Meconium microbiome associates with the development of neonatal jaundice/Experiment 2

From BugSigDB


Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Aiyshaaaa, ChiomaBlessing, Joan Chuks

Subjects

Location of subjects
China
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
Neonatal jaundice neonatal hyperbilirubinemia,neonatal icterus,neonatal jaundice,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 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
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

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)?
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
alcohol drinking, birth weight, gestational age, smoking behavior, maternal age, sex, 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, gestational diabetes, feeding practices, preterm premature rupture of the membranes, mode of birth

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

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 Quality ControlLinks
Clostridium perfringens

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

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 Quality ControlLinks
Rothia mucilaginosa
Streptococcus

Revision editor(s): WikiWorks