Characterization of oral and gut microbiome temporal variability in hospitalized cancer patients/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/5
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
- Buccal mucosa Buccal mucosa,buccal mucosa
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Acute myeloid leukemia acute granulocytic leukemia,acute myeloblastic leukemia,acute myelocytic leukemia,acute myelogenous leukemia,acute myelogenous leukemias,acute myeloid leukemia,acute myeloid leukemia (AML),acute non lymphoblastic leukemia,acute Nonlymphocytic leukemia,acute nonlymphocytic leukemia,AML,AML - acute myeloid leukemia,ANLL,hematopoeitic - acute Myleogenous leukemia (AML),leukemia, acute myelogenous,leukemia, acute myeloid,leukemia, acute myeloid, susceptibility to,leukemia, myelocytic, acute,myeloid leukemia, acute,Acute myeloid leukemia
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- no infection
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- infection
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- acute myeloid leukemia patients that were microbiologically documented with infection during induction chemotherapy before neutrophil recovery
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- Mann-Whitney (Wilcoxon)
- 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
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/5
Source: Figure 5e
Description: Differential microbial abundance between patients who experienced infection and patients who did not
Abundance in Group 1: increased abundance in infection
| NCBI | Quality Control | Links |
|---|---|---|
| Stenotrophomonas |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/5
Source: Figure 5e
Description: Differential microbial abundance between patients who experienced infection and patients who did not
Abundance in Group 1: decreased abundance in infection
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus |
Revision editor(s): Claregrieve1
