Characterization of gut microbiota in children with pulmonary tuberculosis/Experiment 1
From BugSigDB
Subjects
- 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
- Pulmonary tuberculosis lung TB,lung tuberculosis,pulmonary TB,pulmonary tuberculosis,Tuberculosis, Pulmonary,Pulmonary tuberculosis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PTB patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Positive smear/culture or clinical‐radiological diagnosis per national guidelines
- Group 0 sample size Number of subjects in the control (unexposed) group
- 18
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No probiotics, prebiotics or antibiotics within one month prior to sampling
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
- T-Test
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex design, Matched on: "weight" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.weight
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- antibiotic exposure, Confounders controlled for: "demographic" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.demographic, Confounders controlled for: "co-infections" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.co-infections
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: Fig. 2, Fig. 3, Fig. 4
Description: Fig 2: Family‐level barplots Fig 3: Genus‐level barplots Fig 4: Species‐level barplots
Abundance in Group 1: increased abundance in PTB patients
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus agilisEnterococcus agilis | ||
| Prevotella copriPrevotella copri |
Revision editor(s): Nuerteye
Signature 2
Source: Fig. 2, Fig. 3, Fig. 4
Description: Fig 2: Family‐level barplots Fig 3: Genus‐level barplots Fig 4: Species‐level barplots
Abundance in Group 1: decreased abundance in PTB patients
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides vulgatusBacteroides vulgatus | ||
| Faecalibacterium prausnitzii | ||
| Ruminococcus |
Revision editor(s): Nuerteye
