Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Acute Ischemic Stroke and the Subsequent Risk for Poor Functional Outcomes

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Curated date: 2024/10/07

Curator: InimfonD

Revision editor(s): InimfonD

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: Ischemic stroke Ischaemic stroke,Ischemic stroke,ischemic stroke

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy control group (HC)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Acute ischemic stroke (AIS)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: All acute ischemic stroke patients with ischemic stroke onset within 48 hours.

Group 0 sample size Number of subjects in the control (unexposed) group: 92

Group 1 sample size Number of subjects in the case (exposed) group: 140

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): No antibiotics, prebiotics or probiotics taken in the past 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: 2.5

Signature 1

Needs review

Curated date: 2024/10/22

Curator: InimfonD

Revision editor(s): InimfonD

Source: figure 2D

Description: The difference between the gut microbiota of patients with acute ischemic stroke and healthy controls by LEfSE

Abundance in Group 1: decreased abundance in Acute ischemic stroke (AIS)

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Alcaligenaceae
Bacteroidaceae
Lachnospiraceae
Moraxellaceae
Pasteurellaceae
Prevotellaceae

Revision editor(s): InimfonD

Experiment 2

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Curated date: 2024/10/22

Curator: InimfonD

Revision editor(s): InimfonD

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy control/moderate AIS/ severe AIS

Group 1 name Corresponds to the case (exposed) group for case-control studies: Mild acute ischemic stroke

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Ischemic stroke Patients with a NIHSS score < 5 points

Group 0 sample size Number of subjects in the control (unexposed) group: 154

Group 1 sample size Number of subjects in the case (exposed) group: 78

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): No antibiotic, probiotics or prebiotic taken in the past 3 months.

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/10/23

Curator: InimfonD

Revision editor(s): InimfonD

Source: figure 2D

Description: These taxons show an increased abundance in mild acute ischemic patients as compared to the moderate/severe AIS patients and healthy controls by LEfSE

Abundance in Group 1: increased abundance in Mild acute ischemic stroke

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Deferribacteraceae
Helicobacteraceae
Lactobacillaceae
Micrococcaceae
unclassified Bradyrhizobiaceae

Revision editor(s): InimfonD

Experiment 3

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Curated date: 2024/10/23

Curator: InimfonD

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy control/mild AIS/ severe AIS

Group 1 name Corresponds to the case (exposed) group for case-control studies: Moderate acute ischemic stroke

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Ischemic stroke Patients with a NIHSS score between 5 and 15 points

Group 0 sample size Number of subjects in the control (unexposed) group: 185

Group 1 sample size Number of subjects in the case (exposed) group: 47

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/10/23

Curator: InimfonD

Revision editor(s): InimfonD

Source: Figure 2D

Description: These taxons are increased in moderate AIS as compared to healthy control/mild AIS/severe AIS

Abundance in Group 1: increased abundance in Moderate acute ischemic stroke

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Enterobacteriaceae
Enterococcaceae
Erysipelotrichaceae
Methanobacteriaceae
Corynebacteriaceae
Eubacteriaceae

Revision editor(s): InimfonD

Experiment 4

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Curated date: 2024/10/23

Curator: InimfonD

Revision editor(s): InimfonD

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy control/mild AIS/ moderate AIS

Group 1 name Corresponds to the case (exposed) group for case-control studies: Severe acute ischemic stroke

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Ischemic stroke Patients with a NIHSS score >15 points

Group 0 sample size Number of subjects in the control (unexposed) group: 217

Group 1 sample size Number of subjects in the case (exposed) group: 15

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/10/23

Curator: InimfonD

Revision editor(s): InimfonD

Source: figure 2D

Description: These taxa show increase in severe AIS compared to healthy control/mild AIS/moderate AIS by LEfSE

Abundance in Group 1: increased abundance in Severe acute ischemic stroke

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Porphyromonadaceae
Mycoplasmataceae
Phyllobacteriaceae
Carnobacteriaceae
Staphylococcaceae

Revision editor(s): InimfonD

Experiment 5

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Curated date: 2024/10/27

Curator: InimfonD

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy control group (HC)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Acute ischemic stroke (AIS)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: All acute ischemic stroke patients with ischemic stroke onset within 48 hours.

Group 0 sample size Number of subjects in the control (unexposed) group: 92

Group 1 sample size Number of subjects in the case (exposed) group: 140

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): No antibiotics, prebiotics or probiotics taken in the past 3 months.

Lab analysis

Statistical Analysis

Statistical test: LEfSe; Spearman Correlation

Signature 1

Needs review

Curated date: 2024/10/27

Curator: InimfonD

Revision editor(s): InimfonD

Source: Figure 3

Description: Comparison of the abundance of short-chain fatty acid-producing gut microbiota between healthy controls and Acute Ischemic Stroke patients.

Abundance in Group 1: increased abundance in Acute ischemic stroke (AIS)

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Akkermansia
Enterobacteriaceae
Porphyromonadaceae
unclassified Lactobacillaceae

Revision editor(s): InimfonD

Signature 2

Needs review

Curated date: 2024/10/27

Curator: InimfonD

Revision editor(s): InimfonD

Source: Figure 3

Description: comparison of the abundance of short-chain fatty acid-producing microbiota in healthy controls versus acute ischemic stroke patients

Abundance in Group 1: decreased abundance in Acute ischemic stroke (AIS)

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Anaerostipes
Bacteroides
Blautia
Faecalibacterium
Lachnospiraceae
Roseburia

Revision editor(s): InimfonD

Experiment 6

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2024/10/27

Curator: InimfonD

Revision editor(s): InimfonD

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Moderate Acute ischemic stroke (AIS)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Mild (AIS)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Acute ischemic stroke Patients with National Institutes of Health Stroke Scale (NIHSS) score < 5 points

Group 0 sample size Number of subjects in the control (unexposed) group: 47

Group 1 sample size Number of subjects in the case (exposed) group: 78

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/10/27

Curator: InimfonD

Revision editor(s): InimfonD

Source: Figure 3

Description: comparison of the abundance of short-chain fatty acid-producing gut microbiota between moderate and mild acute ischemic patients

Abundance in Group 1: increased abundance in Mild (AIS)

NCBI	Quality Control	Links
Bacteroides
Faecalibacterium
Porphyromonadaceae
Roseburia
unclassified Lactobacillaceae

Revision editor(s): InimfonD

Signature 2

Needs review

Curated date: 2024/10/27

Curator: InimfonD

Revision editor(s): InimfonD

Source: Figure 3

Description: comparison of the abundance of short-chain fatty acid-producing gut microbiota between moderate and mild acute ischemic patients

Abundance in Group 1: decreased abundance in Mild (AIS)

NCBI	Quality Control	Links
Akkermansia
Anaerostipes
Blautia
Enterobacteriaceae
Lachnospiraceae

Revision editor(s): InimfonD

Experiment 7

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2024/10/27

Curator: InimfonD

Revision editor(s): InimfonD

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Mild Acute ischemic stroke (AIS)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Severe AIS

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Acute ischemic stroke Patients with National Institutes of Health Stroke Scale (NIHSS) score > 15 points

Group 0 sample size Number of subjects in the control (unexposed) group: 78

Group 1 sample size Number of subjects in the case (exposed) group: 15

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/10/27

Curator: InimfonD

Revision editor(s): InimfonD

Source: Figure 3

Description: comparison of the abundance of short-chain fatty acid-producing gut microbiota in severe acute ischemic stroke patients versus mild ischemic stroke patients

Abundance in Group 1: increased abundance in Severe AIS

NCBI	Quality Control	Links
Akkermansia
Anaerostipes
Enterobacteriaceae
Porphyromonadaceae

Revision editor(s): InimfonD

Signature 2

Needs review

Curated date: 2024/10/27

Curator: InimfonD

Revision editor(s): InimfonD

Source: Figure 3

Description: comparison of the abundance of short-chain fatty acid-producing gut microbiota in severe acute ischemic stroke patients versus mild ischemic stroke patients

Abundance in Group 1: decreased abundance in Severe AIS

NCBI	Quality Control	Links
Bacteroides
Blautia
Faecalibacterium
Lachnospiraceae
Roseburia
unclassified Lactobacillaceae

Revision editor(s): InimfonD

Experiment 8

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2024/10/27

Curator: InimfonD

Revision editor(s): InimfonD

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Severe Acute ischemic stroke (AIS)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Moderate AIS

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Acute ischemic stroke Patients with National Institutes of Health Stroke Scale (NIHSS) score between 5 and 15 points

Group 0 sample size Number of subjects in the control (unexposed) group: 15

Group 1 sample size Number of subjects in the case (exposed) group: 47

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2024/10/28

Curator: InimfonD

Revision editor(s): InimfonD

Source: Figure 3

Description: comparison of the abundance of short-chain fatty acid-producing gut microbiota in severe acute ischemic stroke patients versus moderate ischemic stroke patients

Abundance in Group 1: increased abundance in Moderate AIS

NCBI	Quality Control	Links
Akkermansia
Anaerostipes
Bacteroides
Blautia
Enterobacteriaceae
Lachnospiraceae
Roseburia
unclassified Lactobacillaceae

Revision editor(s): InimfonD

Signature 2