High-throughput 16S rRNA gene sequencing reveals alterations of intestinal microbiota in myalgic encephalomyelitis/chronic fatigue syndrome patients

Study information

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

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

23791918

DOI Digital object identifier for electronic documents.

10.1016/j.anaerobe.2013.06.002

URI

Authors

Frémont M, Coomans D, Massart S, De Meirleir K

Journal

Anaerobe

Year

2013

Keywords:

Chronic fatigue syndrome, High-throughput sequencing, Intestinal microbiota, Myalgic encephalomyelitis

Human intestinal microbiota plays an important role in the maintenance of host health by providing energy, nutrients, and immunological protection. Intestinal dysfunction is a frequent complaint in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) patients, and previous reports suggest that dysbiosis, i.e. the overgrowth of abnormal populations of bacteria in the gut, is linked to the pathogenesis of the disease. We used high-throughput 16S rRNA gene sequencing to investigate the presence of specific alterations in the gut microbiota of ME/CFS patients from Belgium and Norway. 43 ME/CFS patients and 36 healthy controls were included in the study. Bacterial DNA was extracted from stool samples, PCR amplification was performed on 16S rRNA gene regions, and PCR amplicons were sequenced using Roche FLX 454 sequencer. The composition of the gut microbiota was found to differ between Belgian controls and Norwegian controls: Norwegians showed higher percentages of specific Firmicutes populations (Roseburia, Holdemania) and lower proportions of most Bacteroidetes genera. A highly significant separation could be achieved between Norwegian controls and Norwegian patients: patients presented increased proportions of Lactonifactor and Alistipes, as well as a decrease in several Firmicutes populations. In Belgian subjects the patient/control separation was less pronounced, however some abnormalities observed in Norwegian patients were also found in Belgian patients. These results show that intestinal microbiota is altered in ME/CFS. High-throughput sequencing is a useful tool to diagnose dysbiosis in patients and could help designing treatments based on gut microbiota modulation (antibiotics, pre and probiotics supplementation).

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, Victoria

Subjects

Location of subjects: Belgium

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: 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: Belgian controls

Group 1 name Corresponds to the case (exposed) group for case-control studies: Norweigan controls

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients were diagnosed for CFS according to the clinical criteria of Fukuda et al

Group 0 sample size Number of subjects in the control (unexposed) group: 19

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): 4 weeks

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V5-V6

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Roche454

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): 0.05

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

Signature 1

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

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Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks

Source: table 1

Description: Differentiately abundant mictobiota between Norwegian controls and Belgian controls.

Abundance in Group 1: increased abundance in Norweigan controls

NCBI	Quality Control	Links
Roseburia
Holdemania

Revision editor(s): 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: table 1

Description: Differentiately abundant mictobiota between Norwegian controls and Belgian controls

Abundance in Group 1: decreased abundance in Norweigan controls

NCBI	Quality Control	Links
Bacteroides
Alistipes
Barnesiella
Prevotella
Parabacteroides

Revision editor(s): WikiWorks

Experiment 2

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

Curated date: 2021/01/10

Curator: WikiWorks

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Differences from previous experiment shown

Subjects

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

Group 1 name Corresponds to the case (exposed) group for case-control studies: Norweigan CFS/ME patients

Group 0 sample size Number of subjects in the control (unexposed) group: 17

Group 1 sample size Number of subjects in the case (exposed) group: 25

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: Not specified