Normal gut microbiome in NMDA receptor encephalitis/Experiment 1
From BugSigDB
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
- Intestine Bowel,Intestinal tract,Intestine,intestine
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Encephalitis brain inflammation,Encephalitis,encephalitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- NMDAR encephalitis Patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with anti-NMDA receptor encephalitis, an antibody-mediated disease of the central nervous system
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Patients who received antibiotic treatment within the last 6 weeks before stool collection were excluded
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- PERMANOVA
- Negative Binomial Regression
- 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
- life style, diet
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- life style, age, sex, diet, smoking status, body weight
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 1
Description: Average gut flora profiles of patients with NMDAR encephalitis and healthy controls
Abundance in Group 1: increased abundance in NMDAR encephalitis Patients
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae | ||
| Lachnospiraceae | ||
| Parabacteroides | ||
| Prevotella | ||
| ClostridialesClostridiales |
Revision editor(s): Aishat
Signature 2
Needs review
Source: Figure 1
Description: Average gut flora profiles of patients with NMDAR encephalitis and healthy controls
Abundance in Group 1: decreased abundance in NMDAR encephalitis Patients
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Bacteroides | ||
| Dialister | ||
| Faecalibacterium | ||
| Oscillospiraceae |
Revision editor(s): Aishat, Fiddyhamma
