The gut microbiota and metabolite profiles are altered in patients with spinal cord injury/Experiment 1
From BugSigDB
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
