Abundance alteration of nondominant species in fecal-associated microbiome of patients with SAPHO syndrome

Study information

Reviewed Marked as Reviewed by Peace Sandy on 2024-3-26

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

34053449

DOI Digital object identifier for electronic documents.

https://doi.org/10.1186/s12866-021-02221-2

URI

Authors

Zhen J, Sun Y, Zhao P, Li C, Wang H, Li Y, Zhao L, Wang L, Huang G, Xu A

Journal

BMC microbiology

Year

2021

Keywords:

Biomarkers, Fecal-associated microbiome, SAPHO syndrome

BACKGROUND: SAPHO syndrome is a group of symptoms consisting of synovitis, acne, pustulosis, hyperostosis and osteosis. There is no specific laboratory index assist in the diagnosis of SAPHO because of its highly heterogeneous clinical manifestations. Pathogenic microorganisms had been identified in biopsies of some SAPHO cases and particular gene mutations were also linked to the occurrence of SAPHO. It is largely unknown whether intestinal microbiome plays a role in pathogenesis of SAPHO. To explore the intestinal microbiome structure of SAPHO syndrome, fecal samples from 17 SAPHO patients and 14 healthy controls (HC) were collected for 16S rDNA sequencing. RESULTS: Our results showed that there was no significant difference in alpha indexes and beta diversity between SAPHO and HC samples, while there were 14 operational taxonomic units (OTUs) in the Wilcoxon rank-sum test and 42 OTUs in the MetagenomeSeq analysis showed significant difference in distribution between the SAPHO and HC groups, 3 of which in Firmicutes were also observed in the random forest analysis and used to construct a receiver operating characteristic curve to evaluate the diagnostic value, the area under the curve was 0.86. CONCLUSION: Fecal-associated microbiome in the SAPHO samples was characterized by the alteration in abundance of some nondominant species, and the 3 selected OTUs in Firmicutes could serve as candidate biomarkers for SAPHO syndrome diagnosis.

Experiment 1

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Reviewed Marked as Reviewed by Peace Sandy on 2024-3-26

Curated date: 2024/03/06

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin, Peace Sandy

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: SAPHO syndrome Acquired Hyperostosis Syndrome,acquired hyperostosis syndrome,PPHS,Pustulo-psoriatic hyperostotic Spondyloarthritis,SAPHO syndrome,synovitis acne pustulosis hyperostosis osteitis,synovitis, acne, Pustlosis, hyperostosis, and osteomyelitis,Synovitis, acne, pustulosis palmaris, hyperostosis, osteomyelitis syndrome,synovitis, acne, pustulosis palmaris, hyperostosis, osteomyelitis syndrome,synovitis, acne, pustulosis, hyperostosis, and osteitis syndrome,synovitis-acne-pustulosis-hyperostosis-osteitis syndrome,sAPHO syndrome

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy control group

Group 1 name Corresponds to the case (exposed) group for case-control studies: SAPHO syndrome Patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: SAPHO (synovitis, acne, pustulosis, hyperostosis and osteosis) syndrome, The main features of SAPHO syndrome consist of cutaneous and osteoarticular manifestations, the latter more often affects the anterior chest wall and has a typical radiologic finding called the “bull’s head sign”

Group 0 sample size Number of subjects in the control (unexposed) group: 14

Group 1 sample size Number of subjects in the case (exposed) group: 17

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 3months

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-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).: relative abundances

Statistical test: LEfSe

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)?: No

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Chao1 Abundance-based estimator of species richness: unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness: unchanged

Richness Number of species: unchanged

Signature 1

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Reviewed Marked as Reviewed by Peace Sandy on 2024-3-26

Curated date: 2024/03/08

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin, Peace Sandy

Source: Figure 3

Description: Distingushing taxa identified in the HC and SAPHO groups using LEfSe analysis. (a) Cladogram and (b) LDA score bar chart constructed using the LEfSe method. HC, healthy control; SAPHO, SAPHO syndrome

Abundance in Group 1: increased abundance in SAPHO syndrome Patients

NCBI	Quality Control	Links
Bacillales
Gemella

Revision editor(s): Omojokunoluwatomisin, Peace Sandy

Signature 2

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Reviewed Marked as Reviewed by Peace Sandy on 2024-3-26

Curated date: 2024/03/09

Curator: Omojokunoluwatomisin

Revision editor(s): Omojokunoluwatomisin, Peace Sandy

Source: Figure 3

Description: Distingushing taxa identified in the HC and SAPHO groups using LEfSe analysis. (a) Cladogram and (b) LDA score bar chart constructed using the LEfSe method. HC, healthy control; SAPHO, SAPHO syndrome

Abundance in Group 1: decreased abundance in SAPHO syndrome Patients

NCBI	Quality Control	Links
Oscillospiraceae
Ruminiclostridium

Revision editor(s): Omojokunoluwatomisin, Peace Sandy