuals characterized by the progressive loss of skin pigmentation in various areas of the body, resulting in depigmented white patches that is mostly widespread in distribution.
Group 0 sample size Number of subjects in the control (unexposed) group
25
Group 1 sample size Number of subjects in the case (exposed) group
25
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
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
BGISEQ-500 Sequencing

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
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
2.0
Matched on Factors on which subjects have been matched on in a case-control study
age, sex, body mass index

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Signature 1

Reviewed Marked as Reviewed by Chloe on 2023-10-30

Curated date: 2023/10/16

Curator: Deacme

Revision editor(s): Deacme

Source: Figure 2b, 3

Description: Increased abundant species in Non-segmental Vitiligo patients

Abundance in Group 1: increased abundance in Non-segmental Vitiligo patients

NCBI Quality ControlLinks
Agathobacter rectalis
Alistipes putredinis
Amedibacillus dolichus
Anaerobutyricum hallii
Anaerostipes hadrus
Bacteroides fragilis
Bacteroides stercoris
Bacteroides uniformis
Barnesiella intestinihominis
Bifidobacterium pseudocatenulatum
Blautia wexlerae
Escherichia coli
Faecalibacterium prausnitzii
Fusicatenibacter saccharivorans
Lachnospiraceae bacterium OF09-6
Massilioclostridium coli
Megamonas funiformis
Phocaeicola coprocola
Phocaeicola dorei
Phocaeicola plebeius
Phocaeicola vulgatus
Roseburia faecis
Roseburia intestinalis
Roseburia inulinivorans
Ruminococcus bromii
TM7 phylum sp. oral taxon 348
[Ruminococcus] torques
Dialister hominis

Revision editor(s): Deacme

Signature 2

Reviewed Marked as Reviewed by Chloe on 2023-10-30

Curated date: 2023/10/16

Curator: Deacme

Revision editor(s): Deacme

Source: Figure 2d, 3

Description: Decreased abundant species in non-segmental Vitiligo patients

Abundance in Group 1: decreased abundance in Non-segmental Vitiligo patients

NCBI Quality ControlLinks
Actinomyces sp. ICM58
Allisonella histaminiformans
Bacteroides bouchesdurhonensis
Bacteroides eggerthii
Clostridia bacterium
Clostridium sp. AF20-17LB
Coprobacter secundus
Coprococcus comes
Desulfovibrio desulfuricans
Dorea longicatena
Eggerthellaceae bacterium
Isoptericola variabilis
Oscillospiraceae bacterium
Parvimonas micra
Rikenellaceae bacterium
Sellimonas intestinalis
Trueperella pyogenes
Veillonella rogosae
Streptococcus thermophilus
Faecalicatena fissicatena
Faecalimonas umbilicata
Alistipes senegalensis
Butyricimonas faecalis
Neobittarella massiliensis
Alistipes ihumii
Holdemanella biformis

Revision editor(s): Deacme