Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life/Experiment 8

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Reviewed Marked as Reviewed by Lwaldron on 2022/03/2

Curated date: 2022/03/02

Curator: Shaimaa

Revision editor(s): Lwaldron, Shaimaa, WikiWorks, Aiyshaaaa

Subjects

Location of subjects

Luxembourg

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 0 sample size Number of subjects in the control (unexposed) group

4

Group 1 sample size Number of subjects in the case (exposed) group

6

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

11 mothers (6 controls and 5 cases) used antibiotics 12 hours before and after delivery, 3 VD mothers were positive group B Streptococcus screening.

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

Illumina

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)?

Yes

Alpha Diversity

Pielou Quantifies how equal the community is numerically

unchanged

Shannon Estimator of species richness and species evenness: more weight on species richness

unchanged

Richness Number of species

increased