The gut microbiota and metabolite profiles are altered in patients with spinal cord injury
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Kong G, Zhang W, Zhang S, Chen J, He K, Zhang C, Yuan X, Xie B
Journal
Molecular brain
Year
2023
Keywords:
16S rRNA gene sequencing, Gut microbiota, Spinal cord injury, Untargeted metabolomics
BACKGROUND: Metabolites secreted by the gut microbiota may play an essential role in microbiota-gut-central nervous system crosstalk. In this study, we explored the changes occurring in the gut microbiota and their metabolites in patients with spinal cord injury (SCI) and analyzed the correlations among them. METHODS: The structure and composition of the gut microbiota derived from fecal samples collected from patients with SCI (n = 11) and matched control individuals (n = 10) were evaluated using 16S rRNA gene sequencing. Additionally, an untargeted metabolomics approach was used to compare the serum metabolite profiles of both groups. Meanwhile, the association among serum metabolites, the gut microbiota, and clinical parameters (including injury duration and neurological grade) was also analyzed. Finally, metabolites with the potential for use in the treatment of SCI were identified based on the differential metabolite abundance analysis. RESULTS: The composition of the gut microbiota was different between patients with SCI and healthy controls. At the genus level, compared with the control group, the abundance of UBA1819, Anaerostignum, Eggerthella, and Enterococcus was significantly increased in the SCI group, whereas that of Faecalibacterium, Blautia, Escherichia-Shigella, Agathobacter, Collinsella, Dorea, Ruminococcus, Fusicatenibacter, and Eubacterium was decreased. Forty-one named metabolites displayed significant differential abundance between SCI patients and healthy controls, including 18 that were upregulated and 23 that were downregulated. Correlation analysis further indicated that the variation in gut microbiota abundance was associated with changes in serum metabolite levels, suggesting that gut dysbiosis is an important cause of metabolic disorders in SCI. Finally, gut dysbiosis and serum metabolite dysregulation was found to be associated with injury duration and severity of motor dysfunction after SCI. CONCLUSIONS: We present a comprehensive landscape of the gut microbiota and metabolite profiles in patients with SCI and provide evidence that their interaction plays a role in the pathogenesis of SCI. Furthermore, our findings suggested that uridine, hypoxanthine, PC(18:2/0:0), and kojic acid may be important therapeutic targets for the treatment of this condition.
Experiment 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-5
Subjects
- Location of subjects
- United States of America
- 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
- Spinal cord injury Post-Traumatic Myelopathy,Spinal Cord Contusion,Spinal Cord Injuries,Spinal Cord Laceration,Spinal Cord Transection,Spinal Cord Trauma,Traumatic Myelopathy,Spinal cord injury,spinal cord injury
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy control (without SCI)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- SCI (spinal cord injury)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Spinal cord injury (SCI), which is typically caused by severe trauma such as falls and traffic accidents, is one of the most severe forms of central nervous system injury (CNS).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Patients taking antibiotics or probiotics one month prior to the study were excluded from the SCI group for this experiment.
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)?
- Yes
- 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, geographic area, sex
Alpha Diversity
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-5
Source: Figure 2e
Description: The species with different abundances are listed in the genus, class, phylum, order, and family levels for each group.
Abundance in Group 1: decreased abundance in SCI (spinal cord injury)
Revision editor(s): Kahvecirem, Atrayees, Boadiwaa
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-5
Source: Figure 2e
Description: The species with different abundances are listed in the genus, class, phylum, order, and family levels for each group.
Abundance in Group 1: increased abundance in SCI (spinal cord injury)
Revision editor(s): Kahvecirem, Atrayees
Experiment 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-5
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Venous blood Blood in vein,Portion of venous blood,Venous blood,venous blood
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-5
Source: Figure 2b, 2c
Description: Differential abundance of taxa at phylum and genus level
Abundance in Group 1: decreased abundance in SCI (spinal cord injury)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Blautia | ||
| Faecalibacterium | ||
| Escherichia/Shigella sp. | ||
| Agathobacter | ||
| Collinsella | ||
| Dorea | ||
| Roseburia | ||
| Fusicatenibacter | ||
| Holdemanella | ||
| Ruminococcus | ||
| Clostridia | ||
| Lachnospiraceae |
Revision editor(s): Atrayees
Signature 2
Source: Figure 2b, 2c
Description: Differential abundance of taxa at phylum and genus level
Abundance in Group 1: increased abundance in SCI (spinal cord injury)
| NCBI | Quality Control | Links |
|---|---|---|
| Eggerthella |
Revision editor(s): Atrayees
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