Meconium microbiome analysis identifies bacteria correlated with premature birth
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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, Shaimaa, ChiomaBlessing, Folakunmi
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
- Meconium Meconium,meconium
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cesarean section caesarean section,Cesarean section,cesarean section
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- vaginal delivery
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- C-section
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- the study groups are devided into two groups acc to the gestational age. 1) gestational age < 33 weeks. 2) gestational age >/= 33 weeks
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- Group 1 sample size Number of subjects in the case (exposed) group
- 33
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Ion Torrent
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- birth weight, chorioamnionitis, feeding practices, sex, Confounders controlled for: "infant antibiotic" 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.infant antibiotic, Confounders controlled for: "maternal antibiotic" 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.maternal antibiotic, Confounders controlled for: "insurance" 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.insurance, Confounders controlled for: "ROM>18 h" 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.ROM>18 h
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Table S6 in File S1
Description: Meconium microbiome related to mode of delivery in premature infants
Abundance in Group 1: increased abundance in C-section
NCBI | Quality Control | Links |
---|---|---|
Leuconostoc | ||
Negativicoccus | ||
Vagococcus | ||
Butyrivibrio |
Revision editor(s): WikiWorks
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Premature birth Birth, Premature,Birth, Preterm,Births, Premature,Births, Preterm,Premature Births,Preterm Birth,Preterm Births,Premature birth,premature birth
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- >/=33 weeks
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- infants <33 weeks gestational age
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 35
Lab analysis
Statistical Analysis
- Statistical test
- Spearman Correlation
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table 1
Description: Phyla, family, and genera taxonomy significantly correlated with gestational age
Abundance in Group 1: increased abundance in infants <33 weeks gestational age
Revision editor(s): WikiWorks
Signature 2
Source: Table 1
Description: Phyla, family, and genera taxonomy significantly correlated with gestational age
Abundance in Group 1: decreased abundance in infants <33 weeks gestational age
NCBI | Quality Control | Links |
---|---|---|
Oxalicibacterium |
Revision editor(s): WikiWorks