Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth/Experiment 8
From BugSigDB
Needs review
Subjects
- Location of subjects
- United Kingdom
- 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
- 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,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to antibiotic Response to antibiotic,response to antibiotic
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Abx_mother_labour_IAP on day 4 (n=310) for vaginal delivery[where Abx is antibiotics, and IAP is Intrapartum antibiotic prophylaxis]
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- No Abx_mother_labour_IAP on day 4 (n=310) for vaginal delivery[where Abx is antibiotics, and IAP is Intrapartum antibiotic prophylaxis]
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mothers who did not receive antibiotics during labour.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 23
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- Statistical test
- Linear 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
- maternal age, Confounders controlled for: "mode of delivery" 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.mode of delivery, Confounders controlled for: "maternal intrapartum antibiotics" 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 intrapartum antibiotics, Confounders controlled for: "postnatal stay in hospital" 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.postnatal stay in hospital, Confounders controlled for: "partial breastfeeding" 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.partial breastfeeding, Confounders controlled for: "exclusive breastfeeding" 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.exclusive breastfeeding, Confounders controlled for: "hospital site" 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.hospital site, Confounders controlled for: "immediate breastfeeding after birth" 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.immediate breastfeeding after birth, Confounders controlled for: "postnatal antibiotics" 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.postnatal antibiotics, Confounders controlled for: "gender" 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.gender
Signature 1
Needs review
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: increased abundance in No Abx_mother_labour_IAP on day 4 (n=310) for vaginal delivery[where Abx is antibiotics, and IAP is Intrapartum antibiotic prophylaxis]
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium breve |
Revision editor(s): Ameenatoloko
Signature 2
Needs review
Source: Table S5
Description: Significant metagenomic species associated with clinical covariates after adjusting for potentially confounding covariates with MaAsLin.
Abundance in Group 1: decreased abundance in No Abx_mother_labour_IAP on day 4 (n=310) for vaginal delivery[where Abx is antibiotics, and IAP is Intrapartum antibiotic prophylaxis]
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium bifidum |
Revision editor(s): Ameenatoloko
