Gut Microbiome Composition Predicts Infection Risk During Chemotherapy in Children With Acute Lymphoblastic Leukemia/Experiment 1

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Needs review

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

Subjects

Location of subjects Country from which study subjects were recruited
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
97

Lab analysis

Sequencing type Experimental technique used for quantifying microbial abundance
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

Statistical test Statistical test or computational tool used for differential abundance testing
"negative binomial regression" is not in the list (ANCOM, ANOSIM, ANOVA, DESeq2, edgeR, Fisher's Exact Test, Kruskall-Wallis, LEfSe, Linear Regression, Logistic Regression, ...) of allowed values for the "Statistical test" property.negative binomial regression
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
"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 for the "Confounders controlled for" property.chemotherapy and acute lymphoblastic leukemia

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

Needs review

Curated date: 2020-06-02

Curator: William Lam

Revision editor(s): WikiWorks743

Source: Table 1, Figure 1 and 2, 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 Links
Firmicutes
Clostridiaceae
Streptococcaceae
Enterococcaceae
Lactobacillaceae

Revision editor(s): WikiWorks743

Signature 2

Needs review

Curated date: 2020-06-02

Curator: William Lam

Revision editor(s): WikiWorks743

Source: Table 1, Figure 1 and 2, 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 Links
Bacteroidota
Faecalibacterium sp.
Oscillospiraceae
Actinobacteria
Verrucomicrobia

Revision editor(s): WikiWorks743