Human milk-associated bacterial communities associate with the infant gut microbiome over the first year of life

Introduction

Microbial communities inhabiting the human infant gut are important for immune system development and lifelong health. One critical exposure affecting the bacterial colonization of the infant gut is consumption of human milk, which contains diverse microbial communities and prebiotics. We hypothesized that human milk-associated microbial profiles are associated with those of the infant gut.

Methods

Maternal-infant dyads enrolled in the New Hampshire Birth Cohort Study (n = 189 dyads) contributed breast milk and infant stool samples collected approximately at 6 weeks, 4 months, 6 months, 9 months, and 12 months postpartum (n = 572 samples). Microbial DNA was extracted from milk and stool and the V4-V5 region of the bacterial 16S rRNA gene was sequenced.

Results

Clustering analysis identified three breast milk microbiome types (BMTs), characterized by differences in Streptococcus, Staphylococcus, Pseudomonas, Acinetobacter, and microbial diversity. Four 6-week infant gut microbiome types (6wIGMTs) were identified, differing in abundances of Bifidobacterium, Bacteroides, Clostridium, Streptococcus, and Escherichia/Shigella, while two 12-month IGMTs (12mIGMTs) differed primarily by Bacteroides presence. At 6 weeks, BMT was associated with 6wIGMT (Fisher's exact test value of p = 0.039); this association was strongest among infants delivered by Cesarean section (Fisher's exact test value of p = 0.0028). The strongest correlations between overall breast milk and infant stool microbial community structures were observed when comparing breast milk samples to infant stool samples collected at a subsequent time point, e.g., the 6-week breast milk microbiome associated with the 6-month infant gut microbiome (Mantel test Z-statistic = 0.53, value of p = 0.001). Streptoccous and Veillonella species abundance were correlated in 6-week milk and infant stool, and 4- and 6-month milk Pantoea species were associated with infant stool Lachnospiraceae genera at 9 and 12  months.

Discussion

We identified clusters of human milk and infant stool microbial communities that were associated in maternal-infant dyads at 6 weeks of life and found that milk microbial communities were more strongly associated with infant gut microbial communities in infants delivered operatively and after a lag period. These results suggest that milk microbial communities have a long-term effect on the infant gut microbiome both through sharing of microbes and other molecular mechanisms.

Validation of the Emotional Tone Index for Families (ETIF): A Multi-Informant Measure of Emotional Closeness

Despite the importance of emotional closeness (EC) in families, few researchers have accurately measured the construct in a systemic way. Additionally, existing measures rely on ratings from one informant, typically the mother, to provide information on closeness within the entire family system. We examined EC in 140 individuals (37 families) using the Emotional Tone Index for Families (ETIF), a novel, multi-informant measure that obtains bidirectional information about EC within every family relationship. The parent identified as most familiar with the family also completed two widely used single-informant measures: The McMaster Family Assessment Device and the Family Adaptability and Cohesion Evaluation Scales, version IV. The ETIF exhibited good test-retest reliability, high internal consistency, and concurrent validity with the single-informant measures. Though the primary respondent scores correlated highly with overall family closeness, results revealed only a modest association between closeness ratings within each dyad and parents rated higher levels of closeness toward their children than children rated closeness toward parents. These findings suggest that ratings from multiple informants provide valuable information about discrepancies in perceived closeness between family members and other complex family dynamics that cannot be captured by single-informant measures. Limitations, future directions, and implications for practice are discussed.

Prediagnostic breast milk DNA methylation alterations in women who develop breast cancer

Prior candidate gene studies have shown tumor suppressor DNA methylation in breast milk related with history of breast biopsy, an established risk factor for breast cancer. To further establish the utility of breast milk as a tissue-specific biospecimen for investigations of breast carcinogenesis, we measured genome-wide DNA methylation in breast milk from women with and without a diagnosis of breast cancer in two independent cohorts. DNA methylation was assessed using Illumina HumanMethylation450k in 87 breast milk samples. Through an epigenome-wide association study we explored CpG sites associated with a breast cancer diagnosis in the prospectively collected milk samples from the breast that would develop cancer compared with women without a diagnosis of breast cancer using linear mixed effects models adjusted for history of breast biopsy, age, RefFreeCellMix cell estimates, time of delivery, array chip and subject as random effect. We identified 58 differentially methylated CpG sites associated with a subsequent breast cancer diagnosis (q-value <0.05). Nearly all CpG sites associated with a breast cancer diagnosis were hypomethylated in cases compared with controls and were enriched for CpG islands. In addition, inferred repeat element methylation was lower in breast milk DNA from cases compared to controls, and cases exhibited increased estimated epigenetic mitotic tick rate as well as DNA methylation age compared with controls. Breast milk has utility as a biospecimen for prospective assessment of disease risk, for understanding the underlying molecular basis of breast cancer risk factors and improving primary and secondary prevention of breast cancer.

Microbial Communities in Human Milk Relate to Measures of Maternal Weight

The process of breastfeeding exposes infants to bioactive substances including a diversity of bacteria from breast milk as well as maternal skin. Knowledge of the character of and variation in these microbial communities, as well as the factors that influence them, is limited. We aimed to identify profiles of breastfeeding-associated microbial communities and their association with maternal and infant factors. Bilateral milk samples were collected from women in the New Hampshire Birth Cohort Study at approximately 6 weeks postpartum without sterilization of the skin in order to capture the infant-relevant exposure. We sequenced the V4-V5 hypervariable region of the bacterial 16S rRNA gene in 155 human milk samples. We used unsupervised clustering (partitioning around medoids) to identify microbial profiles in milk samples, and multinomial logistic regression to test their relation with maternal and infant variables. Associations between alpha diversity and maternal and infant factors were tested with linear models. Four breastfeeding microbiome types (BMTs) were identified, which differed in alpha diversity and in Streptococcus, Staphylococcus, Acinetobacter, and Pseudomonas abundances. Higher maternal pre-pregnancy BMI was associated with increased odds of belonging to BMT1 [OR (95% CI) = 1.13 (1.02, 1.24)] or BMT3 [OR (95% CI) = 1.12 (1.01, 1.25)] compared to BMT2. Independently, increased gestational weight gain was related to reduced odds of membership in BMT1 [OR (95% CI) = 0.66 (0.44, 1.00) per 10 pounds]. Alpha diversity was positively associated with gestational weight gain and negatively associated with postpartum sample collection week. There were no statistically significant associations of breastfeeding microbiota with delivery mode. Our results indicate that the breastfeeding microbiome partitions into four profiles and that its composition and diversity is associated with measures of maternal weight.

Sex-specific associations of infants' gut microbiome with arsenic exposure in a US population

Arsenic is a ubiquitous environmental toxicant with antimicrobial properties that can be found in food and drinking water. The influence of arsenic exposure on the composition of the human microbiome in US populations remains unknown, particularly during the vulnerable infant period. We investigated the relationship between arsenic exposure and gut microbiome composition in 204 infants prospectively followed as part of the New Hampshire Birth Cohort Study. Infant urine was analyzed for total arsenic concentration using inductively coupled plasma mass spectrometry. Stool microbiome composition was determined using sequencing of the bacterial 16S rRNA gene. Infant urinary arsenic related to gut microbiome composition at 6 weeks of life (p = 0.05, adjusted for infant feeding type and urine specific gravity). Eight genera, six within the phylum Firmicutes, were enriched with higher arsenic exposure. Fifteen genera were negatively associated with urinary arsenic concentration, including Bacteroides and Bifidobacterium. Upon stratification by both sex and feeding method, we found detectable associations among formula-fed males (p = 0.008), but not other groups (p > 0.05 for formula-fed females and for breastfed males and females). Our findings from a US population indicate that even moderate arsenic exposure may have meaningful, sex-specific effects on the gut microbiome during a critical window of infant development.

Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner

BACKGROUND

The gut microbiome has an important role in infant health and immune development and may be affected by early-life exposures. Maternal diet may influence the infant gut microbiome through vertical transfer of maternal microbes to infants during vaginal delivery and breastfeeding. We aimed to examine the association of maternal diet during pregnancy with the infant gut microbiome 6 weeks post-delivery in mother-infant dyads enrolled in the New Hampshire Birth Cohort Study. Infant stool samples were collected from 145 infants, and maternal prenatal diet was assessed using a food frequency questionnaire. We used targeted sequencing of the 16S rRNA V4-V5 hypervariable region to characterize infant gut microbiota. To account for differences in baseline and trajectories of infant gut microbial profiles, we stratified analyses by delivery mode.

RESULTS

We identified three infant gut microbiome clusters, characterized by increased abundance of Bifidobacterium, Streptococcus and Clostridium, and Bacteroides, respectively, overall and in the vaginally delivered infant stratum. In the analyses stratified to infants born vaginally and adjusted for other potential confounders, maternal fruit intake was associated with infant gut microbial community structure (PERMANOVA, p < 0.05). In multinomial logistic regression analyses, increased fruit intake was associated with an increased odds of belonging to the high Streptococcus/Clostridium group among infants born vaginally (OR (95% CI) = 2.73 (1.36, 5.46)). In infants delivered by Cesarean section, we identified three clusters that differed slightly from vaginally delivered infants, which were characterized by a high abundance of Bifidobacterium, high Clostridium and low Streptococcus and Ruminococcus genera, and high abundance of the family Enterobacteriaceae. Maternal dairy intake was associated with an increased odds of infants belonging to the high Clostridium cluster in infants born by Cesarean section (OR (95% CI) = 2.36 (1.05, 5.30)). Linear models suggested additional associations between maternal diet and infant intestinal microbes in both delivery mode strata.

CONCLUSIONS

Our data indicate that maternal diet influences the infant gut microbiome and that these effects differ by delivery mode.

Abstract 4355: Altered DNA methylation in breast milk from women with breast cancer

Prior candidate gene studies have shown that methylation-induced silencing of tumor suppressor genes in breast milk is related with history of breast biopsy, an established risk factor for breast cancer. To further establish the utility of breast milk as a tissue-specific biospecimen for investigations of breast carcinogenesis we measured genome-wide DNA methylation in breast milk from women with and without a diagnosis of breast cancer. Breast milk provides a source of cells without invasive procedure that is available during a window of increased breast cancer risk. Actively lactating women were enrolled and consented through the University of Massachusetts Amherst breast milk study targeting high risk subjects. Participants completed a questionnaire to provide demographic and breast cancer risk factor data. Genome-wide DNA methylation levels were quantified using the Illumina 450K HumanMethylation array. Data was processed in R using RnBeads. Beta-values were normalized (FUNnorm), low quality probes were filtered and transformed to M-values. Linear mixed effects models were fit including a random effect for subject and adjusted for history of breast biopsy, age, body mass index, age of the baby, and estimated cell type proportions, an interaction term for time of diagnosis was included. DNA methylation in women with breast cancer (n=9), was compared with women without a history of breast cancer (n=22). Among women with a diagnosis of breast cancer there were two groups: those diagnosed within one year of donating breast milk, and those diagnosed more than one year before sample collection. Four women in the control and five women in the cancer group provided bilateral breast milk samples at recruitment and both samples were included in the analyses. CpGs with significant differential methylation were tested for enrichment in gene pathways using the KEGG database. We identified 215 differentially methylated CpG sites in women diagnosed within one year of sample donation compared with women without a diagnosis of breast cancer (Q&lt;0.10). The top sites were in ATF3 (an adaptive-response gene linked to epithelial mesenchymal transition), and in COL5A3 (an extracellular matrix gene related to metastasis potential). In addition, among women with a breast cancer diagnosis more than one year before sample donation we identified 8148 differentially methylated CpG sites compared with women without a breast cancer diagnosis (Q&lt;0.05). Five sites were in OTOF a calcium-sensing protein in cancer. These differentially methylated sites were significantly enriched in relevant pathways such metabolic (Q= 3.12E-116), and cancer pathways (Q= 2.08E-58), PI3K-Akt signaling pathway (Q=7.05E-40), and transcriptional misregulation in cancer (Q=1.41E-29). Future studies are needed to validate our findings in independent subjects and to investigate the utility of breast milk as a biospecimen for understanding the molecular basis of disease risk and prospective risk assessment.

Citation Format: Lucas A. Salas, Sara N. Lundgren, Eva P. Browne, Elizabeth C. Punska, Douglas L. Anderton, Kathleen F. Arcaro, Brock C. Christensen. Altered DNA methylation in breast milk from women with breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4355. doi:10.1158/1538-7445.AM2017-4355

Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants

IMPORTANCE

The intestinal microbiome plays a critical role in infant development, and delivery mode and feeding method (breast milk vs formula) are determinants of its composition. However, the importance of delivery mode beyond the first days of life is unknown, and studies of associations between infant feeding and microbiome composition have been generally limited to comparisons between exclusively breastfed and formula-fed infants, with little consideration given to combination feeding of both breast milk and formula.

OBJECTIVE

To examine the associations of delivery mode and feeding method with infant intestinal microbiome composition at approximately 6 weeks of life.

DESIGN, SETTING, AND PARTICIPANTS

Prospective observational study of 102 infants followed up as part of a US pregnancy cohort study.

EXPOSURES

Delivery mode was abstracted from delivery medical records, and feeding method prior to the time of stool collection was ascertained through detailed questionnaires.

MAIN OUTCOMES AND MEASURES

Stool microbiome composition was characterized using next-generation sequencing of the 16S rRNA gene.

RESULTS

There were 102 infants (mean gestational age, 39.7 weeks; range, 37.1-41.9 weeks) included in this study, of whom 70 were delivered vaginally and 32 by cesarean delivery. In the first 6 weeks of life, 70 were exclusively breastfed, 26 received combination feeding, and 6 were exclusively formula fed. We identified independent associations between microbial community composition and both delivery mode (P< .001; Q < .001) and feeding method (P = .01; Q < .001). Differences in microbial community composition between vaginally delivered infants and infants delivered by cesarean birth were equivalent to or significantly larger than those between feeding groups (P = .003). Bacterial communities associated with combination feeding were more similar to those associated with exclusive formula feeding than exclusive breastfeeding (P = .002). We identified 6 individual bacterial genera that were differentially abundant between delivery mode and feeding groups.

CONCLUSIONS AND RELEVANCE

The infant intestinal microbiome at approximately 6 weeks of age is significantly associated with both delivery mode and feeding method, and the supplementation of breast milk feeding with formula is associated with a microbiome composition that resembles that of infants who are exclusively formula fed. These results may inform feeding choices and shed light on the mechanisms behind the lifelong health consequences of delivery and infant feeding modalities.