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Updated: Jul 7, 2026
A Method for Targeted 16S Sequencing of Human Milk Samples
Published on: March 23, 2018
Single-cell transcriptomics reveals that human milk feeding shapes neonatal immune cell interleukin signaling
Michael L Salinas1, Bharath Kumar Mulakala2, Laurie A Davidson3
1Department of Nutrition, Texas A&M University, College Station, TX, United States; CPRIT Single Cell Data Science Core, Texas A&M University, College Station, TX, United States; Texas A&M AgriLife Institute for Advancing Health Through Agriculture, College Station, TX, United States.
Background:
Several studies have indicated the benefits of human milk feeding to infants however, mechanisms behind positive health outcomes have not been investigated.
Objectives:
The study aimed to characterize circulating immune cell subpopulation gene expression in human milk-fed (HMF) compared with cow milk formula-fed (FF) infants using single-cell transcriptomics.
Methods:
Peripheral blood mononuclear cells (PBMCs) were isolated from healthy HMF (n = 6), and FF (n = 3) infants who were 3-3.5 mo old and enrolled in a nonrandomized clinical trial. Single-cell RNA sequencing was used to generate a PBMC atlas and evaluate gene expression in immune cell subsets. Differential expression analysis was performed on each cell type independently after clustering the cells by similar marker gene expression using the scGEAToolbox. Differentially expressed genes were subjected to pathway analyses using an online functional enrichment analysis program.
Results:
The relative abundance (%) of T and B lymphocytes, natural killer (NK) cells, and plasmacytoid dendritic cells were similar, whereas monocytes were higher in FF infants than in HMF infants (22.6 ± 10.7 compared with 8.3 ± 5.6; P = 0.0314). In addition, innate and adaptive immune cells from FF infants exhibited a higher activation state compared with HMF infants. We identified 16 distinct cell subsets from the major immune cell types: 3 monocyte subsets, 4 NK subsets, 2 B cell subsets, and 7 T cell subsets. Transcriptional profiles of each peripheral innate and adaptive immune cell subtype varied between HMF and FF infants. Pathway enrichment analysis of cell-specific transcriptional changes within subsets of major cell types revealed that the interleukin (IL)-4/IL-13 signaling pathways were upregulated in FF infants relative to HMF infants.
Conclusions:
These findings suggest that human milk downregulates peripheral immune cell cytokine transcriptional signatures linked to allergic inflammation and infection relative to formula feeding.
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