Alterations of the human gut microbiome in multiple sclerosis

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/14

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing

Subjects

Location of subjects: United States of America

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: healthy controls

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: multiple sclerosis patients

Group 0 sample size Number of subjects in the control (unexposed) group: 43

Group 1 sample size Number of subjects in the case (exposed) group: 60

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 6 months

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

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

Statistical test: DESeq2

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)?: Yes

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/15

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

Source: Figure 2a, 2c, Table 2

Description: Compositional differences in fecal microbiota between patients of MS compared to healthy controls using Illumina MiSeq

Abundance in Group 1: increased abundance in multiple sclerosis

NCBI	Quality Control	Links
Methanobrevibacter
Akkermansia
Micromonospora
Methanobacteriota

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/15

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

Source: Figure 2a, 2c, Table 2

Description: Compositional differences in fecal microbiota between patients of MS compared to healthy controls using Illumina MiSeq

Abundance in Group 1: decreased abundance in multiple sclerosis

NCBI	Quality Control	Links
Butyricimonas

Revision editor(s): WikiWorks

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/15

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing

Differences from previous experiment shown

Subjects

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

Group 1 name Corresponds to the case (exposed) group for case-control studies: multiple sclerosis patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: patients with multiple sclerosis

Lab analysis

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V5

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Roche454

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

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/15

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

Source: Figure 2a, 2c, Table 2

Description: Compositional differences in fecal microbiota between patients of MS compared to healthy controls using Roche 454

Abundance in Group 1: increased abundance in multiple sclerosis patients

NCBI	Quality Control	Links
Micromonospora
Methanobrevibacter
Akkermansia
Methanobacteriota

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/15

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

Source: Figure 2a, 2c, Table 2

Description: Compositional differences in fecal microbiota between patients of MS compared to healthy controls using Roche 454

Abundance in Group 1: decreased abundance in multiple sclerosis patients

NCBI	Quality Control	Links
Butyricimonas

Revision editor(s): WikiWorks

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/15

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: untreated multiple sclerosis

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: untreated multiple sclerosis

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

Lab analysis

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

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/15

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 2a, 2c, Table 2

Description: Compositional differences in fecal microbiota between untreated patients of MS compared to healthy controls using Illumina MiSeq

Abundance in Group 1: increased abundance in untreated multiple sclerosis

NCBI	Quality Control	Links
Akkermansia
Verrucomicrobium

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/15

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 2a, 2c, Table 2

Description: Compositional differences in fecal microbiota between untreated patients of MS compared to healthy controls using Illumina MiSeq

Abundance in Group 1: decreased abundance in untreated multiple sclerosis

NCBI	Quality Control	Links
Butyricimonas
Prevotella
Sutterella

Revision editor(s): Claregrieve1, WikiWorks

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/15

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, ChiomaBlessing

Differences from previous experiment shown

Subjects

Lab analysis

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V5

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Roche454

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

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/15

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 2a, 2c, Table 2

Description: compositional differences in fecal microbiota between untreated patients of MS compared to healthy controls using Roche 454

Abundance in Group 1: increased abundance in untreated multiple sclerosis

NCBI	Quality Control	Links
Akkermansia
Methanobacteriota
Methanobrevibacter
Verrucomicrobium

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/15

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 2a, 2c, Table 2

Description: compositional differences in fecal microbiota between untreated patients of MS compared to healthy controls using Roche 454

Abundance in Group 1: decreased abundance in untreated multiple sclerosis

NCBI	Quality Control	Links
Butyricimonas
Prevotella
Sutterella

Revision editor(s): Claregrieve1, WikiWorks

Experiment 5

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/15

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: untreated multiple sclerosis

Group 1 name Corresponds to the case (exposed) group for case-control studies: treated multiple sclerosis

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: treated multiple sclerosis

Group 0 sample size Number of subjects in the control (unexposed) group: 28

Group 1 sample size Number of subjects in the case (exposed) group: 32

Lab analysis

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

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/15

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

Source: Figure 2c, Table 2

Description: Compositional differences in fecal microbiota between treated patients of MS compared to untreated patients using Illumina MiSeq

Abundance in Group 1: increased abundance in treated multiple sclerosis

NCBI	Quality Control	Links
Prevotella
Sutterella

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/15

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

Source: Figure 2c, Table 2

Description: Compositional differences in fecal microbiota between treated patients of MS compared to untreated patients using Illumina MiSeq

Abundance in Group 1: decreased abundance in treated multiple sclerosis

NCBI	Quality Control	Links
Sarcina

Revision editor(s): WikiWorks

Experiment 6