The alteration of gut microbiome and metabolism in amyotrophic lateral sclerosis patients/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-6
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
- 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
- Amyotrophic lateral sclerosis ALS,ALS (Amyotrophic Lateral Sclerosis),ALS - Amyotrophic lateral sclerosis,amyotrophic lateral sclerosis,Amyotrophic lateral sclerosis (disorder),Amyotrophic Lateral Sclerosis With Dementia,Amyotrophic Lateral Sclerosis, Guam Form,Amyotrophic lateral sclerosis, Parkinsonism/Dementia complex of Guam,Amyotrophic Lateral Sclerosis-Parkinsonism/dementia Complex 1,AMYOTROPHIC SCLEROSIS,Bulbar motor neuron disease,Charcot disease,Dementia With Amyotrophic Lateral Sclerosis,Disease, Lou-Gehrigs,Gehrig Disease,Gehrig's Disease,GEHRIGS DIS,Gehrigs Disease,Guam Form of Amyotrophic Lateral Sclerosis,Lateral Scleroses, Amyotrophic,LOU GEHRIG DIS,Lou Gehrig Disease,Lou Gehrig disease,Lou Gehrig's Disease,Lou Gehrig's disease,LOU GEHRIGS DIS,Lou Gehrigs Disease,Lou-Gehrigs Disease,MOTOR NEURON DIS AMYOTROPHIC LATERAL SCLEROSIS,Motor Neuron Disease, Amyotrophic Lateral Sclerosis,Motor neuron disease, bulbar,motor neuron disease, bulbar,Sclerosis, Amyotrophic Lateral,Amyotrophic lateral sclerosis
- 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
- Amyotrophic lateral sclerosis - ALS patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients clinically diagnosed with probably or definite ALS according to the revised El Escorial criteria in the neurology department.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- 4
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-6
Source: Figure 2F
Description: The bar chart shows the biomarkers with diferential abundance between the groups and larger than the preset value (LDA score >4, p<0.05). The LDA score indicates the extent to which the corresponding group is affected by the diferential microbes.
Abundance in Group 1: increased abundance in Amyotrophic lateral sclerosis - ALS patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidales | ||
| Bacteroidia | ||
| Bacteroidota | ||
| Porphyromonadaceae |
Revision editor(s): Fatima, Peace Sandy
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-1-6
Source: Figure 2F
Description: The bar chart shows the biomarkers with diferential abundance between the groups and larger than the preset value (LDA score >4, p<0.05). The LDA score indicates the extent to which the corresponding group is affected by the diferential microbes.
Abundance in Group 1: decreased abundance in Amyotrophic lateral sclerosis - ALS patients
| NCBI | Quality Control | Links |
|---|---|---|
| Megamonas | ||
| Negativicutes | ||
| Selenomonadales | ||
| Veillonellaceae | ||
| unclassified Megamonas |
Revision editor(s): Fatima, Peace Sandy
