Meconium microbiome associates with the development of neonatal jaundice
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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
- China
- 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
- Meconium Meconium
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- neonatal jaundice neonatal hyperbilirubinemia,neonatal icterus,neonatal jaundice
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cesarean infants with jaundice
- Group 0 sample size Number of subjects in the control (unexposed) group
- 160
- Group 1 sample size Number of subjects in the case (exposed) group
- 141
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- among all the participants,11 mothers used antibiotics during pregnancy and 4 infants used antibiotics after birth.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- LEfSe
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.5
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- sex, gestational age, birth weight, Confounders controlled for: "delivery mode" 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.delivery mode, Confounders controlled for: "feeding pattern" 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.feeding pattern, smoking behavior, Confounders controlled for: "alcohol consumption" 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.alcohol consumption, maternal age, Confounders controlled for: "premature rupture of membranes" 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.premature rupture of membranes, Confounders controlled for: "gestational diabetes mellitus" 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.gestational diabetes mellitus, Confounders controlled for: "subclinical hypothyroidism in pregnancy" 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.subclinical hypothyroidism in pregnancy
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 3
Description: LDA Score (log10) between control and case groups in cesarean infants with jaundice
Abundance in Group 1: increased abundance in cesarean infants with jaundice
NCBI | Links |
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Cupriavidus ⚠ |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 3
Description: LDA Score (log10) between control and case groups in cesarean infants with jaundice
Abundance in Group 1: decreased abundance in cesarean infants with jaundice
NCBI | Links |
---|---|
Clostridiaceae | |
Pasteurellaceae | |
Bifidobacterium pseudolongum subsp. globosum | |
Pasteurellales |
Revision editor(s): WikiWorks
Experiment 2
Subjects
- Location of subjects
- China
- 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
- Meconium Meconium
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- neonatal jaundice neonatal hyperbilirubinemia,neonatal icterus,neonatal jaundice
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- infants with jaundice
- Group 0 sample size Number of subjects in the control (unexposed) group
- 160
- Group 1 sample size Number of subjects in the case (exposed) group
- 141
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- among all the participants,11 mothers used antibiotics during pregnancy and 4 infants used antibiotics after birth.
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- LEfSe
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.5
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- sex, gestational age, birth weight, Confounders controlled for: "delivery mode" 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.delivery mode, Confounders controlled for: "feeding pattern" 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.feeding pattern, smoking behavior, Confounders controlled for: "alcohol consumption" 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.alcohol consumption, maternal age, Confounders controlled for: "premature rupture of membranes" 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.premature rupture of membranes, Confounders controlled for: "gestational diabetes mellitus" 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.gestational diabetes mellitus, Confounders controlled for: "subclinical hypothyroidism in pregnancy" 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.subclinical hypothyroidism in pregnancy
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Figure 2
Description: LDA Score (log10) between control and case groups in all infants
Abundance in Group 1: increased abundance in infants with jaundice
NCBI | Links |
---|---|
Clostridium perfringens |
Revision editor(s): WikiWorks
Signature 2
Source: Supplementary Figure 2
Description: LDA Score (log10) between control and case groups in all infants
Abundance in Group 1: decreased abundance in infants with jaundice
NCBI | Links |
---|---|
Rothia mucilaginosa | |
Streptococcus |
Revision editor(s): WikiWorks