Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut/Experiment 5
From BugSigDB
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
- Stroke Acute Cerebrovascular Accident,Acute Cerebrovascular Accidents,Acute Stroke,Acute Strokes,Apoplexy,Apoplexy, Cerebrovascular,Brain Vascular Accident,Brain Vascular Accidents,cerebral infarction,Cerebral Stroke,Cerebral Strokes,Cerebrovascular Accident,cerebrovascular accident,Cerebrovascular accident (disorder),Cerebrovascular accident (disorder) [Ambiguous],CEREBROVASCULAR ACCIDENT, (CVA),cerebrovascular accident, (CVA),Cerebrovascular Accident, Acute,Cerebrovascular Accidents,Cerebrovascular Accidents, Acute,Cerebrovascular Apoplexy,Cerebrovascular Apoplexya,Cerebrovascular Stroke,Cerebrovascular Strokes,CVA,CVA (cerebral vascular accident),CVA (Cerebrovascular Accident),CVA - Cerebrovascular accident,CVA - Cerebrovascular accident unspecified,CVA, CEREBROVASCULAR ACCIDENT,CVA, cerebrovascular accident,CVAs (Cerebrovascular Accident),ischemic stroke,stroke,Stroke and cerebrovascular accident unspecified,Stroke and cerebrovascular accident unspecified (disorder),stroke disorder,Stroke NOS,Stroke NOS (disorder),STROKE SYNDROME,stroke syndrome,Stroke, Acute,Stroke, Cerebral,Stroke, Cerebrovascular,Stroke/CVA - undefined,Strokes,Strokes, Acute,Strokes, Cerebral,Strokes, Cerebrovascular,SYNDROME, STROKE,syndrome, stroke,undetermined stroke,Vascular Accident, Brain,Vascular Accidents, Brain,Stroke
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Risk (LR) and High Risk (HR) Without Medication use
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Medium Risk (MR) Without Medication use
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Medium-risk (MR) group comprised of participants with less than three risk factors, chronic diseases and without medication use. The risk factors Include Hypertension, Atrial fibrillation, Diabetes mellitus, Dyslipidemias, Smoking, Physical inactivity, Overweight and Family history of stroke.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 51
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "medication" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.medication
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Supplementary Figure 5
Description: Differentially Abundant taxa between the Low Risk (LR)/High Risk (HR) and Medium Risk (MR) groups Without medication use determined using linear discriminant analysis effect size (LEfSe) analysis
Abundance in Group 1: increased abundance in Medium Risk (MR) Without Medication use
| NCBI | Quality Control | Links |
|---|---|---|
| Mitsuokella | ||
| Plesiomonas | ||
| Veillonella |
Revision editor(s): MyleeeA
