Gut Microbiome Composition Predicts Infection Risk During Chemotherapy in Children With Acute Lymphoblastic Leukemia
-
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
- 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 lymphoblastic leukemia acute lymphoblastic leukemia,acute lymphoblastic leukemia (ALL),acute lymphoblastic leukemia (disease),acute lymphoblastic leukemia/lymphoma,acute lymphocytic leukaemia,acute lymphocytic leukemia,acute lymphocytic leukemias,acute lymphogenous leukemia,acute lymphoid leukemia,ALL,ALL - acute lymphocytic leukemia,leukemia, lymphoblastic, malignant,lymphoblastic leukemia,lymphoblastic leukemia, acute,precursor cell lymphoblastic leukemia,precursor Lymphoblasic leukemia,precursor lymphoblastic leukemia
- 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
- post-induction therapy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 6 weeks of remission induction therapy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 112
- Group 1 sample size Number of subjects in the case (exposed) group
- 87
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- antibiotic exposure, demographics
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Supplemental Table S3
Description: Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to post induction
Abundance in Group 1: increased abundance in post-induction therapy
NCBI | Quality Control | Links |
---|---|---|
Bacillota | ||
Clostridiaceae | ||
Streptococcaceae | ||
Enterococcaceae | ||
Lactobacillaceae |
Signature 2
Source: Supplemental Table S3
Description: Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to post induction
Abundance in Group 1: decreased abundance in post-induction therapy
NCBI | Quality Control | Links |
---|---|---|
Faecalibacterium sp. | ||
Actinomycetota | ||
Verrucomicrobiota |
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- post-consolidation therapy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 8 weeks of consolidation
- Group 1 sample size Number of subjects in the case (exposed) group
- 107
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "chemotherapy and acute lymphoblastic leukemia" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.chemotherapy and acute lymphoblastic leukemia
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: Supplemental Table S3
Description: Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to postconsildation
Abundance in Group 1: increased abundance in post-consolidation therapy
NCBI | Quality Control | Links |
---|---|---|
Bacillota | ||
Lactobacillaceae |
Signature 2
Source: Table 1, Figure 1 and 2, Supplemental Table S3
Description: Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to postconsildation
Abundance in Group 1: decreased abundance in post-consolidation therapy
NCBI | Quality Control | Links |
---|---|---|
Bacteroidota | ||
Actinomycetota | ||
Verrucomicrobiota |
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- post re-induction therapy
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 120 weeks of continuation phase with the last 17-20 weeks of reinduction II therapy
- Group 1 sample size Number of subjects in the case (exposed) group
- 90
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Supplemental Table S3
Description: Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to post re-induction
Abundance in Group 1: increased abundance in post re-induction therapy
NCBI | Quality Control | Links |
---|---|---|
Bacillota | ||
Clostridiaceae | ||
Enterococcaceae | ||
Lactobacillaceae |
Signature 2
Source: Supplemental Table S3
Description: Change in gut microbiota diversity in acute lymphoblastic leukemia children from baseline to post re-induction
Abundance in Group 1: decreased abundance in post re-induction therapy
NCBI | Quality Control | Links |
---|---|---|
Oscillospiraceae | ||
Faecalibacterium sp. | ||
Actinomycetota | ||
Verrucomicrobiota |
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non-febrile neutropenia
- 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
- fever as an oral temperature more than 38.0°C persisting for more than 1 hour; neutropenia as an absolute neutrophil count less than or equal to 500 cells per microliter after baseline first sampled
- Group 0 sample size Number of subjects in the control (unexposed) group
- 47
- Group 1 sample size Number of subjects in the case (exposed) group
- 65
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
- unchanged
Signature 1
Source: Supplemental Table S6, Figure 5a
Description: Comparison of baseline diversity and composition between acute lymphoblastic leukemia children with and without febrile neutropenia occurring throughout therapy
Abundance in Group 1: increased abundance in febrile neutropenia
NCBI | Quality Control | Links |
---|---|---|
Pseudomonadota |
Revision editor(s): WikiWorks