Gut microbiota in early pediatric multiple sclerosis: a case-control study/Experiment 3

From BugSigDB


Needs review

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

Subjects

Location of subjects Country from which study subjects were recruited
United States of America
Host species Species from which microbiome was sampled (if applicable)
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
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
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
IMD naive cases multiple sclerosis
Group 0 sample size Number of subjects in the control (unexposed) group
16
Group 1 sample size Number of subjects in the case (exposed) group
9
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
2 months

Lab analysis

Sequencing type Experimental technique used for quantifying microbial abundance
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

Statistical test Statistical test or computational tool used for differential abundance testing
"negative binomial regression" is not in the list (ANCOM, ANOSIM, ANOVA, DESeq2, edgeR, Fisher's Exact Test, Kruskall-Wallis, LEfSe, Linear Regression, Logistic Regression, ...) of allowed values for the "Statistical test" property.negative binomial regression
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

Richness Number of species
unchanged

Signature 1

Needs review

Curated date: 2020-05-27

Curator: Rimsha Azhar

Revision editor(s): Lwaldron, WikiWorks743

Source: Supplementary Table 7a, Supp Table 7b

Description: Taxa enriched and depleted in the IMD naive cases vs. controls

Abundance in Group 1: increased abundance in IMD naive cases multiple sclerosis

NCBI Links
Acidaminococcus
Akkermansia muciniphila
Atopobium
Bacteroides caccae
Bacteroides ovatus
Bifidobacterium
Bilophila
Blautia producta
Catenibacterium
Christensenellaceae
Comamonadaceae
Coprococcus
Coriobacteriaceae
Desulfovibrio
Dorea
Eubacteriales
Eubacterium
Faecalibacterium prausnitzii
Haemophilus parainfluenzae
Lachnospiraceae
Megamonas
Megasphaera
Methanobrevibacter
Oscillospira
Oscillospiraceae
Parabacteroides distasonis
Phascolarctobacterium
Phocaeicola plebeius
Prevotella copri
Prevotella stercorea
Pseudoramibacter
Ruminococcus
Sutterella
Veillonella dispar
[Ruminococcus] gnavus

Revision editor(s): Lwaldron, WikiWorks743

Signature 2

Needs review

Curated date: 2020-05-27

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743

Source: Supplementary Table 7a, Supp Table 7b

Description: Taxa enriched and depleted in the IMD naive cases vs. controls

Abundance in Group 1: decreased abundance in IMD naive cases multiple sclerosis

NCBI Links
Oscillospiraceae
Prevotella copri
Ligilactobacillus ruminis
Paraprevotella
Lachnospiraceae
Rikenellaceae
Bacteroides
Ruminococcus
Parabacteroides distasonis
Bacteroides uniformis
Butyricimonas
Mitsuokella multacida
Coprococcus
Peptostreptococcus anaerobius
Anaerostipes
Akkermansia muciniphila
Bacteroides eggerthii
Sutterella
Faecalibacterium prausnitzii
Bacteroides fragilis
Catenibacterium
Dialister
Phocaeicola coprophilus
Bacteroides ovatus
Dorea

Revision editor(s): WikiWorks743