Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut

From BugSigDB
Needs review
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


Needs review

Curated date: 2024/10/26

Curator: MyleeeA

Revision editor(s): MyleeeA

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

Signature 1

Needs review

Curated date: 2024/10/26

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 2C

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

Abundance in Group 1: increased abundance in High Risk (HR)

NCBI Quality ControlLinks
Enterobacterales
Enterobacteriaceae

Revision editor(s): MyleeeA

Experiment 2


Needs review

Curated date: 2024/10/26

Curator: MyleeeA

Revision editor(s): MyleeeA

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

Signature 1

Needs review

Curated date: 2024/10/26

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 2C

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

Abundance in Group 1: increased abundance in Medium Risk (MR)

NCBI Quality ControlLinks
Cloacibacillus
Clostridium
Plesiomonas

Revision editor(s): MyleeeA

Experiment 3


Needs review

Curated date: 2024/10/26

Curator: MyleeeA

Revision editor(s): MyleeeA

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

Signature 1

Needs review

Curated date: 2024/10/26

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Figure 2C

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

Abundance in Group 1: increased abundance in Low Risk (LR)

NCBI Quality ControlLinks
Aggregatibacter
Erysipelotrichaceae
Erysipelotrichales
Faecalibacterium
Lachnospira
Lachnospiraceae
Oscillospiraceae
Roseburia
RF32RF32
ErysipelotrichiErysipelotrichi

Revision editor(s): MyleeeA

Experiment 4


Needs review

Curated date: 2024/10/26

Curator: MyleeeA

Revision editor(s): MyleeeA

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

Signature 1

Needs review

Curated date: 2024/10/26

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Figure 5

Description: Differentially Abundant taxa between the Low Risk (LR)/Medium Risk (MR) and High Risk (HR) groups Without medication use determined using linear discriminant analysis effect size (LEfSe) analysis.

Abundance in Group 1: increased abundance in High Risk (HR) Without Medication use

NCBI Quality ControlLinks
Actinomycetaceae
Porphyromonas
Sphingobacterium
Actinobaculum
Thermoplasmata
Raoultella
E2E2
Pseudoxanthomonas
Desulfovibrio
Desulfovibrionaceae
Desulfovibrionales
Deltaproteobacteria
Burkholderiales
Betaproteobacteria

Revision editor(s): MyleeeA

Experiment 5


Needs review

Curated date: 2024/10/26

Curator: MyleeeA

Revision editor(s): MyleeeA

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

Needs review

Curated date: 2024/10/26

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Mitsuokella
Plesiomonas
Veillonella

Revision editor(s): MyleeeA

Experiment 6


Needs review

Curated date: 2024/10/26

Curator: MyleeeA

Revision editor(s): MyleeeA

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

Signature 1

Needs review

Curated date: 2024/10/26

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Figure 5

Description: Differentially Abundant taxa between the High Risk (HR)/Medium Risk (MR) and Low Risk (LR) groups Without medication use determined using linear discriminant analysis effect size (LEfSe) analysis

Abundance in Group 1: increased abundance in Low Risk (LR) Without Medication use

NCBI Quality ControlLinks
Faecalibacterium
Peptostreptococcaceae

Revision editor(s): MyleeeA

Experiment 7


Needs review

Curated date: 2024/10/26

Curator: MyleeeA

Revision editor(s): MyleeeA

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

Signature 1

Needs review

Curated date: 2024/10/26

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Figure 6

Description: Differentially Abundant taxa between the Low Risk (LR)/Medium Risk (MR) and High Risk (HR) groups With medication use determined using linear discriminant analysis effect size (LEfSe) analysis.

Abundance in Group 1: increased abundance in High Risk (HR) With Medication use

NCBI Quality ControlLinks
Veillonellaceae

Revision editor(s): MyleeeA

Experiment 8


Needs review

Curated date: 2024/10/26

Curator: MyleeeA

Revision editor(s): MyleeeA

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

Signature 1

Needs review

Curated date: 2024/10/26

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Figure 6

Description: Differentially Abundant taxa between the Low Risk (LR)/High Risk (HR) and Medium Risk (MR) groups With medication use determined using linear discriminant analysis effect size (LEfSe) analysis

Abundance in Group 1: increased abundance in Medium Risk (MR) With Medication use

NCBI Quality ControlLinks
Oscillospira

Revision editor(s): MyleeeA

Experiment 9


Needs review

Curated date: 2024/10/26

Curator: MyleeeA

Revision editor(s): MyleeeA

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

Signature 1

Needs review

Curated date: 2024/10/26

Curator: MyleeeA

Revision editor(s): MyleeeA

Source: Supplementary Figure 6

Description: Differentially Abundant taxa between the High Risk (HR)/Medium Risk (MR) and Low Risk (LR) groups With medication use determined using linear discriminant analysis effect size (LEfSe) analysis

Abundance in Group 1: increased abundance in Low Risk (LR) With Medication use

NCBI Quality ControlLinks
Oscillospiraceae
Lachnospiraceae
Hylemonella
Roseburia
Lysinibacillus
Vagococcus
Lachnospira
Blautia
Aggregatibacter
SMB53SMB53
RF32RF32
02d0602d06
Et0H8Et0H8

Revision editor(s): MyleeeA

Experiment 10


Needs review

Curated date: 2024/10/26

Curator: MyleeeA

Revision editor(s): MyleeeA

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

Needs review

Curated date: 2024/10/26

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Escherichia
Veillonella
Lactobacillaceae
Lactobacillus
Cetobacterium
Serratia

Revision editor(s): MyleeeA

Experiment 11


Needs review

Curated date: 2024/10/26

Curator: MyleeeA

Revision editor(s): MyleeeA

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

Needs review

Curated date: 2024/10/26

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Plesiomonas
RF3RF3
ML615J_28ML615J_28

Revision editor(s): MyleeeA

Experiment 13


Needs review

Curated date: 2024/11/01

Curator: MyleeeA

Revision editor(s): MyleeeA

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

Needs review

Curated date: 2024/11/01

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Pseudomonadota

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/11/01

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Roseburia

Revision editor(s): MyleeeA

Experiment 14


Needs review

Curated date: 2024/10/28

Curator: Princess Ben

Revision editor(s): Princess Ben, MyleeeA

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

Curated date: 2024/10/28

Curator: Princess Ben

Revision editor(s): Princess Ben, MyleeeA

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)

NCBI Quality ControlLinks
Pseudomonadota
Enterobacterales
Enterobacteriaceae
Gammaproteobacteria
Veillonellaceae
Corynebacteriaceae
Corynebacterium
Megasphaera
Streptococcaceae
Streptococcus
Christensenella
Methylobacterium
Delftia
Leuconostoc
Plesiomonas
Anaerostipes

Revision editor(s): Princess Ben, MyleeeA

Signature 2

Needs review

Curated date: 2024/11/01

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Oscillospiraceae
Faecalibacterium
Verrucomicrobiota
Verrucomicrobiales
Akkermansia
Verrucomicrobiaceae
Verrucomicrobiia
Ruminococcus
Roseburia
Sphingomonas
Lachnobacterium

Revision editor(s): MyleeeA

Experiment 15


Needs review

Curated date: 2024/11/01

Curator: MyleeeA

Revision editor(s): MyleeeA

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

Needs review

Curated date: 2024/11/01

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Veillonellaceae

Revision editor(s): MyleeeA

Signature 2

Needs review

Curated date: 2024/11/01

Curator: MyleeeA

Revision editor(s): MyleeeA

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 ControlLinks
Lachnospiraceae
Oscillospiraceae
Faecalibacterium
Roseburia

Revision editor(s): MyleeeA