Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut
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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.
URI
Authors
Zeng X, Gao X, Peng Y, Wu Q, Zhu J, Tan C, Xia G, You C, Xu R, Pan S, Zhou H, He Y, Yin J
Journal
Frontiers in cellular and infection microbiology
Year
2019
Keywords:
16S rRNA, fecal, microbiota, short-chain fatty acids, stroke risk
Objective: Gut microbiota is a newly identified risk factor for stroke, and there are no large prospective studies linking the baseline gut microbiome to long-term risk of stroke. We present here the correlation between the gut microbiota and stroke risk in people with no prior stroke history. Methods: A total of 141 participants aged ≥60 years without prior history of stroke were recruited and divided into low-risk, medium-risk, and high-risk groups based on known risk factors and whether they were suffering from chronic diseases. The composition of their gut microbiomes was compared using 16S rRNA gene amplicon next-generation-sequencing and Quantitative Insights into Microbial Ecology (QIIME) analysis. Levels of fecal short-chain fatty acids were measured using gas chromatography. Results: We found that opportunistic pathogens (e.g., Enterobacteriaceae and Veillonellaceae) and lactate-producing bacteria (e.g., Bifidobacterium and Lactobacillus) were enriched, while butyrate-producing bacteria (e.g., Lachnospiraceae and Ruminococcaceae) were depleted, in the high-risk group compared to the low-risk group. Butyrate concentrations were also lower in the fecal samples obtained from the high-risk group than from the low-risk group. The concentrations of other short-chain fatty acids (e.g., acetate, propionate, isobutyrate, isovalerate, and valerate) in the gut were comparable among the three groups. Conclusion: Participants at high risk of stroke were characterized by the enrichment of opportunistic pathogens, low abundance of butyrate-producing bacteria, and reduced concentrations of fecal butyrate. More researches into the gut microbiota as a risk factor in stroke should be carried out in the near future.
Experiment 1
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 Medium Risk (MR)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Risk (HR)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The high-risk (HR) group comprised of participants with three or more risk factors. 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
- 105
- Group 1 sample size Number of subjects in the case (exposed) group
- 36
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- 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
Experiment 2
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Risk (LR) and High Risk (HR)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Medium Risk (MR)
- 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 and chronic diseases. 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
- 87
- Group 1 sample size Number of subjects in the case (exposed) group
- 54
Lab analysis
Statistical Analysis
Alpha Diversity
- 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
Experiment 3
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High Risk (HR) and Medium Risk (MR)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low Risk (LR)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Low-risk (LR) group comprised of participants with less than three risk factors without chronic diseases. 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
- 90
- Group 1 sample size Number of subjects in the case (exposed) group
- 51
Lab analysis
Statistical Analysis
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
Alpha Diversity
- 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
Experiment 4
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Risk (LR) and Medium Risk (MR) Without Medication use
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Risk (HR) Without Medication use
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The high-risk (HR) group comprised of participants with three or more risk factors 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
- 56
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
- 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
Experiment 5
Differences from previous experiment shown
Subjects
- 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
Lab analysis
Statistical Analysis
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
Experiment 6
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High Risk (HR) and Medium Risk (MR) Without Medication use
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low Risk (LR) Without Medication use
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Low-risk (LR) group comprised of participants with less than three risk factors without chronic diseases and 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
- 19
- Group 1 sample size Number of subjects in the case (exposed) group
- 44
- 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
Statistical Analysis
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
Experiment 7
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Risk (LR) and Medium Risk (MR) With Medication use
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Risk (HR) With Medication use
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The high-risk (HR) group comprised of participants with three or more risk factors with 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
- 49
- Group 1 sample size Number of subjects in the case (exposed) group
- 29
- 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
Statistical Analysis
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
Experiment 8
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Risk (LR) and High Risk (HR) With Medication use
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Medium Risk (MR) With 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 with 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
- 36
- Group 1 sample size Number of subjects in the case (exposed) group
- 42
- 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
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
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
Experiment 9
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High Risk (HR) and Medium Risk (MR) With Medication use
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low Risk (LR) With Medication use
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Low-risk (LR) group comprised of participants with less than three risk factors with chronic diseases and 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
- 71
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
- 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
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Experiment 10
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Risk (LR) and Medium Risk (MR)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Risk (HR)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The high-risk (HR) group comprised of participants with three or more risk factors. 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
- 103
- Group 1 sample size Number of subjects in the case (exposed) group
- 36
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
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 2G
Description: Differentially Abundant taxa between the Low Risk (LR)/Medium Risk (MR) and High Risk (HR) groups determined using linear discriminant analysis effect size (LEfSe) analysis. DADA2 sequencing was used.
Abundance in Group 1: increased abundance in High Risk (HR)
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia | ||
| Veillonella | ||
| Lactobacillaceae | ||
| Lactobacillus | ||
| Cetobacterium | ||
| Serratia |
Revision editor(s): MyleeeA
Experiment 11
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Risk (LR) and High Risk (HR)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Medium Risk (MR)
- 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 and chronic diseases. 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
- 87
- Group 1 sample size Number of subjects in the case (exposed) group
- 52
Lab analysis
Statistical Analysis
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 2G
Description: Differentially Abundant taxa between the Low Risk (LR)/High Risk (HR) and Medium Risk (MR) groups determined using linear discriminant analysis effect size (LEfSe) analysis. DADA2 sequencing was used.
Abundance in Group 1: increased abundance in Medium Risk (MR)
| NCBI | Quality Control | Links |
|---|---|---|
| Plesiomonas | ||
| RF3RF3 | ||
| ML615J_28ML615J_28 |
Revision editor(s): MyleeeA
Experiment 12
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High Risk (HR) and Medium Risk (MR)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low Risk (LR)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Low-risk (LR) group comprised of participants with less than three risk factors without chronic diseases. 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
- 88
- Group 1 sample size Number of subjects in the case (exposed) group
- 51
Lab analysis
Statistical Analysis
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 2G
Description: Differentially Abundant taxa between the High Risk (HR)/Medium Risk (MR) and Low Risk (LR) groups determined using linear discriminant analysis effect size (LEfSe) analysis. DADA2 sequencing was used.
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospiraceae | ||
| Faecalibacterium | ||
| Roseburia | ||
| Lachnospiraceae | ||
| Lachnospira | ||
| Anaerostipes |
Revision editor(s): MyleeeA
Experiment 13
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Risk (LR)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Risk (HR)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The high-risk (HR) group comprised of participants with three or more risk factors. 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
- 36
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Kruskall-Wallis
- 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
- Not specified
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: Figure 4E
Description: The relative abundance of butyrate and lactate-producing bacteria in the gut, between the High Risk (HR) and Low Risk (LR) groups.
Abundance in Group 1: increased abundance in High Risk (HR)
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 3E
Description: The relative abundance of butyrate and lactate-producing bacteria in the gut, between the High Risk (HR) and Low Risk (LR) groups.
Abundance in Group 1: decreased abundance in High Risk (HR)
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia |
Revision editor(s): MyleeeA
Experiment 14
Needs review
Differences from previous experiment shown
Subjects
- Group 0 sample size Number of subjects in the control (unexposed) group
- 41
- Group 1 sample size Number of subjects in the case (exposed) group
- 31
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- 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
- 2.0
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
Needs review
Source: Supplementary Figure 1G
Description: Differentially Abundant taxa in the High Risk (HR) compared to Low Risk (LR) groups were determined using linear discriminant analysis effect size (LEfSe) analysis.
Abundance in Group 1: increased abundance in High Risk (HR)
Revision editor(s): Princess Ben, MyleeeA
Signature 2
Source: Supplementary Figure 1G
Description: Differentially Abundant taxa in the High Risk (HR) compared to Low Risk (LR) groups were determined using linear discriminant analysis effect size (LEfSe) analysis.
Abundance in Group 1: decreased abundance in High Risk (HR)
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospiraceae | ||
| Faecalibacterium | ||
| Verrucomicrobiota | ||
| Verrucomicrobiales | ||
| Akkermansia | ||
| Verrucomicrobiaceae | ||
| Verrucomicrobiia | ||
| Ruminococcus | ||
| Roseburia | ||
| Sphingomonas | ||
| Lachnobacterium |
Revision editor(s): MyleeeA
Experiment 15
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Medium Risk (MR)
- 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 and chronic diseases. 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
- 54
Lab analysis
Statistical Analysis
- Statistical test
- Kruskall-Wallis
- 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
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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: Figure 4G
Description: The relative abundance of butyrate and lactate-producing bacteria in the gut, between the Medium Risk (MR) and Low Risk (LR) groups.
Abundance in Group 1: increased abundance in Medium Risk (MR)
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonellaceae |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 3A, B, D and E
Description: The relative abundance of butyrate and lactate-producing bacteria in the gut, between the Medium Risk (MR) and Low Risk (LR) groups.
Abundance in Group 1: decreased abundance in Medium Risk (MR)
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae | ||
| Oscillospiraceae | ||
| Faecalibacterium | ||
| Roseburia |
Revision editor(s): MyleeeA
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