Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia/Experiment 6

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Reviewed Marked as Reviewed by Svetlana up on 2024-7-16

Curated date: 2024/07/04

Curator: Jacob A. De Jesus

Revision editor(s): WikiWorks, Scholastica, Jacob A. De Jesus

Subjects

Location of subjects
Australia
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
Treatment refractory schizophrenia refractory schizophrenia,treatment resistant schizophrenia,treatment-refractory schizophrenia,TRS,Treatment refractory schizophrenia,treatment refractory schizophrenia
Group 0 name Corresponds to the control (unexposed) group for case-control studies
control individuals without a psychiatric diagnosis of schizophrenia
Group 1 name Corresponds to the case (exposed) group for case-control studies
CNR: individuals with treatment-resistant schizophrenia nonresponsive to clozapine
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
CNR: individuals with treatment-resistant schizophrenia who were clozapine nonresponsive (total PANSS score >60).
Group 0 sample size Number of subjects in the control (unexposed) group
25
Group 1 sample size Number of subjects in the case (exposed) group
22
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
WMS
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Not specified
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).
centered log-ratio
Statistical test
ANCOM
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes
Matched on Factors on which subjects have been matched on in a case-control study
age, body mass index, sex
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, body mass index, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
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 Svetlana up on 2024-7-16

Curated date: 2024/07/04

Curator: Jacob A. De Jesus

Revision editor(s): Jacob A. De Jesus, WikiWorks

Source: Figure 3

Description: Differentially abundant species identified for CR and CNR group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.

Abundance in Group 1: increased abundance in CNR: individuals with treatment-resistant schizophrenia nonresponsive to clozapine

NCBI Quality ControlLinks
Ruthenibacterium lactatiformans
Faecalicatena gnavusFaecalicatena gnavus
CAG 83 sp000431575CAG 83 sp000431575

Revision editor(s): Jacob A. De Jesus, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-7-16

Curated date: 2024/07/04

Curator: Jacob A. De Jesus

Revision editor(s): Jacob A. De Jesus, WikiWorks

Source: Figure 3

Description: Differentially abundant species identified for CR and CNR group comparisons. Analyses were performed using ANCOM-BC, adjusting for age, sex, and body mass index.

Abundance in Group 1: decreased abundance in CNR: individuals with treatment-resistant schizophrenia nonresponsive to clozapine

NCBI Quality ControlLinks
Romboutsia timonensis
Faecalibacterium MIC7145Faecalibacterium MIC7145
ER4 sp000765235ER4 sp000765235
Faecalibacterium prausnitzii DFaecalibacterium prausnitzii D
UBA7182 MIC8422UBA7182 MIC8422
Gemmiger MIC9530Gemmiger MIC9530
GCA 900066135 MIC6659GCA 900066135 MIC6659

Revision editor(s): Jacob A. De Jesus, WikiWorks