Gut microbiota composition can reflect immune responses of latent tuberculosis infection in patients with poorly controlled diabetes/Experiment 1
Subjects
- Location of subjects
- Taiwan
- 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 , Diabetes mellitus active tuberculosis,Kochs disease,TB,tuberculosis,tuberculosis disease,Tuberculosis,Diabetes,diabetes,diabetes mellitus,diabetes mellitus (disease),Diabetes mellitus (disorder),Diabetes mellitus, NOS,Diabetes NOS,DM,DM - Diabetes mellitus,Diabetes mellitus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- poorly-controlled diabetes mellitus (pDM) without latent tuberculosis infection (LTBI)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- poorly-controlled diabetes mellitus with latent tuberculosis infection (pDM + LTBI)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- poorly-controlled diabetes mellitus with latent tuberculosis infection (pDM + LTBI)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 87
- Group 1 sample size Number of subjects in the case (exposed) group
- 43
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
- 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
- 2
- 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
- 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. 3A and B
Description: Differential abundance analysis and identification of representative genera as predictive signatures through linear discriminant analysis (LDA) with effect size measurements (LEfSe) analysis and a random forest model to discriminate between patients with poorly controlled diabetes with and without latent tuberculosis infection (LTBI). (A) Significantly different taxa in the cladogram according to a LDA score of ≥ 2 (each circle represents phylogenetic levels from phylum to genus [inside to outside], and each diameter is proportional to the taxon’s abundance). (B) Significantly different genera in terms of relative abundance (LDA score of ≥ 2) between LTBI and non-LTBI groups.
Abundance in Group 1: increased abundance in poorly-controlled diabetes mellitus with latent tuberculosis infection (pDM + LTBI)
Revision editor(s): Nuerteye
Signature 2
Source: Figure 3A and B
Description: Differential abundance analysis and identification of representative genera as predictive signatures through linear discriminant analysis (LDA) with effect size measurements (LEfSe) analysis and a random forest model to discriminate between patients with poorly controlled diabetes with and without latent tuberculosis infection (LTBI). A) Significantly different taxa in the cladogram according to a LDA score of ≥ 2 (each circle represents phylogenetic levels from phylum to genus [inside to outside], and each diameter is proportional to the taxon’s abundance). B) Significantly different genera in terms of relative abundance (LDA score of ≥ 2) between LTBI and non-LTBI groups.
Abundance in Group 1: decreased abundance in poorly-controlled diabetes mellitus with latent tuberculosis infection (pDM + LTBI)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella 9Prevotella 9 | ||
| Streptococcus | ||
| Actinomyces | ||
| Haemophilus | ||
| RothiaRothia | ||
| Intestinimonas | ||
| Acidaminococcus | ||
| Muribaculaceae metagenomeMuribaculaceae metagenome |
Revision editor(s): Nuerteye
