Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis

Study information

Reviewed Marked as Reviewed by Chloe on 2023-4-3

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

28750650

DOI Digital object identifier for electronic documents.

10.1186/s13059-017-1271-6

URI

https://pubmed.ncbi.nlm.nih.gov/28750650/

Authors

Wen C, Zheng Z, Shao T, Liu L, Xie Z, Le Chatelier E, He Z, Zhong W, Fan Y, Zhang L, Li H, Wu C, Hu C, Xu Q, Zhou J, Cai S, Wang D, Huang Y, Breban M, Qin N, Ehrlich SD

Journal

Genome biology

Year

2017

Keywords:

Ankylosing spondylitis, Biomarkers, Human gut microbiome, Pathogenesis

BACKGROUND: The assessment and characterization of the gut microbiome has become a focus of research in the area of human autoimmune diseases. Ankylosing spondylitis is an inflammatory autoimmune disease and evidence showed that ankylosing spondylitis may be a microbiome-driven disease. RESULTS: To investigate the relationship between the gut microbiome and ankylosing spondylitis, a quantitative metagenomics study based on deep shotgun sequencing was performed, using gut microbial DNA from 211 Chinese individuals. A total of 23,709 genes and 12 metagenomic species were shown to be differentially abundant between ankylosing spondylitis patients and healthy controls. Patients were characterized by a form of gut microbial dysbiosis that is more prominent than previously reported cases with inflammatory bowel disease. Specifically, the ankylosing spondylitis patients demonstrated increases in the abundance of Prevotella melaninogenica, Prevotella copri, and Prevotella sp. C561 and decreases in Bacteroides spp. It is noteworthy that the Bifidobacterium genus, which is commonly used in probiotics, accumulated in the ankylosing spondylitis patients. Diagnostic algorithms were established using a subset of these gut microbial biomarkers. CONCLUSIONS: Alterations of the gut microbiome are associated with development of ankylosing spondylitis. Our data suggest biomarkers identified in this study might participate in the pathogenesis or development process of ankylosing spondylitis, providing new leads for the development of new diagnostic tools and potential treatments.

Experiment 1

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Reviewed Marked as Reviewed by Chloe on 2023-4-3

Curated date: 2023/03/15

Curator: Ufuoma Ejite

Revision editor(s): Ufuoma Ejite

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: Ankylosing spondylitis Ankylosing Spondylarthritides,Ankylosing Spondylarthritis,ankylosing spondylitis,Ankylosing Spondyloarthritides,Ankylosing Spondyloarthritis,BECHTEREW DIS,Bechterew Disease,Bechterew's Disease,BECHTEREWS DIS,Bechterews Disease,Bekhterev syndrome,Bekhterev's disease,MARIE STRUEMPELL DIS,Marie Struempell Disease,Marie-Struempell Disease,Marie-Strumpell disease,Rheumatoid Spondylitis,Spondylarthritides, Ankylosing,Spondylarthritis Ankylopoietica,Spondylarthritis, Ankylosing,Spondylitis, Ankylosing,Spondylitis, Rheumatoid,Spondyloarthritides, Ankylosing,Spondyloarthritis, Ankylosing,Ankylosing spondylitis

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: Ankylosing spondylitis patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Ankylosing spondylitis confirmed by calculating the Bath Ankylosing Spondylitis Functional Index (BASFI) and Bath Ankylosing Spondylitis Disease Activity Index (BASDAI)

Group 0 sample size Number of subjects in the control (unexposed) group: 114

Group 1 sample size Number of subjects in the case (exposed) group: 97

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 4 weeks

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: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: Mann-Whitney (Wilcoxon)

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.001

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

Richness Number of species: decreased

Signature 1

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Reviewed Marked as Reviewed by Chloe on 2023-4-3

Curated date: 2023/03/15

Curator: Ufuoma Ejite

Revision editor(s): Chloe, Atrayees, Ufuoma Ejite, Aiyshaaaa

Source: Table S4

Description: Differences of phylogenetic abundance between AS patients and healthy controls

Abundance in Group 1: increased abundance in Ankylosing spondylitis patients

NCBI	Quality Control	Links
Actinomyces
Bifidobacterium
Collinsella
Corynebacterium
Eggerthella
Faecalibacterium
Flavonifractor plautii ATCC 29863
Lachnospiraceae bacterium 7_1_58FAA
Megamonas
Megasphaera
Neisseria
Prevotella
Rothia
Sutterella
Anaerostipes hadrus

Revision editor(s): Chloe, Atrayees, Ufuoma Ejite, Aiyshaaaa

Signature 2

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Reviewed Marked as Reviewed by Chloe on 2023-4-3

Curated date: 2023/03/15

Curator: Ufuoma Ejite

Revision editor(s): Ufuoma Ejite, Chloe, Aiyshaaaa

Source: Table S4

Description: Differences of phylogenetic abundance between AS patients and healthy controls

Abundance in Group 1: decreased abundance in Ankylosing spondylitis patients

NCBI	Quality Control	Links
Butyrivibrio
Citrobacter
Clostridium
Enterobacter
Erysipelotrichaceae
Eubacterium
Fusobacterium
Klebsiella
Lachnoanaerobaculum sp. OBRC5-5
Odoribacter
Parabacteroides
Peptostreptococcaceae
Roseburia
[Bacteroides] pectinophilus ATCC 43243
butyrate-producing bacterium SS3/4
Lachnospiraceae bacterium 6_1_63FAA
Intestinibacter bartlettii DSM 16795
Lachnospiraceae bacterium 9_1_43BFAA
Lachnospiraceae bacterium 3_1_46FAA
Lachnospiraceae bacterium 1_1_57FAA
Campylobacter
Enterococcus
Lachnospiraceae bacterium 5_1_57FAA
Lachnospiraceae bacterium 3_1_57FAA_CT1
Amedibacillus dolichus DSM 3991
Lachnospiraceae bacterium 2 1 46FAA
Clostridioides difficile 70-100-2010
Erysipelotrichaceae bacterium 2_2_44A
Erysipelotrichaceae bacterium 3_1_53

Revision editor(s): Ufuoma Ejite, Chloe, Aiyshaaaa