Meconium microbiome associates with the development of neonatal jaundice/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by Shaimaa Elsafoury on 9 February 2021

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

Subjects

Location of subjects Country from which study subjects were recruited
China
Host species Species from which microbiome was sampled (if applicable)
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Meconium Meconium
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
neonatal jaundice neonatal hyperbilirubinemia,neonatal icterus,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
cesarean 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 Experimental technique used for quantifying microbial abundance
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

Statistical test Statistical test or computational tool used for differential abundance testing
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
sex, gestational age, birth weight, "delivery mode" 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 for the "Confounders controlled for" property.delivery mode, "feeding pattern" 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 for the "Confounders controlled for" property.feeding pattern, smoking behavior, "alcohol consumption" 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 for the "Confounders controlled for" property.alcohol consumption, maternal age, "premature rupture of membranes" 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 for the "Confounders controlled for" property.premature rupture of membranes, "gestational diabetes mellitus" 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 for the "Confounders controlled for" property.gestational diabetes mellitus, "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 for the "Confounders controlled for" property.subclinical hypothyroidism in pregnancy

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 9 February 2021

Curated date: 2019-02-19

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743

Source: Figure 3

Description: LDA Score (log10) between control and case groups in cesarean infants with jaundice

Abundance in Group 1: increased abundance in cesarean infants with jaundice

NCBI Links
Cupriavidus

Revision editor(s): WikiWorks743

Signature 2

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 9 February 2021

Curated date: 2019-02-19

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743

Source: Figure 3

Description: LDA Score (log10) between control and case groups in cesarean infants with jaundice

Abundance in Group 1: decreased abundance in cesarean infants with jaundice

NCBI Links
Clostridiaceae
Pasteurellaceae
Bifidobacterium pseudolongum subsp. globosum
Pasteurellales

Revision editor(s): WikiWorks743