10.3390/Experiment 1
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
- Extrapulmonary tuberculosis Extrapulmonary tuberculosis,extrapulmonary tuberculosis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy volunteers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Lymph node tuberculosis (LNTB) patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- All Lymph node tuberculosis (LNTB) patients cases included in this study were newly diagnosed
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- prior use of therapeutic medications (including antibiotics)
Lab analysis
- Sequencing type
- WMS
- 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
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Figure 3A-B
Description: Gut microbiota characteristics in patients with lymph node tuberculosis. (A) The phylogenetic tree generated by LEfSe analysis showing the distribution of microbial taxa from the phylum to genus level between the LNTB group and the control group. (B) The histogram of LDA scores identifying significantly different bacterial taxa between patients and controls (LDA score > 2.0).
Abundance in Group 1: increased abundance in
Revision editor(s): Nuerteye
Signature 2
Source: Figure 3A-B
Description: Gut microbiota characteristics in patients with lymph node tuberculosis. (A) The phylogenetic tree generated by LEfSe analysis showing the distribution of microbial taxa from the phylum to genus level between the LNTB group and the control group. (B) The histogram of LDA scores identifying significantly different bacterial taxa between patients and controls (LDA score > 2.0).
Abundance in Group 1: decreased abundance in
Revision editor(s): Nuerteye
