Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Subjects
- Location of subjects
- Finland
- 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
- placenta
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- colostrum
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- maternal colostrum samples
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- prior to or during c-section
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
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- 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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Figure 4D
Description: Differentially abundant bacteria in colostrum samples compared to placenta samples from LEfSe analysis
Abundance in Group 1: increased abundance in colostrum
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillaceae | ||
| Streptococcaceae |
Revision editor(s): Merit, WikiWorks, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Figure 4D
Description: Differentially abundant bacteria in colostrum samples compared to placenta samples from LEfSe analysis
Abundance in Group 1: decreased abundance in colostrum
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae |
Revision editor(s): WikiWorks, ChiomaBlessing
