Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis
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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
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- 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
- Multiple sclerosis Disseminated Sclerosis,generalized multiple sclerosis,insular sclerosis,MS,MS (Multiple Sclerosis),multiple sclerosis,MULTIPLE SCLEROSIS ACUTE FULMINATING,Multiple Sclerosis, Acute Fulminating,Sclerosis, Disseminated,Sclerosis, Multiple,Multiple sclerosis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pre-Experimental Autoimmune Encephalomyelitis induction(pre-EAE induction/Day 0): 0 day post immunization(0 DPI)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 3 days post immunization(3 DPI)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 3 days post immunization(3 DPI), refers to fecal samples collected three days after immunization. Mice were immunized with Myelin oligodendrocyte glycoprotein(MOG) for EAE induction. EAE was induced by injecting 8- to 10-week-old female C57BL/6J mice with 150 mg MOG35–55 peptide (Genemed Synthesis) emulsified in complete Freund’s adjuvant (CFA) (BD Difco) per mouse subcutaneously in the flanks, followed by intraperitoneal administration of 150 ng pertussis toxin (List Biological Laboratories, Inc.) per mouse on days 0 and 2.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 11
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
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
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: Fig. 1F
Description: Differentially abundant taxa between 3 days post immunization(3 DPI) and 0 day post immunization(0 DPI)
Abundance in Group 1: increased abundance in Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 3 days post immunization(3 DPI)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium ruminantium | ||
| Ruminococcus flavefaciens | ||
| Thomasclavelia cocleata | ||
| Clostridium chauvoei |
Revision editor(s): KateRasheed
Signature 2
Source: Fig. 1F
Description: Differentially abundant taxa between 3 days post immunization(3 DPI) and 0 day post immunization(0 DPI)
Abundance in Group 1: decreased abundance in Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 3 days post immunization(3 DPI)
| NCBI | Quality Control | Links |
|---|---|---|
| Dorea formicigenerans | ||
| Lacrimispora indolis | ||
| [Clostridium] viride | ||
| Lactobacillus gasseri/hominis/johnsonii/taiwanensisLactobacillus gasseri/hominis/johnsonii/taiwanensis |
Revision editor(s): KateRasheed
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 8 days post immunization(8 DPI)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 8 days post immunization(8 DPI), refers to the timepoint for fecal sample collection(eight days after immunization). EAE was induced by injecting 8- to 10-week-old female C57BL/6J mice with 150 mg MOG35–55 peptide (Genemed Synthesis) emulsified in complete Freund’s adjuvant (CFA) (BD Difco) per mouse subcutaneously in the flanks, followed by intraperitoneal administration of 150 ng pertussis toxin (List Biological Laboratories, Inc.) per mouse on days 0 and 2.
Lab analysis
Statistical Analysis
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: Fig. 1F
Description: Differentially abundant taxa between 8 days post immunization(8 DPI) and 0 day post immunization(0 DPI)
Abundance in Group 1: increased abundance in Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 8 days post immunization(8 DPI)
Revision editor(s): KateRasheed
Signature 2
Source: Fig. 1F
Description: Differentially abundant taxa between 8 days post immunization(8 DPI) and 0 day post immunization(0 DPI)
Abundance in Group 1: decreased abundance in Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 8 days post immunization(8 DPI)
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospira guilliermondii |
Revision editor(s): KateRasheed
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post-Experimental Autoimmune Encephalomyelitis induction-peak disease(post-EAE induction): 15 days post immunization(15 DPI)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Post-Experimental Autoimmune Encephalomyelitis induction-peak disease(post-EAE induction): 15 days post immunization(15 DPI), refers to the timepoint for fecal sample collection(fifteen days after immunization). This was also the peak of multiple sclerosis disease.
Lab analysis
Statistical Analysis
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: Fig. 1F
Description: Differentially abundant taxa between 15 days post immunization(15 DPI) and 0 day post immunization(0 DPI)
Abundance in Group 1: increased abundance in Post-Experimental Autoimmune Encephalomyelitis induction-peak disease(post-EAE induction): 15 days post immunization(15 DPI)
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| Ruminococcus flavefaciens | ||
| Clostridium ruminantium | ||
| [Clostridium] scindens |
Revision editor(s): KateRasheed
Signature 2
Source: Fig. 1F
Description: Differentially abundant taxa between 15 days post immunization(15 DPI) and 0 day post immunization(0 DPI)
Abundance in Group 1: decreased abundance in Post-Experimental Autoimmune Encephalomyelitis induction-peak disease(post-EAE induction): 15 days post immunization(15 DPI)
Revision editor(s): KateRasheed
Experiment 4
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
- Single-treatment housed control mice - 0 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Single-treatment housed vancomycin mice - 0 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Single-treatment housed vancomycin mice - 0 DPI refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 0 day post immunization(0 DPI).
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Fig. S4A
Description: Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 0 day post immunization(0 DPI) using LEfSe
Abundance in Group 1: increased abundance in Single-treatment housed vancomycin mice - 0 DPI
Revision editor(s): KateRasheed
Signature 2
Source: Fig. S4A
Description: Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 0 day post immunization(0 DPI) using LEfSe
Abundance in Group 1: decreased abundance in Single-treatment housed vancomycin mice - 0 DPI
Revision editor(s): KateRasheed
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Single-treatment housed control mice - 3 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Single-treatment housed vancomycin mice - 3 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Single-treatment housed vancomycin mice - 3 DPI refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 3 days post immunization(3 DPI).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Fig. S4A
Description: Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 3 days post immunization(3 DPI) using LEfSe
Abundance in Group 1: decreased abundance in Single-treatment housed vancomycin mice - 3 DPI
Revision editor(s): KateRasheed
Signature 2
Source: Fig. S4A
Description: Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 3 days post immunization(3 DPI) using LEfSe
Abundance in Group 1: increased abundance in Single-treatment housed vancomycin mice - 3 DPI
Revision editor(s): KateRasheed
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Single-treatment housed control mice - 8 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Single-treatment housed vancomycin mice - 8 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Single-treatment housed vancomycin mice refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 8 days post immunization(8 DPI).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Fig. S4A
Description: Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 8 day post immunization(8 DPI) using LEfSe
Abundance in Group 1: decreased abundance in Single-treatment housed vancomycin mice - 8 DPI
Revision editor(s): KateRasheed
Signature 2
Source: Fig. S4A
Description: Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 8 days post immunization(8 DPI) using LEfSe
Abundance in Group 1: increased abundance in Single-treatment housed vancomycin mice - 8 DPI
Revision editor(s): KateRasheed
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Single-treatment housed control mice - 15 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Single-treatment housed vancomycin mice - 15 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Single-treatment housed vancomycin mice refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 15 days post immunization(15 DPI).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Fig. S4A
Description: Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 15 days post immunization(15 DPI) using LEfSe
Abundance in Group 1: increased abundance in Single-treatment housed vancomycin mice - 15 DPI
Revision editor(s): KateRasheed
Signature 2
Source: Fig. S4A
Description: Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 15 days post immunization(15 DPI) using LEfSe
Abundance in Group 1: decreased abundance in Single-treatment housed vancomycin mice - 15 DPI
Revision editor(s): KateRasheed
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Single-treatment housed vancomycin mice (vancomycin) - 0 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 0 day post immunization(0 DPI).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Fig. S4B
Description: Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 0 day post immunization(0 DPI) using LEfSe
Abundance in Group 1: increased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI
Revision editor(s): KateRasheed
Signature 2
Source: Fig. S4B
Description: Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 0 day post immunization(0 DPI) using LEfSe
Abundance in Group 1: decreased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI
Revision editor(s): KateRasheed
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Single-treatment housed vancomycin mice (vancomycin) - 3 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 3 days post immunization(3 DPI).
Lab analysis
Statistical Analysis
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: Fig. S4B
Description: Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 3 days post immunization(3 DPI) using LEfSe
Abundance in Group 1: increased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI
Revision editor(s): KateRasheed
Signature 2
Source: Fig. S4B
Description: Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 3 days post immunization(3 DPI) using LEfSe
Abundance in Group 1: decreased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI
Revision editor(s): KateRasheed
Experiment 10
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Single-treatment housed vancomycin mice (vancomycin) - 8 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 8 days post immunization(8 DPI).
Lab analysis
Statistical Analysis
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: Fig. S4B
Description: Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 8 days post immunization(8 DPI) using LEfSe
Abundance in Group 1: increased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus colihominis | ||
| Enterocloster aldenensis | ||
| Lacrimispora indolis | ||
| Roseburia intestinalis | ||
| [Clostridium] polysaccharolyticum | ||
| Clostridium XIVaClostridium XIVa |
Revision editor(s): KateRasheed
Signature 2
Source: Fig. S4B
Description: Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 8 days post immunization(8 DPI) using LEfSe
Abundance in Group 1: decreased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI
Revision editor(s): KateRasheed
Experiment 11
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Single-treatment housed vancomycin mice (vancomycin) - 15 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 15 days post immunization(15 DPI).
Lab analysis
Statistical Analysis
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: Fig. S4B
Description: Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 15 days post immunization(15 DPI) using LEfSe
Abundance in Group 1: increased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI
Revision editor(s): KateRasheed
Signature 2
Source: Fig. S4B
Description: Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 15 days post immunization(15 DPI) using LEfSe
Abundance in Group 1: decreased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Olsenella profusa | ||
| Clostridium asparagiforme/lavalenseClostridium asparagiforme/lavalense | ||
| Clostridium chauvoei/quiniiClostridium chauvoei/quinii |
Revision editor(s): KateRasheed
Experiment 12
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Untreated mice cohoused with vancomycin-treated mice (ControlCoho) - 0 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 0 day post immunization(0 DPI)
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Fig. S4C
Description: Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 0 day post immunization(0 DPI) using LEfSe
Abundance in Group 1: increased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI
Revision editor(s): KateRasheed
Signature 2
Source: Fig. S4C
Description: Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 0 day post immunization(0 DPI) using LEfSe
Abundance in Group 1: decreased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI
Revision editor(s): KateRasheed
Experiment 13
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Untreated mice cohoused with vancomycin-treated mice (ControlCoho) - 3 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 3 days post immunization(3 DPI).
Lab analysis
Statistical Analysis
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: Fig. S4C
Description: Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 3 days post immunization(3 DPI) using LEfSe
Abundance in Group 1: increased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| Coprobacillus cateniformis | ||
| Faecalicatena orotica | ||
| Oscillibacter valericigenes | ||
| Oscillospira guilliermondii | ||
| Thomasclavelia cocleata |
Revision editor(s): KateRasheed
Signature 3
Source: Fig. S4C
Description: Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 3 days post immunization(3 DPI) using LEfSe
Abundance in Group 1: decreased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia intestinalis |
Revision editor(s): KateRasheed
Experiment 14
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Untreated mice cohoused with vancomycin-treated mice (ControlCoho) - 8 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 8 days post immunization(8 DPI)
Lab analysis
Statistical Analysis
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: Fig. S4C
Description: Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 8 days post immunization(8 DPI) using LEfSe
Abundance in Group 1: increased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| Gracilibacter thermotolerans |
Revision editor(s): KateRasheed
Signature 2
Source: Fig. S4C
Description: Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 8 days post immunization(8 DPI) using LEfSe
Abundance in Group 1: decreased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Enterocloster bolteae | ||
| Enterocloster clostridioformis | ||
| Faecalicatena orotica | ||
| Robinsoniella peoriensis | ||
| Clostridium chauvoei/quiniiClostridium chauvoei/quinii |
Revision editor(s): KateRasheed
Experiment 15
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Untreated mice cohoused with vancomycin-treated mice (ControlCoho) - 15 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 15 days post immunization(15 DPI)
Lab analysis
Statistical Analysis
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: Fig. S4C
Description: Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 15 days post immunization(15 DPI) using LEfSe
Abundance in Group 1: increased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerocolumna jejuensis | ||
| Lacrimispora indolis |
Revision editor(s): KateRasheed
Signature 2
Source: Fig. S4C
Description: Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 15 days post immunization(15 DPI)
Abundance in Group 1: decreased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Dorea formicigenerans | ||
| Enterocloster bolteae | ||
| Enterocloster clostridioformis | ||
| Faecalicatena orotica | ||
| Oscillibacter valericigenes |
Revision editor(s): KateRasheed
Experiment 16
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Single-treatment housed control mice - 0 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Single-treatment housed vancomycin mice - 0 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Single-treatment housed vancomycin mice refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin.
Lab analysis
Statistical Analysis
- Statistical test
- Spearman Correlation
- 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
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Fig. 5A
Description: Differentially abundant taxa between single-treatment housed untreated mice (control) and single-treatment housed vancomycin mice (vancomycin) at 0 day post immunization(3 DPI) using spearman correlation matrix.
Abundance in Group 1: increased abundance in Single-treatment housed vancomycin mice - 0 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus | ||
| Turicibacter | ||
| Akkermansia |
Revision editor(s): KateRasheed
Signature 2
Source: Fig. 5A
Description: Differentially abundant taxa between single-treatment housed untreated mice (control) and single-treatment housed vancomycin mice (vancomycin) at 0 day post immunization(0 DPI) using spearman correlation matrix.
Abundance in Group 1: decreased abundance in Single-treatment housed vancomycin mice - 0 DPI
Revision editor(s): KateRasheed
Experiment 17
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Single-treatment housed control mice - 3 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Single-treatment housed vancomycin mice - 3 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Single-treatment housed vancomycin mice refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 3 days post immunization(3 DPI).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Fig. 5A
Description: Differentially abundant taxa between single-treatment housed untreated mice (control) and single-treatment housed vancomycin mice (vancomycin) at 3 days post immunization(3 DPI) using spearman correlation matrix.
Abundance in Group 1: increased abundance in Single-treatment housed vancomycin mice - 3 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus | ||
| Clostridium XVIIIClostridium XVIII | ||
| Turicibacter | ||
| Akkermansia |
Revision editor(s): KateRasheed
Signature 2
Source: Fig. 5A
Description: Differentially abundant taxa between single-treatment housed untreated mice (control) and single-treatment housed vancomycin mice (vancomycin) at 3 days post immunization(3 DPI) using spearman correlation matrix.
Abundance in Group 1: decreased abundance in Single-treatment housed vancomycin mice - 3 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerosporobacter | ||
| Roseburia | ||
| Ruminococcus | ||
| Clostridium IIIClostridium III | ||
| Holdemania | ||
| Anaeroplasma |
Revision editor(s): KateRasheed
Experiment 18
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Single-treatment housed control mice - 8 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Single-treatment housed vancomycin mice - 8 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Single-treatment housed vancomycin mice refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 8 days post immunization(8 DPI).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Fig. 5A
Description: Differentially abundant taxa between single-treatment housed untreated mice (control) and single-treatment housed vancomycin mice (vancomycin) at 8 day post immunization(8 DPI) using spearman correlation matrix.
Abundance in Group 1: decreased abundance in Single-treatment housed vancomycin mice - 8 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Holdemania | ||
| Anaerotruncus colihominis | ||
| Hydrogenoanaerobacterium | ||
| Roseburia intestinalis | ||
| Dorea formicigenerans | ||
| Anaerocolumna jejuensis | ||
| Clostridium XIVaClostridium XIVa |
Revision editor(s): KateRasheed
Experiment 19
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Single-treatment housed control mice - 15 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Single-treatment housed vancomycin mice - 15 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Single-treatment housed vancomycin mice - 15 DPI refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 15 days post immunization(15 DPI).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Fig. 5A
Description: Differentially abundant taxa between single-treatment housed untreated mice (control) and single-treatment housed vancomycin mice (vancomycin) at 15 days post immunization(15 DPI) using spearman correlation matrix.
Abundance in Group 1: decreased abundance in Single-treatment housed vancomycin mice - 15 DPI
Revision editor(s): KateRasheed
Signature 2
Source: Fig. 5A
Description: Differentially abundant taxa between single-treatment housed untreated mice (control) and single-treatment housed vancomycin mice (vancomycin) at 15 days post immunization(15 DPI) using spearman correlation matrix.
Abundance in Group 1: increased abundance in Single-treatment housed vancomycin mice - 15 DPI
Revision editor(s): KateRasheed
Experiment 20
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Multiple sclerosis Disseminated Sclerosis,generalized multiple sclerosis,insular sclerosis,MS,MS (Multiple Sclerosis),multiple sclerosis,MULTIPLE SCLEROSIS ACUTE FULMINATING,Multiple Sclerosis, Acute Fulminating,Sclerosis, Disseminated,Sclerosis, Multiple,Multiple sclerosis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pre-Experimental Autoimmune Encephalomyelitis induction(pre-EAE induction/Day 0): 0 day post immunization(0 DPI)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 3 days post immunization(3 DPI)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 3 days post immunization(3 DPI), refers to fecal samples collected three days after immunization. Mice were immunized with Myelin oligodendrocyte glycoprotein(MOG) for EAE induction. EAE was induced by injecting 8- to 10-week-old female C57BL/6J mice with 150 mg MOG35–55 peptide (Genemed Synthesis) emulsified in complete Freund’s adjuvant (CFA) (BD Difco) per mouse subcutaneously in the flanks, followed by intraperitoneal administration of 150 ng pertussis toxin (List Biological Laboratories, Inc.) per mouse on days 0 and 2.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 11
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
Lab analysis
Statistical Analysis
- Statistical test
- ANOVA
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
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: Fig. 1G
Description: Differentially abundant taxa between 3 days post immunization(3 DPI) and 0 day post immunization(0 DPI) using Mann-Whitney
Abundance in Group 1: decreased abundance in Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 3 days post immunization(3 DPI)
| NCBI | Quality Control | Links |
|---|---|---|
| Lacrimispora indolis | ||
| Lactobacillus gasseri/hominis/johnsonii/taiwanensisLactobacillus gasseri/hominis/johnsonii/taiwanensis |
Revision editor(s): KateRasheed
Experiment 21
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 8 days post immunization(8 DPI)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 8 days post immunization(8 DPI), refers to the timepoint for fecal sample collection(eight days after immunization). EAE was induced by injecting 8- to 10-week-old female C57BL/6J mice with 150 mg MOG35–55 peptide (Genemed Synthesis) emulsified in complete Freund’s adjuvant (CFA) (BD Difco) per mouse subcutaneously in the flanks, followed by intraperitoneal administration of 150 ng pertussis toxin (List Biological Laboratories, Inc.) per mouse on days 0 and 2.
Lab analysis
Statistical Analysis
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: Fig. 1G
Description: Differentially abundant taxa between 8 days post immunization(8 DPI) and 0 day post immunization(0 DPI) using Mann-Whitney
Abundance in Group 1: decreased abundance in Post-Experimental Autoimmune Encephalomyelitis induction-latent period(post-EAE induction): 8 days post immunization(8 DPI)
| NCBI | Quality Control | Links |
|---|---|---|
| [Clostridium] scindens |
Revision editor(s): KateRasheed
Experiment 22
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post-Experimental Autoimmune Encephalomyelitis induction-peak disease(post-EAE induction): 15 days post immunization(15 DPI)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Post-Experimental Autoimmune Encephalomyelitis induction-peak disease(post-EAE induction): 15 days post immunization(15 DPI), refers to the timepoint for fecal sample collection(fifteen days after immunization). This was also the peak of multiple sclerosis disease.
Lab analysis
Statistical Analysis
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: Fig. 1G
Description: Differentially abundant taxa between 15 days post immunization(15 DPI) and 0 day post immunization(0 DPI) using Mann-Whitney
Abundance in Group 1: increased abundance in Post-Experimental Autoimmune Encephalomyelitis induction-peak disease(post-EAE induction): 15 days post immunization(15 DPI)
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| [Clostridium] scindens |
Revision editor(s): KateRasheed
Signature 2
Source: Fig. 1G
Description: Differentially abundant taxa between 15 days post immunization(15 DPI) and 0 day post immunization(0 DPI) using Mann-Whitney
Abundance in Group 1: decreased abundance in Post-Experimental Autoimmune Encephalomyelitis induction-peak disease(post-EAE induction): 15 days post immunization(15 DPI)
| NCBI | Quality Control | Links |
|---|---|---|
| Lacrimispora indolis | ||
| Turicibacter sanguinis | ||
| Lactobacillus gasseri/hominis/johnsonii/taiwanensisLactobacillus gasseri/hominis/johnsonii/taiwanensis |
Revision editor(s): KateRasheed
Experiment 23
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
- Single-treatment housed control mice - 0 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Single-treatment housed vancomycin mice - 0 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Single-treatment housed vancomycin mice - 0 DPI refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 0 day post immunization(0 DPI).
- 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
- Statistical test
- Mann-Whitney (Wilcoxon)
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Fig. 4A
Description: Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 0 day post immunization(0 DPI) using Mann-Whitney
Abundance in Group 1: increased abundance in Single-treatment housed vancomycin mice - 0 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| Turicibacter sanguinis | ||
| Enterococcus casseliflavus/gallinarum/saccharolyticusEnterococcus casseliflavus/gallinarum/saccharolyticus |
Revision editor(s): KateRasheed
Signature 2
Source: Fig. 4A
Description: Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 0 day post immunization(0 DPI) using Mann-Whitney
Abundance in Group 1: decreased abundance in Single-treatment housed vancomycin mice - 0 DPI
Revision editor(s): KateRasheed
Experiment 24
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Single-treatment housed control mice - 3 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Single-treatment housed vancomycin mice - 3 DPI refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 3 days post immunization(3 DPI).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Fig. 4A
Description: Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 3 days post immunization(3 DPI) using Mann-Whitney
Abundance in Group 1: decreased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus colihominis |
Revision editor(s): KateRasheed
Signature 2
Source: Fig. 4A
Description: Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 3 days post immunization(3 DPI) using Mann-Whitney
Abundance in Group 1: increased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI
Revision editor(s): KateRasheed
Experiment 25
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Single-treatment housed control mice - 8 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Single-treatment housed vancomycin mice - 8 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Single-treatment housed vancomycin mice refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 8 days post immunization(8 DPI).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Fig. 4A
Description: Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 8 day post immunization(8 DPI) using Mann-Whitney
Abundance in Group 1: decreased abundance in Single-treatment housed vancomycin mice - 8 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus colihominis |
Revision editor(s): KateRasheed
Signature 2
Source: Fig. 4A
Description: Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 8 day post immunization(8 DPI) using Mann-Whitney
Abundance in Group 1: increased abundance in Single-treatment housed vancomycin mice - 8 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| Thomasclavelia cocleata | ||
| [Clostridium] scindens | ||
| Lactobacillus gasseri/hominis/johnsonii/taiwanensisLactobacillus gasseri/hominis/johnsonii/taiwanensis |
Revision editor(s): KateRasheed
Experiment 26
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Single-treatment housed control mice - 15 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Single-treatment housed vancomycin mice - 15 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Single-treatment housed vancomycin mice refers to conventionally raised mice with multiple sclerosis, who were treated with vancomycin. Mice were fed 200 μL of the vancomycin cecal slurry by oral gavage once for 2 weeks. This was done 4 weeks before EAE induction. These vancomycin-treated mice were housed with the same treatment group (single treatment) at 15 days post immunization(15 DPI).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 2
Source: Fig. 4A
Description: Differentially abundant taxa between single-treatment housed vancomycin mice and single-treatment housed control mice at 15 days post immunization(15 DPI) using Mann-Whitney
Abundance in Group 1: increased abundance in Single-treatment housed vancomycin mice - 15 DPI
Revision editor(s): KateRasheed
Experiment 27
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Single-treatment housed vancomycin mice (vancomycin) - 0 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 0 day post immunization(0 DPI).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Fig. 4B
Description: Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 0 day post immunization(0 DPI) using Mann-Whitney
Abundance in Group 1: decreased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila |
Revision editor(s): KateRasheed
Signature 2
Source: Fig. 4B
Description: Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 0 day post immunization(0 DPI) using Mann-Whitney
Abundance in Group 1: increased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Thomasclavelia cocleata | ||
| Lactobacillus gasseri/hominis/johnsonii/taiwanensisLactobacillus gasseri/hominis/johnsonii/taiwanensis |
Revision editor(s): KateRasheed
Experiment 28
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Single-treatment housed vancomycin mice (vancomycin) - 3 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 3 days post immunization(3 DPI).
Lab analysis
Statistical Analysis
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: Fig. 4B
Description: Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 3 days post immunization(3 DPI) using Mann-Whitney
Abundance in Group 1: increased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus colihominis | ||
| Clostridium asparagiforme/lavalenseClostridium asparagiforme/lavalense |
Revision editor(s): KateRasheed
Signature 2
Source: Fig. 4B
Description: Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 3 days post immunization(3 DPI) using Mann-Whitney
Abundance in Group 1: decreased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| Thomasclavelia cocleata |
Revision editor(s): KateRasheed
Experiment 29
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Single-treatment housed vancomycin mice (vancomycin) - 8 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 8 days post immunization(8 DPI).
Lab analysis
Statistical Analysis
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: Fig. 4B
Description: Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 8 days post immunization(8 DPI) using Mann-Whitney
Abundance in Group 1: increased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus colihominis |
Revision editor(s): KateRasheed
Signature 2
Source: Fig. 4B
Description: Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 8 days post immunization(8 DPI) using Mann-Whitney
Abundance in Group 1: decreased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| Thomasclavelia cocleata | ||
| Lactobacillus gasseri/hominis/johnsonii/taiwanensisLactobacillus gasseri/hominis/johnsonii/taiwanensis |
Revision editor(s): KateRasheed
Experiment 30
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Single-treatment housed vancomycin mice (vancomycin) - 15 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 15 days post immunization(15 DPI).
Lab analysis
Statistical Analysis
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: Fig. 4B
Description: Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 15 days post immunization(15 DPI) using Mann-Whitney
Abundance in Group 1: increased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus colihominis |
Revision editor(s): KateRasheed
Signature 2
Source: Fig. 4B
Description: Differentially abundant taxa between single-treatment housed vancomycin mice (vancomycin) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 15 days post immunization(15 DPI) using Mann-Whitney
Abundance in Group 1: decreased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium asparagiforme/lavalenseClostridium asparagiforme/lavalense |
Revision editor(s): KateRasheed
Experiment 31
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Untreated mice cohoused with vancomycin-treated mice (ControlCoho) - 0 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 0 day post immunization(0 DPI)
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Fig. 4C
Description: Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 0 day post immunization(0 DPI)
Abundance in Group 1: increased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 0 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Coprobacillus cateniformis | ||
| Thomasclavelia cocleata |
Revision editor(s): KateRasheed
Experiment 32
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Untreated mice cohoused with vancomycin-treated mice (ControlCoho) - 3 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 3 days post immunization(3 DPI).
Lab analysis
Statistical Analysis
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: Fig. 4C
Description: Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 3 days post immunization(3 DPI) using Mann-Whitney
Abundance in Group 1: increased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 3 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| Coprobacillus cateniformis | ||
| Faecalicatena orotica | ||
| Thomasclavelia cocleata |
Revision editor(s): KateRasheed
Experiment 33
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Untreated mice cohoused with vancomycin-treated mice (ControlCoho) - 8 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 8 days post immunization(8 DPI)
Lab analysis
Statistical Analysis
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: Fig. 4C
Description: Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 8 days post immunization(8 DPI) using Mann-Whitney
Abundance in Group 1: increased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 8 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila |
Revision editor(s): KateRasheed
Experiment 34
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Untreated mice cohoused with vancomycin-treated mice (ControlCoho) - 15 DPI
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI refers to conventionally raised mice treated with vancomycin daily via oral gavage for 2 weeks. These mice were cohoused with control mice(untreated mice) at 15 days post immunization(15 DPI)
Lab analysis
Statistical Analysis
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: Fig. 4C
Description: Differentially abundant taxa between untreated mice cohoused with vancomycin-treated mice (ControlCoho) and vancomycin-treated mice cohoused with untreated mice (VancoCoho) at 15 days post immunization(15 DPI) using Mann-Whitney
Abundance in Group 1: increased abundance in Vancomycin-treated mice cohoused with untreated mice (VancoCoho) - 15 DPI
| NCBI | Quality Control | Links |
|---|---|---|
| Lacrimispora indolis | ||
| Anaerocolumna jejuensis |
Revision editor(s): KateRasheed
Contents
- 1 Experiment 1
- 2 Experiment 2
- 3 Experiment 3
- 4 Experiment 4
- 5 Experiment 5
- 6 Experiment 6
- 7 Experiment 7
- 8 Experiment 8
- 9 Experiment 9
- 10 Experiment 10
- 11 Experiment 11
- 12 Experiment 12
- 13 Experiment 13
- 14 Experiment 14
- 15 Experiment 15
- 16 Experiment 16
- 17 Experiment 17
- 18 Experiment 18
- 19 Experiment 19
- 20 Experiment 20
- 21 Experiment 21
- 22 Experiment 22
- 23 Experiment 23
- 24 Experiment 24
- 25 Experiment 25
- 26 Experiment 26
- 27 Experiment 27
- 28 Experiment 28
- 29 Experiment 29
- 30 Experiment 30
- 31 Experiment 31
- 32 Experiment 32
- 33 Experiment 33
- 34 Experiment 34
