Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Encephalitis: A Chinese Pilot Study/Experiment 1
From BugSigDB
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
- Viral encephalitis Arbovirus encephalitis,arbovirus encephalitis,Arbovirus encephalitis (disorder),Arbovirus encephalitis (disorder) [Ambiguous],Arthropod-borne viral encephalitis, vector unknown,Arthropod-borne viral encephalitis, vector unknown (disorder),Encephalitis - viral,Encephalitis in viral disease NOS (disorder),Encephalitis, Arbovirus,Epidemic Encephalitis,Epidemic encephalitis,epidemic encephalitis,Epidemic encephalitis (disorder),mosquito-borne viral encephalitis,tick-borne viral encephalitis,Unspecified viral encephalitis (disorder),Viral Encephalitis,viral encephalitis,Viral encephalitis (disorder),Viral encephalitis NOS,Viruses caused encephalitis,Viruses encephalitis,Viral encephalitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy controls (CON)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Encephalitis (ENC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who suffered from brain inflammation (encephalitis)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 28
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Last year
Lab analysis
- Sequencing type
- 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
- 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
- 3.5
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
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
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: FIG 1 (G)
Description: Cladogram based on LEfSe results of the encephalitis patients (ENC) and healthy subjects serving as controls (CON).
Abundance in Group 1: increased abundance in Encephalitis (ENC)
Revision editor(s): Rahila
Signature 2
Source: FIG 1 (G)
Description: Cladogram based on LEfSe results of the encephalitis patients (ENC) and healthy subjects serving as controls (CON).
Abundance in Group 1: decreased abundance in Encephalitis (ENC)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Clostridiaceae | ||
| Lachnospiraceae | ||
| Veillonellaceae | ||
| Alcaligenaceae | ||
| Burkholderiales | ||
| Betaproteobacteria |
Revision editor(s): Rahila
