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
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): WikiWorks, Folakunmi, ChiomaBlessing
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
- 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,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,Acute myeloid leukemia
- 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 receiving low-intensity remission induction chemotherapy at a later timepoint T6
- 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
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
Lab analysis
- Sequencing type
- ITS / ITS2
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- 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)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- decreased
Signature 2
Curated date: 2021/01/10
Curator: William Lam
Revision editor(s): Atrayees, WikiWorks, Folakunmi, ChiomaBlessing
Source: Figure 4
Description: Significantly enriched taxa in patients who received high-intensity chemotherapies compared to those who received low-intensity chemotherapy
Abundance in Group 1: decreased abundance in High Intensity Chemotherapy
NCBI | Quality Control | Links |
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Malassezia |
Revision editor(s): Atrayees, WikiWorks, Folakunmi, ChiomaBlessing
Experiment 2
Curated date: 2021/01/10
Curator: WikiWorks
Revision editor(s): WikiWorks, Folakunmi, ChiomaBlessing
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients without bacterial infections at T3
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with bacterial infections at T3
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Acute Myeloid Leukemia patients that experienced microbiologically defined bacterial infections during remission induction chemotherapy at midpoint timepoint T3
- 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
Signature 1
Curated date: 2021/01/10
Curator: William Lam
Revision editor(s): Atrayees, WikiWorks, Folakunmi, ChiomaBlessing
Source: Figure S2 + Figure 6
Description: Differential abundance among acute leukemia patients who had infections during induction chemotherapy compared to those who did not experience infections at midpoint time point (T3)
Abundance in Group 1: increased abundance in Patients with bacterial infections at T3
NCBI | Quality Control | Links |
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Candida | ||
Debaryomycetaceae | ||
Saccharomycetales | ||
Saccharomycetes |
Revision editor(s): Atrayees, WikiWorks, Folakunmi, ChiomaBlessing
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients with no bacterial infections at T6
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with bacterial infections at T6
- 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 at endpoint timepoint T6
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 6 + Figure S3
Description: Differential abundance among acute leukemia patients who had infections during induction chemotherapy compared to those who did not experience infections at a later time point (T6)
Abundance in Group 1: decreased abundance in Patients with bacterial infections at T6
NCBI | Quality Control | Links |
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Fusarium | ||
Nectriaceae | ||
Sordariomycetes | ||
Hypocreales | ||
Fungi |
Revision editor(s): Folakunmi, ChiomaBlessing
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Antimicrobial agent antibiotic,antibiotics,Antibiotika,Antibiotikum,antibiotique,antimicrobial,antimicrobial agents,microbicide,microbicides,Antimicrobial agent,antimicrobial agent
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients who did not receive Amphotericin B
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients who received Amphotericin B
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Acute Myeloid Leukemia patients who received amphotericin B.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 66
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
Signature 1
Source: Figure 5
Description: Effect of amphotericin B on the composition of the oral fungal community at T6 in those who received amphotericin B compared to those who did not
Abundance in Group 1: increased abundance in Patients who received Amphotericin B
NCBI | Quality Control | Links |
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Fusarium |
Revision editor(s): Folakunmi, ChiomaBlessing