Breastfeeding patterns are associated with human milk microbiome composition: The Mother-Infant Microbiomes, Behavior, and Ecology Study (MIMBES)/Experiment 4

From BugSigDB


Reviewed Marked as Reviewed by Chloe on 2023-11-6

Curated date: 2023/10/12

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Subjects

Location of subjects
United States of America
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
Milk Mammary gland milk,Milk,milk
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Breastfeeding duration Breastfeeding duration,breastfeeding duration
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Medium Breastfeeding Bouts
Group 1 name Corresponds to the case (exposed) group for case-control studies
High Breastfeeding Bouts
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Breastfeeding pattern
Group 0 sample size Number of subjects in the control (unexposed) group
30
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)
Any antibiotics consumed by or administered to the mother or infant in the past 30 days

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
Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
centered log-ratio
Statistical test
ANCOM
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

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

Signature 1

Reviewed Marked as Reviewed by Chloe on 2023-11-6

Curated date: 2023/10/12

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: Figure 3B

Description: Log-fold change estimates relative to the medium group of genera identified as differentially abundant across [B] Breastfeeding bouts in the ANCOM-BC global test. Low < -1 Z-score, medium [-1 1] Z-score high > 1 Z-Score

Abundance in Group 1: increased abundance in High Breastfeeding Bouts

NCBI Quality ControlLinks
Bifidobacterium

Revision editor(s): Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Chloe on 2023-11-6

Curated date: 2023/10/12

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: Figure 3B

Description: Log-fold change estimates relative to the medium group of genera identified as differentially abundant across [B] Breastfeeding bouts in the ANCOM-BC global test. Low < -1 Z-score, medium [-1 1] Z-score high > 1 Z-Score

Abundance in Group 1: decreased abundance in High Breastfeeding Bouts

NCBI Quality ControlLinks
Micrococcus
Pedobacter
Acidocella
Achromobacter

Revision editor(s): Peace Sandy