Predominance of Escherichia-Shigella in Gut Microbiome and Its Potential Correlation with Elevated Level of Plasma Tumor Necrosis Factor Alpha in Patients with Tuberculous Meningitis/Experiment 2

From BugSigDB


Reviewed Marked as Reviewed by Aiyshaaaa on 2023-6-8

Curated date: 2023/03/19

Curator: Chondatondaponda

Revision editor(s): Chondatondaponda, Aiyshaaaa

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
Meningeal tuberculosis meningeal tuberculosis,TB meningitis,Meningeal tuberculosis
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Healthy Control (HC)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Pulmonary tuberculosis (PTB)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
The patients who have been diagnosed from Pulmonary tuberculosis (PTB).
Group 0 sample size Number of subjects in the control (unexposed) group
9
Group 1 sample size Number of subjects in the case (exposed) group
13
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
therapy for 1+ week in previous 6 months. also, prior treatment of systemic antituberculous therapy for more than 1 week.

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
Welch's T-Test
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

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

Reviewed Marked as Reviewed by Aiyshaaaa on 2023-6-8

Curated date: 2023/06/08

Curator: Aiyshaaaa

Revision editor(s): Aiyshaaaa

Source: Supplementary Figure. 1 and 2(B)

Description: Welch’s t-test was used to analyze phylum-level differences in microbiota compositions between pairs of groups: HC and PTB

Abundance in Group 1: increased abundance in Pulmonary tuberculosis (PTB)

NCBI Quality ControlLinks
Pseudomonadota
Bacteroidia
Bacteroides
Escherichia/Shigella sp.

Revision editor(s): Aiyshaaaa

Signature 2

Reviewed Marked as Reviewed by Aiyshaaaa on 2023-6-8

Curated date: 2023/06/08

Curator: Aiyshaaaa

Revision editor(s): Aiyshaaaa, Atrayees

Source: Supplementary Figure. 1 and 2(B)

Description: Welch’s t-test was used to analyze phylum-level differences in microbiota compositions between pairs of groups: HC and PTB

Abundance in Group 1: decreased abundance in Pulmonary tuberculosis (PTB)

NCBI Quality ControlLinks
Bacillota
Blautia
Fusicatenibacter
Dorea
Romboutsia
Coprococcus

Revision editor(s): Aiyshaaaa, Atrayees