Observational Cohort Study of Oral Mycobiome and Interkingdom Interactions over the Course of Induction Therapy for Leukemia
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled (if applicable)
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Mouth Adult mouth,Cavital oralis,Cavitas oris,Cavum oris,Mouth cavity,Oral region,Oral vestibule,Regio oralis,Rima oris,Stoma,Stomatodaeum,Trophic apparatus,Vestibule of mouth,Vestibulum oris,Mouth
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Intensity Chemotherapy
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Intensity Chemotherapy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Acute Myeloid Leukemia patients with receiving low- intensity remission induction chemotherapy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 11
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
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
- Statistical test
- ANOVA
- 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
- increased
Signature 1
Source: Figure S1 and text, Table S1, Figure 4
Description: Mycobiome characteristics correlate with chemotherapy intensity at later point of sample collection (T6)
Abundance in Group 1: increased abundance in High Intensity Chemotherapy
NCBI | Quality Control | Links |
---|---|---|
Fusarium | ||
Candida | ||
Saccharomyces | ||
Cladosporium | ||
Malassezia |
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No bacterial infections
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- bacterial infections
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Acute Myeloid Leukemia patients that experience microbiologically defined bacterial infections during remission induction chemotherapy
- 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
- 9
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Figure 6 and text, Table S2 and S3
Description: Relative abundance differences of taxa at individual time points among Acute Myeloid Leukemia patients who did and did not experience bacterial infection during remission induction chemotherapy at midpoint time point (T3) prior to neutrophil recovery
Abundance in Group 1: increased abundance in bacterial infections
NCBI | Quality Control | Links |
---|---|---|
Candida |
Signature 2
Source: Figure 6 and text, Table S2 and S3
Description: Relative abundance differences of taxa at individual time points among Acute Myeloid Leukemia patients who did and did not experience bacterial infection during remission induction chemotherapy at midpoint time point (T3) prior to neutrophil recovery
Abundance in Group 1: decreased abundance in bacterial infections
NCBI | Quality Control | Links |
---|---|---|
Candida | ||
Cladosporium | ||
Fusarium | ||
Malassezia | ||
Saccharomyces |
Signature 3
Source: Figure 6 and text, Table S2 and S3
Description: Relative abundance differences of taxa at individual time points among Acute Myeloid Leukemia patients who did and did not experience bacterial infection during remission induction chemotherapy at later time point (T6) prior to neutrophil recovery
Abundance in Group 1: increased abundance in bacterial infections
NCBI | Quality Control | Links |
---|---|---|
Candida | ||
Cladosporium | ||
Fusarium | ||
Malassezia | ||
Saccharomyces |
Signature 4
Source: Figure 6 and text, Table S2 and S3
Description: Relative abundance differences of taxa at individual time points among Acute Myeloid Leukemia patients who did and did not experience bacterial infection during remission induction chemotherapy at later time point (T6) prior to neutrophil recovery
Abundance in Group 1: decreased abundance in bacterial infections
NCBI | Quality Control | Links |
---|---|---|
Fusarium |