Gut microbial dysbiosis exacerbates long-term cognitive impairments by promoting intestinal dysfunction and neuroinflammation following neonatal hypoxia-ischemia
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Rattus norvegicus
- 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
- Brain hypoxia-Ischemia Hypoxia-Ischemia, Brain,Brain hypoxia-Ischemia,brain hypoxia-Ischemia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Sham Group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HI (hypoxic-ischemic) Group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Neonatal rats that underwent hypoxia-ischema (HI) to induce brain injury
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 2I and 2J
Description: Taxonomic significant differences in gut microbiota between rats in sham group and HI (hypoxic-ischemic) group using Lefse analysis
Abundance in Group 1: increased abundance in HI (hypoxic-ischemic) Group
Revision editor(s): IsaacImitini, Tosin
Signature 2
Source: Figure 2I and 2J
Description: Taxonomic significant differences in gut microbiota between rats in sham group and HI (hypoxic-ischemic) group using LeFse analysis
Abundance in Group 1: decreased abundance in HI (hypoxic-ischemic) Group
NCBI | Quality Control | Links |
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Akkermansiaceae | ||
Bacteroidaceae | ||
Enterococcaceae | ||
Terriglobia | ||
Verrucomicrobiales | ||
Verrucomicrobiia | ||
Victivallaceae | ||
Helicobacteraceae | ||
Caryophanaceae |
Revision editor(s): IsaacImitini, Tosin
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Sham group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HI (hypoxic-ischemic) group
Lab analysis
Statistical Analysis
- Statistical test
- T-Test
- 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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 2G and Figure 2K-O
Description: Relative abundance of significant differential taxa between Sham and HI (hypoxic ischemia) groups
Abundance in Group 1: increased abundance in HI (hypoxic-ischemic) group
NCBI | Quality Control | Links |
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Pseudomonadota | ||
Fusobacteriaceae | ||
Enterobacteriaceae | ||
Prevotellaceae |
Revision editor(s): IsaacImitini, Tosin
Signature 2
Source: Figure 2G and Figure 2K-O
Description: Relative abundance of significant differential taxa between Sham and HI (hypoxic ischemia) groups
Abundance in Group 1: decreased abundance in HI (hypoxic-ischemic) group
NCBI | Quality Control | Links |
---|---|---|
Enterococcaceae | ||
Akkermansiaceae |
Revision editor(s): IsaacImitini, Tosin
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to transplant Response to transplant,response to transplant
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Sham + Sham FMT (fecal microbiota transplantation) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Sham + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Sham group and HI (hypoxic-ischemic) donor rats who transferred fecal microbiota to sham group.
- 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
- Sequencing type
- PCR
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Signature 1
Source: Figure 7B
Description: Quantification of f_Enterobacteriaceae and f_Akkermansiaceae in fecal samples between [Sham + Sham FMT (fecal microbiota transplantation) group and Sham + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation) group]
Abundance in Group 1: increased abundance in Sham + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation) group
NCBI | Quality Control | Links |
---|---|---|
Enterobacteriaceae |
Revision editor(s): Tosin
Signature 2
Source: Figure 7C
Description: Quantification of f_Enterobacteriaceae and f_Akkermansiaceae in fecal samples between [Sham + Sham FMT (fecal microbiota transplantation) group and Sham + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation) group]
Abundance in Group 1: decreased abundance in Sham + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation) group
NCBI | Quality Control | Links |
---|---|---|
Akkermansiaceae |
Revision editor(s): Tosin
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HI (hypoxic-ischemic) + Sham FMT (fecal microbiota transplantation) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HI (hypoxic-ischemic) + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HI (hypoxic-ischemic) group recipient rats who received fecal microbiota from HI group and sham group donor rats.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 7B
Description: Quantification of f_Enterobacteriaceae and f_Akkermansiaceae in fecal samples between [HI (hypoxic-ischemic) + Sham FMT (fecal microbiota transplantation) and HI (hypoxic-ischemic) + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation) groups].
Abundance in Group 1: increased abundance in HI (hypoxic-ischemic) + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation) group
NCBI | Quality Control | Links |
---|---|---|
Enterobacteriaceae |
Revision editor(s): Tosin
Signature 2
Source: Figure 7C
Description: Quantification of f_Enterobacteriaceae and f_Akkermansiaceae in fecal samples between [HI (hypoxic-ischemic) + Sham FMT (fecal microbiota transplantation) and HI (hypoxic-ischemic) + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation) groups].
Abundance in Group 1: decreased abundance in HI (hypoxic-ischemic) + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation) group
NCBI | Quality Control | Links |
---|---|---|
Akkermansiaceae |
Revision editor(s): Tosin
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HI (hypoxic-ischemic) + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HI (hypoxic-ischemic) + DEX (dexamethasone) FMT (fecal microbiota transplantation) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The rats in the HI+DEX (hypoxic-ischemic + dexamethasone) group were administered (dexamethasone) DEX (ST1254, beyotime, China) orally at a dosage of 1 mg/kg daily from the 7th postnatal day to the 3rd day after HI insult.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 10C
Description: Quantification of f_Enterobacteriaceae and f_Akkermansiaceae in fecal samples between [HI (hypoxic-ischemic) + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation and HI (hypoxic-ischemic) + DEX (dexamethasone) FMT (fecal microbiota transplantation) groups].
Abundance in Group 1: increased abundance in HI (hypoxic-ischemic) + DEX (dexamethasone) FMT (fecal microbiota transplantation) group
NCBI | Quality Control | Links |
---|---|---|
Akkermansiaceae |
Revision editor(s): Tosin
Signature 2
Source: Figure 10B
Description: Quantification of f_Enterobacteriaceae and f_Akkermansiaceae in fecal samples between [HI (hypoxic-ischemic) + HI (hypoxic-ischemic) FMT (fecal microbiota transplantation and HI (hypoxic-ischemic) + DEX (dexamethasone) FMT (fecal microbiota transplantation) groups].
Abundance in Group 1: decreased abundance in HI (hypoxic-ischemic) + DEX (dexamethasone) FMT (fecal microbiota transplantation) group
NCBI | Quality Control | Links |
---|---|---|
Enterobacteriaceae |
Revision editor(s): Tosin
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Treatment outcome measurement Treatment outcome measurement,treatment outcome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Sham Group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HI (hypoxic-ischemic) Group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Neonatal rats that underwent hypoxia-ischema (HI) to induce brain injury
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- 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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure S3a
Description: The effects of oral DEX (dexamethasone) treatment on the gut microbiota in the neonatal HIBD rats. Quantification of f_Enterobacteriaceae and f_Akkermansiaceae in the fecal samples between Sham and HI (hypoxic-ischemic) Groups.
Abundance in Group 1: increased abundance in HI (hypoxic-ischemic) Group
NCBI | Quality Control | Links |
---|---|---|
Enterobacteriaceae |
Revision editor(s): Tosin
Signature 2
Source: Figure S3b
Description: The effects of oral DEX treatment on the gut microbiota in the neonatal HIBD rats. Quantification of f_Enterobacteriaceae and f_Akkermansiaceae in the fecal samples between Sham and HI (hypoxic-ischemic) Groups.
Abundance in Group 1: decreased abundance in HI (hypoxic-ischemic) Group
NCBI | Quality Control | Links |
---|---|---|
Akkermansiaceae |
Revision editor(s): Tosin
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HI (hypoxic-ischemic) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HI (hypoxic-ischemic) + DEX (dexamethasone) groups
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The rats in the HI+DEX (hypoxic-ischemic + dexamethasone) group were administered (dexamethasone) DEX (ST1254, beyotime, China) orally at a dosage of 1 mg/kg daily from the 7th postnatal day to the 3rd day after HI insult.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure S3b
Description: The effects of oral DEX treatment on the gut microbiota in the neonatal HIBD rats. Quantification of f_Enterobacteriaceae and f_Akkermansiaceae in the fecal samples between HI (hypoxic-ischemic) and HI + DEX (hypoxic-ischemic + dexamethasone) groups.
Abundance in Group 1: increased abundance in HI (hypoxic-ischemic) + DEX (dexamethasone) groups
NCBI | Quality Control | Links |
---|---|---|
Akkermansiaceae |
Revision editor(s): Tosin
Signature 2
Source: Figure S3a
Description: The effects of oral DEX treatment on the gut microbiota in the neonatal HIBD rats. Quantification of f_Enterobacteriaceae and f_Akkermansiaceae in the fecal samples between HI (hypoxic-ischemic) and HI + DEX (hypoxic-ischemic + HI (Groups.
Abundance in Group 1: decreased abundance in HI (hypoxic-ischemic) + DEX (dexamethasone) groups
NCBI | Quality Control | Links |
---|---|---|
Enterobacteriaceae |
Revision editor(s): Tosin