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

From BugSigDB
Reviewed Marked as Reviewed by Chloe on 2023-11-6
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Holdsworth EA, Williams JE, Pace RM, Lane AA, Gartstein M, McGuire MA, McGuire MK, Meehan CL
Journal
PloS one
Year
2023
The human milk microbiome (HMM) is hypothesized to be seeded by multiple factors, including the infant oral microbiome during breastfeeding. However, it is not known whether breastfeeding patterns (e.g., frequency or total time) impact the composition of the HMM. As part of the Mother-Infant Microbiomes, Behavior, and Ecology Study (MIMBES), we analyzed data from naturalistic observations of 46 mother-infant dyads living in the US Pacific Northwest and analyzed milk produced by the mothers for its bacterial diversity and composition. DNA was extracted from milk and the V1-V3 region of the 16S rRNA gene was amplified and sequenced. We hypothesized that number of breastfeeding bouts (breastfeeding sessions separated by >30 seconds) and total time breastfeeding would be associated with HMM α-diversity (richness, diversity, or evenness) and differential abundance of HMM bacterial genera. Multiple linear regression was used to examine associations between HMM α-diversity and the number of breastfeeding bouts or total time breastfeeding and selected covariates (infant age, maternal work outside the home, frequency of allomother physical contact with the infant, non-household caregiving network). HMM richness was inversely associated with number of breastfeeding bouts and frequency of allomother physical contact, but not total time breastfeeding. Infants' non-household caregiving network was positively associated with HMM evenness. In two ANCOM-BC analyses, abundances of 5 of the 35 most abundant genera were differentially associated with frequency of breastfeeding bouts (Bifidobacterium, Micrococcus, Pedobacter, Acidocella, Achromobacter); 5 genera (Bifidobacterium, Agreia, Pedobacter, Rugamonas, Stenotrophomonas) were associated with total time breastfeeding. These results indicate that breastfeeding patterns and infant caregiving ecology may play a role in influencing HMM composition. Future research is needed to identify whether these relationships are consistent in other populations and if they are associated with variation in the infant's gastrointestinal (including oral) microbiome.

Experiment 1


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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
breastfeeding duration breastfeeding duration
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Medium Total Time Breastfeeding
Group 1 name Corresponds to the case (exposed) group for case-control studies
Low Total Time Breastfeeding
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
28
Group 1 sample size Number of subjects in the case (exposed) group
10
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 3A

Description: Log-Fold Change estimates relative to the medium group of genera identified as differentially abundant across [A] total time breastfeeding group 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 Low Total Time Breastfeeding

NCBI Quality ControlLinks
Agreia
Bifidobacterium
Pedobacter
Stenotrophomonas
Rugamonas

Revision editor(s): Peace Sandy

Experiment 2


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

Curated date: 2023/10/12

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
High Total Time Breastfeeding
Group 1 sample size Number of subjects in the case (exposed) group
8

Lab analysis

Statistical Analysis

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 3A

Description: Log-Fold Change estimates relative to the medium group of genera identified as differentially abundant across [A] total time breastfeeding group 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 Total Time Breastfeeding

NCBI Quality ControlLinks
Agreia
Bifidobacterium
Pedobacter
Stenotrophomonas
Rugamonas

Revision editor(s): Peace Sandy

Experiment 3


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

Curated date: 2023/10/12

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Differences from previous experiment shown

Subjects

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
Low Breastfeeding Bouts
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
10

Lab analysis

Statistical Analysis

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 Low Breastfeeding Bouts

NCBI Quality ControlLinks
Bifidobacterium
Micrococcus

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 Low Breastfeeding Bouts

NCBI Quality ControlLinks
Pedobacter
Acidocella
Achromobacter

Revision editor(s): Peace Sandy

Experiment 4


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

Curated date: 2023/10/12

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
High Breastfeeding Bouts
Group 1 sample size Number of subjects in the case (exposed) group
6

Lab analysis

Statistical Analysis

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