Chronic fatigue syndrome patients have alterations in their oral microbiome composition and function

Study information

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

30204780

DOI Digital object identifier for electronic documents.

10.1371/journal.pone.0203503

URI

Authors

Wang T, Yu L, Xu C, Pan K, Mo M, Duan M, Zhang Y, Xiong H

Journal

PloS one

Year

2018

Host-microbe interactions have been implicated in the pathogenesis of chronic fatigue syndrome (CFS), but whether the oral microbiome is altered in CFS patients is unknown. We explored alterations of the oral microbiome in Chinese Han CFS patients using 16S rRNA gene sequencing and alterations in the functional potential of the oral microbiome using PICRUSt. We found that Shannon and Simpson diversity indices were not different in CFS patients compared to healthy controls, but the overall oral microbiome composition was different (MANOVA, p < 0.01). CFS patients had a higher relative abundance of Fusobacteria compared with healthy controls. Further, the genera Leptotrichia, Prevotella, and Fusobacterium were enriched and Haemophilus, Veillonella, and Porphyromonas were depleted in CFS patients compared to healthy controls. Functional analysis from inferred metagenomes showed that bacterial genera altered in CFS patients were primarily associated with amino acid and energy metabolism. Our findings demonstrate that the oral microbiome in CFS patients is different from healthy controls, and these differences lead to shifts in functional pathways with implications for CFS pathogenesis. These findings increase our understanding of the relationship between the oral microbiota and CFS, which will advance our understanding of CFS pathogenesis and may contribute to future improvements in treatment and diagnosis.

Experiment 1

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Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, LGeistlinger, Victoria

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: Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Chronic fatigue syndrome CFS,chronic fatigue syndrome,myalgic encephalitis,myalgic encephalomeyelitis/chronic fatigue syndrome,Myalgic Encephalomyelitis,myalgic encephalomyelitis,Postviral fatigue syndrome,systemic exertion intolerance disease,Chronic fatigue syndrome

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: Chronic Fatigue patients

Group 0 sample size Number of subjects in the control (unexposed) group: 45

Group 1 sample size Number of subjects in the case (exposed) group: 46

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 2 months for healthy control only

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

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 3

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

Alpha Diversity

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

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

Signature 1

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Reviewed Marked as Reviewed by Fatima on 2021/06/29

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): Fatima, WikiWorks

Source: Figure 3b

Description: LEfSe analysis identified the most differentially abundant taxa between healthy controls and CFS patients.Only taxa with LDA > 3 are shown.

Abundance in Group 1: increased abundance in Chronic Fatigue patients

NCBI	Quality Control	Links
Alkalibacillus
Bacteroidaceae
Bacteroides
Campylobacter
Campylobacteraceae
Campylobacterales
Campylobacterota
Fusobacteriota
Fusobacteriaceae
Fusobacteriales
Fusobacteriia
Fusobacterium
Gemella

Revision editor(s): Fatima, WikiWorks

Signature 2

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Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks

Source: Figure 3b

Description: LEfSe analysis identified the most differentially abundant taxa between healthy controls and CFS patients.Only taxa with LDA > 3 are shown.

Abundance in Group 1: decreased abundance in Chronic Fatigue patients

NCBI	Quality Control	Links
Gammaproteobacteria
Veillonellaceae
Negativicutes
Selenomonadales
Veillonella
Haemophilus
Pasteurellaceae
Pasteurellales
Porphyromonadaceae
Porphyromonas
Moraxella
Azotobacter group
Pseudomonas

Revision editor(s): WikiWorks