Gut microbial dysbiosis, IgA, and Enterococcus in common variable immunodeficiency with immune dysregulation/Experiment 2
From BugSigDB
Subjects
- Location of subjects
- Netherlands
- 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
- Common variable immunodeficiency acquired agammaglobulinemia,acquired hypogammaglobulinemia,common variable agammaglobulinemia,common variable hypogamma-globulinemia,common variable immune deficiency,common variable immunodeficiency,CVID,hypogamma-globulinemia, acquired,Idiopathic immunoglobulin deficiency,idiopathic immunoglobulin deficiency,Immunoglobulin deficiency, late-onset,Primary antibody deficiency,primary antibody deficiency,Primary hypogammaglobulinemia,primary hypogammaglobulinemia,secondary hypogammaglobulinemia,sporadic hypogammaglobulinemia,Common variable immunodeficiency
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Control (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Common Variable Immunodeficiency (CVID-med)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients living with Common Variable Immunodeficiency without use of antibiotics or immunosuppressive therapy 3 months prior to sampling.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
- Group 1 sample size Number of subjects in the case (exposed) group
- 50
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- ANCOM-BC
- 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
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Source: Supplementary Table 5
Description: Differentially abundant bacteria identified in CVID-med patients (Common Variable Immunodeficiency without medications) (n=50) vs Healthy Controls (n=48)
Abundance in Group 1: increased abundance in Common Variable Immunodeficiency (CVID-med)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus | ||
| Caproiciproducens | ||
| Eubacteriaceae | ||
| Lactococcus | ||
| Sellimonas | ||
| Tyzzerella | ||
| Veillonella |
