Dysbiosis of Gut Microbiota Is an Independent Risk Factor of Stroke-Associated Pneumonia: A Chinese Pilot Study

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Curated date: 2024/10/14

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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: Cerebrovascular disorder

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non-Stroke Associated Pneumonia (non-SAP) Training cohort

Group 1 name Corresponds to the case (exposed) group for case-control studies: Stroke Associated Pneumonia (SAP) Training cohort

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with acute ischemic stroke (AIS) as the Training cohort .

Group 0 sample size Number of subjects in the control (unexposed) group: 136

Group 1 sample size Number of subjects in the case (exposed) group: 52

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 3 Month

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): 0.10

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: 4.0

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/10/14

Curator: Rahila

Revision editor(s): Rahila, WikiWorks

Source: FIG 2 (B)

Description: Comparison of the microbial communities of the SAP and non-SAP groups in the training cohort using LEfSe to identified the 13 most differentially abundant taxa.

Abundance in Group 1: increased abundance in

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Bacilli
Bilophila
Enterobacterales
Enterobacteriaceae
Enterococcus
Erwinia
Gammaproteobacteria
Lactobacillales
Parabacteroides
Porphyromonadaceae
Pseudomonadota
Enterococcaceae

Revision editor(s): Rahila, WikiWorks

Signature 2

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Curated date: 2024/10/14

Curator: Rahila

Revision editor(s): Rahila, WikiWorks

Source: FIG 2 (B)

Description: Comparison of the microbial communities of the SAP and non-SAP groups in the training cohort using LEfSe to identified the 13 most differentially abundant taxa.

Abundance in Group 1: decreased abundance in

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Roseburia

Revision editor(s): Rahila, WikiWorks

Experiment 2

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Curated date: 2024/10/14

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non-Stroke Associated Pneumonia (non-SAP) independent cohort

Group 1 name Corresponds to the case (exposed) group for case-control studies: Stroke Associated Pneumonia (SAP) independent cohort

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with acute ischemic stroke (AIS) as the independent cohort .

Group 0 sample size Number of subjects in the control (unexposed) group: 116

Group 1 sample size Number of subjects in the case (exposed) group: 28

Lab analysis

Statistical Analysis

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2.0

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/10/14

Curator: Rahila

Revision editor(s): Rahila, WikiWorks

Source: Figure (S2B)

Description: Comparison of the microbial communities of the SAP and non-SAP groups in the validation cohort using LEfSe to identified the most differentially abundant taxon between the two groups.

Abundance in Group 1: increased abundance in

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Desulfovibrio
Enterobacterales
Enterobacteriaceae
Gammaproteobacteria
Lactobacillales
Pseudomonadota
Rikenellaceae
Enterobacter
Lactobacillus
Lactobacillaceae

Revision editor(s): Rahila, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2024/10/14

Curator: Rahila

Revision editor(s): Rahila, WikiWorks

Source: Figure (S2B)

Description: Comparison of the microbial communities of the SAP and non-SAP groups in the validation cohort using LEfSe to identified the most differentially abundant taxon between the two groups.

Abundance in Group 1: decreased abundance in

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Bacteroidaceae
Bacteroides
Bacteroidia
Bacteroidales
Pasteurellales
Pasteurellaceae
Haemophilus
Burkholderiales
Betaproteobacteria
Sutterella
Alcaligenaceae
Roseburia
Lachnospira
Coprococcus

Revision editor(s): Rahila, WikiWorks

Experiment 3

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Curated date: 2024/10/15

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non-Stroke Associated Pneumonia (non-SAP) subgroup in the training cohort

Group 1 name Corresponds to the case (exposed) group for case-control studies: Stroke Associated Pneumonia (SAP) subgroup in the training cohort

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with acute ischemic stroke (AIS) as the subgroup in the training cohort.

Group 0 sample size Number of subjects in the control (unexposed) group: 25

Group 1 sample size Number of subjects in the case (exposed) group: 25

Lab analysis

Statistical Analysis

Matched on Factors on which subjects have been matched on in a case-control study: age, Matched on: "NIHSS" 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.NIHSS, Matched on: "dysphagia" 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.dysphagia

Signature 1

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Curated date: 2024/10/15

Curator: Rahila

Revision editor(s): Rahila, KateRasheed, WikiWorks

Source: Figure S4B

Description: Comparison of the microbial communities of the SAP and non-SAP groups in the subset of the training cohort using LEfSe to identified the most differentially abundant taxon between the two groups.

Abundance in Group 1: increased abundance in

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Aeromonadales
Enterococcaceae
Enterococcus
Erwinia
Succinivibrio

Revision editor(s): Rahila, KateRasheed, WikiWorks

Signature 2

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Curated date: 2024/10/15

Curator: Rahila

Revision editor(s): Rahila, KateRasheed, WikiWorks

Source: Figure S4B

Description: Comparison of the microbial communities of the SAP and non-SAP groups in the subset of the training cohort using LEfSe to identified the most differentially abundant taxon between the two groups.

Abundance in Group 1: decreased abundance in

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Dehalobacterium
Faecalibacterium
Roseburia
DehalobacteriaceaeDehalobacteriaceae

Revision editor(s): Rahila, KateRasheed, WikiWorks

Experiment 4

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Curated date: 2025/01/08

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non-Stroke Associated Pneumonia (non-SAP) Training cohort

Group 1 name Corresponds to the case (exposed) group for case-control studies: Stroke Associated Pneumonia (SAP) Training cohort

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with acute ischemic stroke (AIS) as the Training cohort .

Group 0 sample size Number of subjects in the control (unexposed) group: 136

Group 1 sample size Number of subjects in the case (exposed) group: 52

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

Statistical test: Mann-Whitney (Wilcoxon)

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: Not specified

Matched on Factors on which subjects have been matched on in a case-control study: Not specified

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2025/01/08

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

Source: Fig. 2C

Description: Comparison of the microbial communities of the SAP and non-SAP groups in the training cohort using Mann-Whitney

Abundance in Group 1: decreased abundance in Stroke Associated Pneumonia (SAP) Training cohort

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Roseburia

Revision editor(s): KateRasheed, WikiWorks

Signature 2

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Curated date: 2025/01/08

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

Source: Fig. 2C

Description: Comparison of the microbial communities of the SAP and non-SAP groups in the training cohort using Mann-Whitney

Abundance in Group 1: increased abundance in Stroke Associated Pneumonia (SAP) Training cohort

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Pseudomonadota
Bacilli
Gammaproteobacteria
Lactobacillales
Enterococcaceae
Enterobacterales
Enterobacteriaceae
Porphyromonadaceae
Erwinia
Enterococcus
Bilophila
Parabacteroides

Revision editor(s): KateRasheed, WikiWorks

Experiment 5

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Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2025/01/08

Curator:

Revision editor(s):

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non-Stroke Associated Pneumonia (non-SAP) subgroup in the training cohort

Group 1 name Corresponds to the case (exposed) group for case-control studies: Stroke Associated Pneumonia (SAP) subgroup in the training cohort

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with acute ischemic stroke (AIS) as the subgroup in the training cohort.

Group 0 sample size Number of subjects in the control (unexposed) group: 25

Group 1 sample size Number of subjects in the case (exposed) group: 25

Lab analysis

Statistical Analysis

Matched on Factors on which subjects have been matched on in a case-control study: age, Matched on: "NIHSS" 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.NIHSS, Matched on: "dyspagia" 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.dyspagia

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2025/01/08

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

Source: Fig. S4C

Description: Comparison of the microbial communities of the subset of SAP and non-SAP groups in the training cohort using Mann-Whitney

Abundance in Group 1: increased abundance in

NCBI	Quality Control	Links
Enterococcaceae
Enterococcus
Erwinia

Revision editor(s): KateRasheed, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2025/01/08

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

Source: Fig. S4C

Description: Comparison of the microbial communities of the subset of SAP and non-SAP groups in the training cohort using Mann-Whitney

Abundance in Group 1: decreased abundance in

NCBI	Quality Control	Links
Roseburia

Revision editor(s): KateRasheed, WikiWorks

Experiment 6

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Curated date: 2025/01/08

Curator:

Revision editor(s):

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non-Stroke Associated Pneumonia (non-SAP)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Stroke Associated Pneumonia (non-SAP)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Stroke Associated Pneumonia (non-SAP) refers to patients with stroke associated pneumonia (SAP)

Group 0 sample size Number of subjects in the control (unexposed) group: Not specified

Group 1 sample size Number of subjects in the case (exposed) group: Not specified

Lab analysis

Statistical Analysis

Matched on Factors on which subjects have been matched on in a case-control study: Not specified

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2025/01/08

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

Source: Fig. S6A

Description: Differential abundance of taxa in stroke patients.

Abundance in Group 1: increased abundance in

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Lactobacillus

Revision editor(s): KateRasheed, WikiWorks

Experiment 7

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Curated date: 2025/01/08

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Pneumonia severity measurement Pneumonia severity measurement,pneumonia severity measurement

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Low Pneumonia Severity Index (Low-PSI)

Group 1 name Corresponds to the case (exposed) group for case-control studies: High Pneumonia Severity Index (High-PSI)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: High Pneumonia Severity Index (High-PSI) refers to patients with severe pneumonia

Lab analysis

Statistical Analysis

Signature 1

Mark reviewed

Needs review

Curated date: 2025/01/08

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

Source: Fig. S6B

Description: Differential abundance of taxa between low pneumonia severity index and high pneumonia severity index.

Abundance in Group 1: increased abundance in High Pneumonia Severity Index (High-PSI)

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Lactobacillus

Revision editor(s): KateRasheed, WikiWorks

Experiment 8

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Curated date: 2025/01/08

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Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Cerebrovascular disorder

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non-Stroke Associated Pneumonia (non-SAP) Training cohort

Group 1 name Corresponds to the case (exposed) group for case-control studies: Stroke Associated Pneumonia (SAP) Training cohort

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with acute ischemic stroke (AIS) as the Training cohort .

Group 0 sample size Number of subjects in the control (unexposed) group: 136

Group 1 sample size Number of subjects in the case (exposed) group: 52

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: log transformation

Statistical test: Logistic Regression

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2025/01/08

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

Source: Table 2

Description: Relative abundance of selected microbial taxa in patients with and without SAP in the training cohort.

Abundance in Group 1: increased abundance in

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Pseudomonadota
Bacilli
Gammaproteobacteria
Lactobacillales
Enterobacterales
Enterobacteriaceae
Enterococcaceae
Porphyromonadaceae
Erwinia
Enterococcus
Bilophila
Parabacteroides

Revision editor(s): KateRasheed, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-10

Curated date: 2025/01/08

Curator: KateRasheed

Revision editor(s): KateRasheed, WikiWorks

Source: Table 2

Description: Relative abundance of selected microbial taxa in patients with and without SAP in the training cohort.

Abundance in Group 1: decreased abundance in

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Roseburia

Revision editor(s): KateRasheed, WikiWorks

Experiment 9