The microbiome in urogenital schistosomiasis and induced bladder pathologies/Experiment 7
Curated date: 2024/05/01
Curator: Adenike Oladimeji-Kasumu
Revision editor(s): Adenike Oladimeji-Kasumu, Scholastica, WikiWorks
Subjects
- Location of subjects
- Nigeria
- 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
- Urine Urine,urine
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Urinary schistosomiasis bladder Schistosomiasis,bladder schistosomiasis,cystitis with bilharziasis,cystitis with bilharziasis (disorder),Schistosoma haematobium,Schistosoma haematobium (& vesical schistosomiasis),Schistosoma haematobium infection,Schistosoma Hematobium Infection,Schistosoma hematobium infection,Schistosoma hematobium infection (disorder),Schistosoma hematobium infectious disease,Schistosomiasis due to schistosoma haematobium,schistosomiasis due to Schistosoma haematobium,Schistosomiasis haematobia,schistosomiasis of bladder,Schistosomiasis of bladder [Ambiguous],urinary bladder schistosomiasis,urinary schistosomiasis,urinary schistosomiasis (disorder),vesical schistosomiasis,Vesical schistosomiasis NOS,Urinary schistosomiasis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-Infected
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Infected
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Not infected with urogenital schistosomiasis.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 46
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Recent use of Antibiotics
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Ion Torrent
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
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Curated date: 2024/05/01
Curator: Adenike Oladimeji-Kasumu
Revision editor(s): Adenike Oladimeji-Kasumu, Scholastica, WikiWorks
Source: Figure 7
Description: Predicted microbial biomarkers in urogenital schistosomiasis cases (infected) and controls (non-infected).
Abundance in Group 1: decreased abundance in Infected
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerococcus | ||
| Peptostreptococcaceae | ||
| Peptostreptococcus | ||
| Streptomycetaceae | ||
| Trabulsiella | ||
| Weissella | ||
| Xenorhabdus | ||
| unclassified Enterobacteriaceae | ||
| Lactobacillaceae |
Revision editor(s): Adenike Oladimeji-Kasumu, Scholastica, WikiWorks
Signature 2
Curated date: 2024/05/01
Curator: Adenike Oladimeji-Kasumu
Revision editor(s): Adenike Oladimeji-Kasumu, Scholastica, WikiWorks
Source: Figure 7
Description: Predicted microbial biomarkers in urogenital schistosomiasis cases (infected) and controls (non-infected).
Abundance in Group 1: increased abundance in Infected
| NCBI | Quality Control | Links |
|---|---|---|
| Sphingobacteriaceae | ||
| Sphingobacteriales | ||
| Sphingobacteriia | ||
| Sphingobacterium | ||
| Stenotrophomonas | ||
| unclassified Bacillales |
Revision editor(s): Adenike Oladimeji-Kasumu, Scholastica, WikiWorks
