The gut microbiota and metabolite profiles are altered in patients with spinal cord injury

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Reviewed Marked as Reviewed by Atrayees on 2023-6-5
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

Curated date: 2023/03/14

Curator: Kahvecirem

Revision editor(s): Kahvecirem, Atrayees, Peace Sandy

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

Curated date: 2023/03/26

Curator: Kahvecirem

Revision editor(s): Kahvecirem, Atrayees, Boadiwaa

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)

NCBI Quality ControlLinks
Agathobacter
Barnesiella
Barnesiellaceae
Blautia
Burkholderiales
Butyricicoccus
Clostridia
Clostridiales bacterium
Collinsella
Coprococcus
Coriobacteriaceae
Dorea
Erysipelotrichaceae
Escherichia/Shigella sp.
Eubacterium xylanophilum
Faecalibacterium
Fenollaria
Fusicatenibacter
Holdemanella
Lachnospiraceae bacterium
Marvinbryantia
Parasutterella
Pasteurellales
Roseburia
Ruminococcus
Slackia
Sutterella
Sutterellaceae
[Eubacterium] siraeum
unclassified Clostridia
unclassified Lachnospiraceae
Eubacteriales

Revision editor(s): Kahvecirem, Atrayees, Boadiwaa

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-5

Curated date: 2023/03/26

Curator: Kahvecirem

Revision editor(s): Kahvecirem, Atrayees

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)

NCBI Quality ControlLinks
Anaerofilum
Candidatus Epulonipiscium
Christensenella
Dysgonomonadaceae
Dysgonomonas
Eggerthella
Enterococcaceae
Enterococcus
Flavonifractor
Intestinibacter
Lactobacillaceae
Lactobacillus
Oscillibacter
Sellimonas
Thomasclavelia

Revision editor(s): Kahvecirem, Atrayees

Experiment 2


Reviewed Marked as Reviewed by Atrayees on 2023-6-5

Curated date: 2023/04/01

Curator: Kahvecirem

Revision editor(s): Kahvecirem, Atrayees

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

Curated date: 2023/06/02

Curator: Atrayees

Revision editor(s): Atrayees

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 ControlLinks
Bacillota
Blautia
Faecalibacterium
Escherichia/Shigella sp.
Agathobacter
Collinsella
Dorea
Roseburia
Fusicatenibacter
Holdemanella
Ruminococcus
Clostridia
Lachnospiraceae

Revision editor(s): Atrayees

Signature 2

Needs review

Curated date: 2023/06/02

Curator: Atrayees

Revision editor(s): Atrayees

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 ControlLinks
Eggerthella

Revision editor(s): Atrayees