Gut microbiome, T cell subsets, and cytokine analysis identify differential biomarkers in tuberculosis/Experiment 2
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
- Tuberculosis active tuberculosis,Kochs disease,TB,tuberculosis,tuberculosis disease,Tuberculosis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of retreated patients (fz group) and healthy controls (jk group)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- TB patients (cz group)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 60
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- never used antituberculosis drugs or were treated with antituberculosis drugs for the first time for less than 1 month
Lab analysis
- Sequencing type
- 16S
- 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).
- relative abundances
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure 3A and 3B
Description: Identification of different genera as biomarkers by relative abundance. (A) The column length signifies the impact of distinct species in terms of relative abundance (linear discriminant analysis scores > 4). (B) The clado-gram displays the species that are markedly distinct. Each circle symbolizes the phylogenetic progression from phylum to genus, encompassing both the interior and exterior. The size of each circle is linked to the number of taxa present, and the biomarker is in agreement with the group indicated by the color.
Abundance in Group 1: increased abundance in TB patients (cz group)
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae | ||
| Gemmiger | ||
| Eubacterium | ||
| Actinomycetaceae | ||
| Actinomyces | ||
| TM7TM7 | ||
| TM7 3TM7 3 | ||
| Bulleidia | ||
| Comamonas | ||
| Coxiellaceae | ||
| Rickettsiella sp. | ||
| Legionellales | ||
| Gaiella |
Revision editor(s): Nuerteye
