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

Study information

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

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

37737154

DOI Digital object identifier for electronic documents.

10.1186/s12866-023-03020-7

URI

Authors

Luan M, Niu M, Yang P, Han D, Zhang Y, Li W, He Q, Zhao Y, Mao B, Chen J, Mou K, Li P

Journal

BMC microbiology

Year

2023

Keywords:

Gut microbiota, Metagenomic sequencing, Vitiligo

BACKGROUND: Vitiligo has been correlated with an abnormal gut microbiota. We aimed to systematically identify characteristics of the gut microbial compositions, genetic functions, and potential metabolic features in patients with non-segmental vitiligo. METHODS: Twenty-five patients with non-segmental vitiligo and 25 matched healthy controls (HCs) were enrolled. Metagenomic sequencing and bioinformatic analysis were performed to determine the gut microbiota profiles. Differences in gut microbiota diversity and composition between patients with vitiligo and HCs were analyzed. Gene functions and gut metabolic modules were predicted with the Kyoto Encyclopedia of Gene and Genomes (KEGG) and MetaCyc databases. RESULTS: Compared with HCs, alpha diversity of intestinal microbiome in vitiligo patients was significantly reduced. At the species level, the relative abundance of Staphylococcus thermophiles was decreased, and that of Bacteroides fragilis was increased in patients with vitiligo compared with those of the HCs. Linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed representative microbial markers of Lachnospiraceae_bacterium_BX3, Massilioclostridium_coli, TM7_phylum_sp_oral_taxon_348 and Bacteroides_fragilis for patients with vitiligo. KEGG gene function analysis showed that the NOD-like receptor signaling pathway was significantly enriched in patients with vitiligo. Gut metabolic modules (GMMs) analysis showed that cysteine degradation was significantly down-regulated, and galactose degradation was up-regulated in patients with vitiligo. A panel of 28 microbial features was constructed to distinguish patients with vitiligo from HCs. CONCLUSIONS: The gut microbial profiles and genetic functions of patients with vitiligo were distinct from those of the HCs. The identified gut microbial markers may potentially be used for earlier diagnosis and treatment targets.

Experiment 1

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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

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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 Control	Links
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

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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 Control	Links
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 (ex Bilen et al. 2018)
Alistipes ihumii
Holdemanella biformis

Revision editor(s): Deacme