Altered fecal microbiota composition in patients with major depressive disorder/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Peace Sandy

Subjects

Location of subjects
China
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
Unipolar depression Depression,Depression, Emotional,Depression, Endogenous,Depression, Involutional,Depression, Neurotic,Depression, Unipolar,Depressions,Depressions, Emotional,Depressions, Endogenous,Depressions, Neurotic,Depressions, Unipolar,DEPRESSIVE DIS,DEPRESSIVE DIS MAJOR,Depressive Disorder,Depressive Disorder, Major,Depressive Disorders,Depressive Disorders, Major,Depressive Neuroses,Depressive Neurosis,Depressive Symptom,Depressive Symptoms,Depressive Syndrome,Depressive Syndromes,Disorder, Depressive,Disorder, Major Depressive,Disorders, Depressive,Disorders, Major Depressive,Emotional Depression,Emotional Depressions,Endogenous Depression,Endogenous Depressions,Involutional Depression,Involutional Psychoses,Involutional Psychosis,MAJOR DEPRESSIVE DIS,major depressive disorder,Major Depressive Disorders,Neuroses, Depressive,Neurosis, Depressive,Neurotic Depression,Neurotic Depressions,Paraphrenia, Involutional,Psychoses, Involutional,Psychosis, Involutional,Symptom, Depressive,Symptoms, Depressive,Syndrome, Depressive,Syndromes, Depressive,Unipolar Depressions,Unipolar depression,unipolar depression
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
Active Major Depressive Disorder
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
The A-MDD group was defined as having an HAMDS score P20. The patients in the R-MDD group were defined as those with a baseline HAMDS scores P20 upon admission to the hospi- tal.
Group 0 sample size Number of subjects in the control (unexposed) group
30
Group 1 sample size Number of subjects in the case (exposed) group
29
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
1 month

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V1-V3
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

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
increased
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): WikiWorks

Source: Figure 2

Description: Taxonomic differences of fecal microbiota between Healthy Controls and Active Major Depressive Disorder groups

Abundance in Group 1: increased abundance in Active Major Depressive Disorder

NCBI Quality ControlLinks
Flavonifractor
Butyricimonas
Enterobacterales
Enterobacteriaceae
Parabacteroides
Porphyromonadaceae
Alistipes
Rikenellaceae

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): WikiWorks

Source: Figure 2

Description: Taxonomic differences of fecal microbiota between Healthy Controls and Active Major Depressive Disorder groups

Abundance in Group 1: decreased abundance in Active Major Depressive Disorder

NCBI Quality ControlLinks
Oscillospiraceae
Faecalibacterium
Dialister
Pasteurellaceae
Pasteurellales
Ruminococcus
Haemophilus
Peptostreptococcaceae
Escherichia
Shigella

Revision editor(s): WikiWorks