Human milk miRNAs associate to maternal dietary nutrients, milk microbiota, infant gut microbiota and body mass index

Authors: Yeruva, Laxmi; MULAKALA, BHARAT - Texas A&M University; RAJASUNDARAM, DHIVYAA - University Of Pittsburgh; GONZALEZ, SONIA - University Of Oviedo; CABRERA-RUBIO, RAUL - Institute Of Agrochemistry And Food Technology; MARTINEZ-COSTA, CECILIA - University Of Valencia; COLLADO, MARIA CARMEN - Institute Of Agrochemistry And Food Technology

Submitted to: Clinical Nutrition
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/11/2023
Publication Date: 10/16/2023
Citation: Yeruva, V., Mulakala, B.K., Rajasundaram, D., Gonzalez, S., Cabrera-Rubio, R., Martinez-Costa, C., Collado, M. 2023. Human milk miRNAs associate to maternal dietary nutrients, milk microbiota, infant gut microbiota and body mass index. Clinical Nutrition. 42(12):2528-2539. https://doi.org/10.1016/j.clnu.2023.10.011.
DOI: https://doi.org/10.1016/j.clnu.2023.10.011

Interpretive Summary: It is well known that human milk provides an infant with the nutrients required for growth and development. Scientists recently identified that human milk also contains functional epigenetic molecules such as microRNAs, required for normal function and development of the mother's mammary gland and infants' health. Many maternal factors, such as maternal diet, can impact the microRNAs profile in human milk, consequently influencing the infant's health. However, little information is available on the impact of maternal diet on microRNA profile in human milk and the association of milk microRNAs to other milk components, maternal dietary components, and the infant's gut microbes and growth. Our study demonstrates that maternal dietary protein source (animal vs. plant protein) influences the expression levels of human milk microRNAs. In addition, we show the association of microRNAs with the milk microbiota, dietary components, and infant gut microbes and growth. This information provides a better understanding of the impact of maternal diet on the microRNAs profile and the association of human milk microRNAs with other factors. Further, these results will aid in developing maternal nutrition strategies for infants' optimal growth and development.

Technical Abstract: Background: Studies have shown that maternal diet influences the milk miRNAs composition, yet little information is available on the influence of maternal dietary protein source on human milk miRNAs composition. Further, despite growing evidence on the association of milk bioactive compounds with maternal factors and infant outcomes, the association of miRNAs to maternal dietary components and milk microbiome and the infant gut microbiota and growth remains unclear. Methods: Milk samples from 60 healthy lactating women (30 plant protein dietary source and 30 animal protein dietary source) of MAMI cohort at <20d post-partum were subjected to miRNA sequencing with HTG molecular diagnostics. Infant anthropometric measures was followed up to 2 years of age. Microbiota was analyzed by 16S rRNA gene V3–V4 variable regions sequencing. An integrative multi-omics data analysis was conducted to identify an association of milk miRNAs to maternal dietary components, milk microbiome, the infant gut microbiome and growth outcomes. Results: We observed 34 miRNAs were differentially expressed between the plant and animal protein groups, with 33 miRNAs being downregulated in the plant protein group. Pathway analysis of the target predicted genes of the up and down-regulated miRNAs revealed that the top enriched pathways were involved in cell growth and proliferation processes. Discriminant analysis revealed that the milk miRNAs were generally clustered in two groups according to the maternal protein source. Further, significant features contributing to the clustering were associated with milk dietary components, dietary lipids, and milk microbiome. The identified significant features miR-3162-5P, -4271, -4734, -658, -6738-5P, -6824-5p, and -6875-5p, which were abundant in the animal protein group were positively correlated to the milk microbial genera Brevibacillus, and Actinobacterium. In addition, 36 milk miRNAs were strongly correlated with the infant microbial genera at 15 days of age. Among these genera, Ruminococccus, Serratia, Micrococcus, Finegoldia, and Peptoniphillu have positive correlation (r = 0.96) with the 29 miRNAs, whereas Blautica Gemmiger, and Fusicatenibacter positively correlated (r = 0.96) with miR-195-bp, miR335-bp, miR16-5p, miR26b-5p and miR-30c-5p. Interestingly, in 30 day old infants, 10 miRNAs (miR-6802-5p, miR-2467-3p, miR-4441, miR-3937, miR-6778-5p, miR-4451, miR-2392, miR-128-1-5p, miR-4269, miR-1238-5p) were strongly correlated (r = 1) with microbial genera Veillonella and Flavonifractor. In addition, miRs-3977, -7157-5p, -329-5p were negatively correlated to the BMI-Z-score at 1 month of age while several miRNAs were positively correlated to the infant weight, and BMI-Z-score and weight/length z-scores measures at 6 months of age. Pathway analysis of the target predicted genes of the combined list of miRNAs associated to infant microbiota revealed that the top enriched pathways were involved in cellular signaling processes. Further, miR-378 and 320 family miRNAs involved in adipogenesis positively correlated to the infant BMI-z-scores, weight, and W/L-z-scores at 6 months of age. Conclusions: Our findings indicate that the maternal dietary protein source influences the milk miRNA expression. Using integrative muti-omics analysis, we observed miRNAs association with maternal dietary components, milk microbiota and to the infant gut microbiota and growth. Additional research is required to characterize these associations and determine the miRNAs functional relevance in human milk fed infants.