The oral microbiome of patients undergoing treatment for severe aplastic anemia: a pilot study/Experiment 1
From BugSigDB
Needs review
Subjects
- Location of subjects
- United States of America
- 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
- Tongue Glossus,Tongue,tongue
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Severe aplastic anemia SAA,Severe aplastic anemia,severe aplastic anemia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- baseline
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- hematopoietic stem cell transplantation engraftment
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- In HSCT patients, The first sample was obtained before transplant conditioning treatment. The second specimen was collected at engraftment, defined as two absolute neutrophil counts of greater than 500 per microliter for at least 2 days. The final specimen collection occurred at the participant’s scheduled clinic visit approximately 100 days following transplant.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V2-V8
- 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)?
- No
Signature 1
Needs review
Curated date: 2021/01/10
Curator: Shaimaa Elsafoury
Source: figure 8a
Description: Statistically significant bacteria as determined by Lefse analysis for hematopoietic stem cell transplantation patients between the baseline timepoint and engraftment timepoint
Abundance in Group 1: increased abundance in hematopoietic stem cell transplantation engraftment
