Gut microbiota profiles of treatment-naïve adult acute myeloid leukemia patients with neutropenic fever during intensive chemotherapy
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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
- Thailand
- 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
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces
- 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
- Pretreatment
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Febrile neutropenia
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with neutropenic fever during intensive chemotherapy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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
- 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
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- increased
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- febrile neutropenia
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Bone marrow recovery
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- After initiation of induction chemotherapy
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- unchanged
Signature 1
Source: S1 table.
Description: The taxa that increased in relative abundance from febrile neutropenia to bone marrow recovery
Abundance in Group 1: increased abundance in Bone marrow recovery
NCBI | Quality Control | Links |
---|---|---|
Enterococcus | ||
Streptococcus | ||
Blautia | ||
Veillonella | ||
Parabacteroides |
Revision editor(s): Cyberian
Signature 2
Source: S1 table.
Description: The taxa that decreased in relative abundance from febrile neutropenia to bone marrow recovery
Abundance in Group 1: decreased abundance in Bone marrow recovery
NCBI | Quality Control | Links |
---|---|---|
Bacteroides | ||
Escherichia |
Revision editor(s): Cyberian
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pre-treatment
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- After initiation of induction chemotherapy treatment
Lab analysis
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V5
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- unchanged
Signature 1
Source: S1 table.
Description: taxa that increased in relative abundance from pretreatment to bone marrow recovery.
Abundance in Group 1: increased abundance in Bone marrow recovery
NCBI | Quality Control | Links |
---|---|---|
Enterococcus | ||
Streptococcus |
Revision editor(s): Cyberian
Signature 2
Source: S1 table.
Description: The taxa that decreased in relative abundance from pretreatment to bone marrow recovery
Abundance in Group 1: decreased abundance in Bone marrow recovery
NCBI | Quality Control | Links |
---|---|---|
Bacteroides | ||
Blautia | ||
Veillonella |
Revision editor(s): Cyberian