Multiple sclerosis and gut microbiota: Lachnospiraceae from the ileum of MS twins trigger MS-like disease in germfree transgenic mice-An unbiased functional study
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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
- Germany
- 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
- 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
- Unaffected twins
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Affected twins
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals with Multiple Sclerosis, from monozygotic twin pairs clinically discordant for multiple sclerosis.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 81
- Group 1 sample size Number of subjects in the case (exposed) group
- 81
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- Chi-Square
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 1E
Description: A phylogenetic tree showing the taxa nominally significant in Chi-squared test. The “Trend” in the legend indicates changes in abundance in affected twins (compared to unaffected twins).
Abundance in Group 1: increased abundance in Affected twins
Revision editor(s): Anne-mariesharp
Signature 2
Source: Figure 1E
Description: A phylogenetic tree showing the taxa nominally significant in Chi-squared test. The “Trend” in the legend indicates changes in abundance in affected twins (compared to unaffected twins).
Abundance in Group 1: decreased abundance in Affected twins
Revision editor(s): Anne-mariesharp
Experiment 2
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- Linear Regression
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 1E
Description: A phylogenetic tree showing the taxa nominally significant in Linear Mixed Model test. The “Trend” in the legend indicates changes in abundance in affected twins (compared to unaffected twins).
Abundance in Group 1: increased abundance in Affected twins
Revision editor(s): Anne-mariesharp
Signature 2
Source: Figure 1E
Description: A phylogenetic tree showing the taxa nominally significant in Linear Mixed Model test. The “Trend” in the legend indicates changes in abundance in affected twins (compared to unaffected twins).
Abundance in Group 1: decreased abundance in Affected twins
Revision editor(s): Anne-mariesharp
Experiment 3
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Experimental autoimmune encephalomyelitis ALLERGIC ENCEPH,ALLERGIC ENCEPH EXPER,Allergic encephalomyelitis,Allergic encephalomyelitis (disorder),Allergic Encephalomyelitis, Experimental,AUTOIMMUNE ENCEPH EXPER,Autoimmune Encephalomyelitis, Experimental,AUTOIMMUNE EXPER ENCEPH,Autoimmune Experimental Encephalomyelitis,EAE,ENCEPH ALLERGIC,ENCEPH AUTOIMMUNE EXPER,ENCEPH EXPER AUTOIMMUNE,Encephalomyelitis, Allergic,Encephalomyelitis, Autoimmune Experimental,Encephalomyelitis, Autoimmune, Experimental,Encephalomyelitis, Experimental Allergic,Encephalomyelitis, Experimental Autoimmune,EXPER ALLERGIC ENCEPH,EXPER AUTOIMMUNE ENCEPH,Experimental Allergic Encephalomyelitides,Experimental Allergic Encephalomyelitis,Experimental allergic encephalomyelitis (disorder),experimental autoimmune encephalomyelitis,Experimental Encephalomyelitis, Autoimmune,Experimental autoimmune encephalomyelitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- EAE (Experimental Autoimmune Encephalomyelitis)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Gnotobiotic mice that developed Experimental Autoimmune Encephalomyelitis after being colonized with ileal microbiota from an MS (Multiple Sclerosis)-affected human twin (MS-Q).
- 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
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not specified
Lab analysis
Statistical Analysis
- Statistical test
- T-Test
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Figure 3F
Description: Relative abundance of fecal microbiota in recipients of MS patient-derived ileal microbiota that showed a significant difference (unpaired t-test) between healthy and diseased animals.
Abundance in Group 1: increased abundance in EAE (Experimental Autoimmune Encephalomyelitis)
| NCBI | Quality Control | Links |
|---|---|---|
| Alcaligenes | ||
| Eisenbergiella |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Figure 3F
Description: Relative abundance of fecal microbiota in recipients of MS patient-derived ileal microbiota that showed a significant difference (unpaired t-test) between healthy and diseased animals.
Abundance in Group 1: decreased abundance in EAE (Experimental Autoimmune Encephalomyelitis)
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Thomasclavelia | ||
| unclassified Bacillota |
Revision editor(s): Anne-mariesharp
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Transplant outcome measurement Transplant outcome measurement,transplant outcome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- GF_HT (Germ Free_Healthy Twin) (Early 2weeks)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GF-MS (Germ Free_Multiple Sclerosis) (Early 2weeks)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Germ-free Gnotobiotic RR (Relapsing Remitting) SJL/J mice colonized with ileal microbiota from the Multiple Sclerosis twin (MS-Q) (2 weeks after colonization)
- 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
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- decreased
Signature 1
Source: Figure 4E
Description: Relative abundance of fecal microbiota from colonized RR mice that showed significant changes (unpaired t-test) at the genus level.
Abundance in Group 1: increased abundance in GF-MS (Germ Free_Multiple Sclerosis) (Early 2weeks)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Escherichia/Shigella sp. |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Figure 4E
Description: Relative abundance of fecal microbiota from colonized RR mice that showed significant changes (unpaired t-test) at the genus level.
Abundance in Group 1: decreased abundance in GF-MS (Germ Free_Multiple Sclerosis) (Early 2weeks)
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Alistipes | ||
| Streptococcus |
Revision editor(s): Anne-mariesharp
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- GF_HT (Germ Free_Healthy Twin) (End)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GF-MS (Germ Free_Multiple Sclerosis) (End)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Germ-free Gnotobiotic RR (Relapsing Remitting) SJL/J mice colonized with ileal microbiota from the Multiple Sclerosis twin (MS-Q) (at endpoint after colonization)
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
Signature 1
Source: Figure 4E
Description: Relative abundance of fecal microbiota from colonized RR mice that showed significant changes (unpaired t-test) at the genus level.
Abundance in Group 1: increased abundance in GF-MS (Germ Free_Multiple Sclerosis) (End)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Lachnoclostridium | ||
| Escherichia/Shigella sp. |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Figure 4E
Description: Relative abundance of fecal microbiota from colonized RR mice that showed significant changes (unpaired t-test) at the genus level.
Abundance in Group 1: decreased abundance in GF-MS (Germ Free_Multiple Sclerosis) (End)
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Alistipes | ||
| Streptococcus |
Revision editor(s): Anne-mariesharp
Experiment 6
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Ileum Distal intestine,Intestinum ileum,Lower intestine,Posterior intestine,Ileum,ileum
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- GF_HT-Q (Germ Free_Healthy Twin)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GF_MS-Q (Germ Free_Multiple Sclerosis)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Germ-free Gnotobiotic RR (Relapsing Remitting) SJL/J mice colonized with ileal microbiota from the Multiple Sclerosis twin (MS-Q)
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
Signature 1
Source: Fig. S4G
Description: Relative abundance of ileal microbiota in humanized gnotobiotic RR mice that showed significant differences (unpaired t-test) at the genus level.
Abundance in Group 1: increased abundance in GF_MS-Q (Germ Free_Multiple Sclerosis)
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnoclostridium | ||
| Escherichia/Shigella sp. |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Fig. S4G
Description: Relative abundance of ileal microbiota in humanized gnotobiotic RR mice that showed significant differences (unpaired t-test) at the genus level.
Abundance in Group 1: decreased abundance in GF_MS-Q (Germ Free_Multiple Sclerosis)
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Thomasclavelia | ||
| Streptococcus |
Revision editor(s): Anne-mariesharp
Experiment 7
Subjects
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- GF_HT (Germ Free_Healthy Twin) (Early 2weeks)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GF_MS (Germ Free_Multiple Sclerosis) (Early 2weeks)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Germ-free Gnotobiotic RR (Relapsing Remitting) SJL/J mice colonized with ileal microbiota from the Multiple sclerosis twin (MS-A) (2weeks after colonization)
- 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
Signature 1
Source: Fig S5
Description: Relative abundance of fecal microbiota from humanized gnotobiotic RR mice that showed significant changes (unpaired t-test) at the genus level 2 weeks after the colonization and at the endpoint.
Abundance in Group 1: increased abundance in GF_MS (Germ Free_Multiple Sclerosis) (Early 2weeks)
| NCBI | Quality Control | Links |
|---|---|---|
| [Clostridium] innocuum |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Fig S5
Description: Relative abundance of fecal microbiota from humanized gnotobiotic RR mice that showed significant changes (unpaired t-test) at the genus level 2 weeks after the colonization and at the endpoint.
Abundance in Group 1: decreased abundance in GF_MS (Germ Free_Multiple Sclerosis) (Early 2weeks)
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus |
Revision editor(s): Anne-mariesharp
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- GF_HT (Germ Free_Healthy Twin) (End)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GF_MS (Germ Free_Multiple Sclerosis) (End)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Germ-free Gnotobiotic RR (Relapsing Remitting) SJL/J mice colonized with ileal microbiota from the Multiple sclerosis twin (MS-A) (at endpoint after colonization)
Lab analysis
Statistical Analysis
Signature 1
Source: Fig S5
Description: Relative abundance of fecal microbiota from humanized gnotobiotic RR mice that showed significant changes (unpaired t-test) at the genus level 2 weeks after the colonization and at the endpoint.
Abundance in Group 1: increased abundance in GF_MS (Germ Free_Multiple Sclerosis) (End)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes | ||
| Clostridium | ||
| Flavonifractor | ||
| Lachnoclostridium | ||
| [Clostridium] innocuum |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Fig S5
Description: Relative abundance of fecal microbiota from humanized gnotobiotic RR mice that showed significant changes (unpaired t-test) at the genus level 2 weeks after the colonization and at the endpoint.
Abundance in Group 1: decreased abundance in GF_MS (Germ Free_Multiple Sclerosis) (End)
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus |
Revision editor(s): Anne-mariesharp
Experiment 9
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Ileum Distal intestine,Intestinum ileum,Lower intestine,Posterior intestine,Ileum,ileum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Experimental autoimmune encephalomyelitis ALLERGIC ENCEPH,ALLERGIC ENCEPH EXPER,Allergic encephalomyelitis,Allergic encephalomyelitis (disorder),Allergic Encephalomyelitis, Experimental,AUTOIMMUNE ENCEPH EXPER,Autoimmune Encephalomyelitis, Experimental,AUTOIMMUNE EXPER ENCEPH,Autoimmune Experimental Encephalomyelitis,EAE,ENCEPH ALLERGIC,ENCEPH AUTOIMMUNE EXPER,ENCEPH EXPER AUTOIMMUNE,Encephalomyelitis, Allergic,Encephalomyelitis, Autoimmune Experimental,Encephalomyelitis, Autoimmune, Experimental,Encephalomyelitis, Experimental Allergic,Encephalomyelitis, Experimental Autoimmune,EXPER ALLERGIC ENCEPH,EXPER AUTOIMMUNE ENCEPH,Experimental Allergic Encephalomyelitides,Experimental Allergic Encephalomyelitis,Experimental allergic encephalomyelitis (disorder),experimental autoimmune encephalomyelitis,Experimental Encephalomyelitis, Autoimmune,Experimental autoimmune encephalomyelitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- EAE (Experimental Autoimmune Encephalomyelitis)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Gnotobiotic mice that developed Experimental Autoimmune Encephalomyelitis after being colonized with ileal microbiota from an MS (Multiple Sclerosis)-affected human twin (MS-Q).
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
Signature 1
Source: Fig. S3F
Description: Relative abundance of Eisenbergiella as sole genus of the ileal microbiota that showed a significant difference (unpaired t-test) between healthy and diseased animals colonized with MSQ derived ileal microbiota.
Abundance in Group 1: increased abundance in EAE (Experimental Autoimmune Encephalomyelitis)
| NCBI | Quality Control | Links |
|---|---|---|
| Eisenbergiella |
Revision editor(s): Anne-mariesharp
Experiment 10
Subjects
- 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
- Timepoint Timepoint,timepoint
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- GF_MS (Germ Free_Multiple Sclerosis) (Early 2weeks)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GF-MS (Germ Free_Multiple Sclerosis) (End)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Germ-free Gnotobiotic RR (Relapsing Remitting) SJL/J mice colonized with ileal microbiota from the Multiple Sclerosis twin (MS-Q) (at endpoint after colonization)
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4E
Description: Relative abundance of fecal microbiota from colonized RR mice that showed significant changes (unpaired t-test) at the genus level.
Abundance in Group 1: increased abundance in GF-MS (Germ Free_Multiple Sclerosis) (End)
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnoclostridium |
Revision editor(s): Anne-mariesharp
Experiment 11
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GF_MS (Germ Free_Multiple Sclerosis) (End)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Germ-free Gnotobiotic RR (Relapsing Remitting) SJL/J mice colonized with ileal microbiota from the Multiple sclerosis twin (MS-A) (at endpoint after colonization)
Lab analysis
Statistical Analysis
Signature 1
Source: Fig S5
Description: Relative abundance of fecal microbiota from humanized gnotobiotic RR mice that showed significant changes (unpaired t-test) at the genus level 2 weeks after the colonization and at the endpoint.
Abundance in Group 1: increased abundance in GF_MS (Germ Free_Multiple Sclerosis) (End)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes | ||
| Clostridium | ||
| Flavonifractor | ||
| Lachnoclostridium |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Fig S5
Description: Relative abundance of fecal microbiota from humanized gnotobiotic RR mice that showed significant changes (unpaired t-test) at the genus level 2 weeks after the colonization and at the endpoint.
Abundance in Group 1: decreased abundance in GF_MS (Germ Free_Multiple Sclerosis) (End)
| NCBI | Quality Control | Links |
|---|---|---|
| [Clostridium] innocuum |
Revision editor(s): Anne-mariesharp
Experiment 12
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- GF_HT (Germ Free_Healthy Twin) (Early 2weeks)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- GF_HT (Germ Free_Healthy Twin) (End)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Germ-free Gnotobiotic RR (Relapsing Remitting) SJL/J mice colonized with ileal microbiota from the healthy twin (HT-A) (at endpoint after colonization)
Lab analysis
Statistical Analysis
Signature 1
Source: Fig S5
Description: Relative abundance of fecal microbiota from humanized gnotobiotic RR mice that showed significant changes (unpaired t-test) at the genus level 2 weeks after the colonization and at the endpoint.
Abundance in Group 1: increased abundance in GF_HT (Germ Free_Healthy Twin) (End)
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus |
Revision editor(s): Anne-mariesharp
