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Front Nutr. 2019 May 16;6:58. doi: 10.3389/fnut.2019.00058. eCollection 2019.

Integrated Analysis of Human Milk Microbiota With Oligosaccharides and Fatty Acids in the CHILD Cohort.

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Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.
Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada.
Developmental Origins of Chronic Diseases in Children Network (DEVOTION), Winnipeg, MB, Canada.
Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran.
Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada.
Department of Pediatrics and Larson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, University of California, San Diego, San Diego, CA, United States.
Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada.
School of Computing, Queen's University, Kingston, ON, Canada.
Department of Pediatrics, University of Alberta, Edmonton, AB, Canada.
Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada.
Division of Respiratory Medicine, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
Department of Medicine, McMaster University, Hamilton, ON, Canada.
Department of Physiology, University of Toronto, Toronto, ON, Canada.
Department of Agricultural Food, and Nutritional Science, University of Alberta, Edmonton, AB, Canada.
Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada.


Background: Human milk contains many bioactive components that are typically studied in isolation, including bacteria. We performed an integrated analysis of human milk oligosaccharides and fatty acids to explore their associations with milk microbiota. Methods: We studied a sub-sample of 393 mothers in the CHILD birth cohort. Milk was collected at 3-4 months postpartum. Microbiota was analyzed by 16S rRNA gene V4 sequencing. Oligosaccharides and fatty acids were analyzed by rapid high-throughput high performance and gas liquid chromatography, respectively. Dimension reduction was performed with principal component analysis for oligosaccharides and fatty acids. Center log-ratio transformation was applied to all three components. Associations between components were assessed using Spearman rank correlation, network visualization, multivariable linear regression, redundancy analysis, and structural equation modeling. P-values were adjusted for multiple comparisons. Key covariates were considered, including fucosyltransferase-2 (FUT2) secretor status of mother and infant, method of feeding (direct breastfeeding or pumped breast milk), and maternal fish oil supplement use. Results: Overall, correlations were strongest between milk components of the same type. For example, FUT2-dependent HMOs were positively correlated with each other, and Staphylococcus was negatively correlated with other core taxa. Some associations were also observed between components of different types. Using redundancy analysis and structural equation modeling, the overall milk fatty acid profile was significantly associated with milk microbiota composition. In addition, some individual fatty acids [22:6n3 (docosahexaenoic acid), 22:5n3, 20:5n3, 17:0, 18:0] and oligosaccharides (fucosyl-lacto-N-hexaose, lacto-N-hexaose, lacto-N-fucopentaose I) were associated with microbiota α diversity, while others (C18:0, 3'-sialyllactose, disialyl-lacto-N-tetraose) were associated with overall microbiota composition. Only a few significant associations between individual HMOs and microbiota were observed; notably, among mothers using breast pumps, Bifidobacterium prevalence was associated with lower abundances of disialyl-lacto-N-hexaose. Additionally, among non-secretor mothers, Staphylococcus was positively correlated with sialylated HMOs. Conclusion: Using multiple approaches to integrate and analyse milk microbiota, oligosaccharides, and fatty acids, we observed several associations between different milk components and microbiota, some of which were modified by secretor status and/or breastfeeding practices. Additional research is needed to further validate and mechanistically characterize these associations and determine their relevance to infant gut and respiratory microbiota development and health.


Bifidobacterium; CHILD cohort; breastmilk; fatty acids; human milk oligosaccharide; microbiota; mode of breastfeeding

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