Neonatal diet alters fecal microbiota and metabolome profiles at different ages in infants fed breast milk or formula

Authors: BRINK, LAUREN - Arkansas Children'S Nutrition Research Center (ACNC); MERCER, KELLY - Arkansas Children'S Nutrition Research Center (ACNC); PICCOLO, BRIAN - Arkansas Children'S Nutrition Research Center (ACNC); CHINTAPALLI, SREE - Arkansas Children'S Nutrition Research Center (ACNC); ELOLIMY, AHMED - Arkansas Children'S Nutrition Research Center (ACNC); BOWLIN, ANNE - Arkansas Children'S Nutrition Research Center (ACNC); MATAZEL, KATELIN - Arkansas Children'S Nutrition Research Center (ACNC); PACK, LINDSAY - Arkansas Children'S Nutrition Research Center (ACNC); Adams, Sean; SHANKAR, KARTIK - Arkansas Children'S Nutrition Research Center (ACNC); Badger, Thomas - Arkansas Children'S Nutrition Research Center (ACNC); ANDRES, ALINE - Arkansas Children'S Nutrition Research Center (ACNC); YERUVA, LAXMI - Arkansas Children'S Nutrition Research Center (ACNC)

Submitted to: The American Journal of Clinical Nutrition
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/24/2020
Publication Date: 4/24/2020
Citation: Brink, L.R., Mercer, K.E., Piccolo, B.D., Chintapalli, S.V., Elolimy, A., Bowlin, A.K., Matazel, K.S., Pack, L., Adams, S.H., Shankar, K., Badger, T.M., Andres, A., Yeruva, L. 2020. Neonatal diet alters fecal microbiota and metabolome profiles at different ages in infants fed breast milk or formula. American Journal of Clinical Nutrition. https://doi.org/10.1093/ajcn/nqaa076.
DOI: https://doi.org/10.1093/ajcn/nqaa076

Interpretive Summary: Exclusive breastfeeding (BF) is recommended by the WHO for the first six months of life. There can be multiple barriers to exclusive BF and thus it is not always an option, in which case infant formula is an appropriate alternative. There is no other period in life where nutrition comes from a sole source (BF or infant formula), and the health implications of early life nutrition have been well described. For example, BF is associated with lower risks of infection during infancy, as well as a long-term decreased risk of atopy (hypersensitivity to allergy triggers) and obesity. There is a growing body of literature describing the ability of the gut microbiome (the repertoire of bacteria normally found in the gut) to modulate host health through molecules (a large suite of metabolites, the "metabolome") that interact with the body. Nutrition provided in early age can significantly affect bacterial colonization and development. In this study, we examine how early-life diet alters the lower-gut microbiome and host metabolism. Fecal samples were utilized from a longitudinal cohort (Beginnings) that examined the effect of early infant diet on growth and body composition. Aside from examining BF vs. formula-fed (FF) infants, this study contained two types of FF models, both a dairy milk-based (MF) and soy-based (SF) formula. To our knowledge, a longitudinal investigation into the fecal microbiome and metabolome of SF infants has not been investigated previously. We describe the infant fecal microbiome and metabolome across the first year of life, both globally and within each age time-point. BF is associated with increased abundances of specific bacteria, primarily Bifidobacteria. These bacteria have been found to produce short chain fatty acids (SCFA), such as butyrate, which promote colonic gut development. We observed significantly higher butyric acid in BF relative to FF infants. In addition, we observed kyneuric acid, D-sphingosine and betaine levels that were higher in BF relative to FF infants. The kynurenine pathway for the amino acid tryptophan metabolism has been implicated in developing tolerance within the immune system and also impact allergy outcomes while D-sphingosine and betaine play a role in immune cell trafficking and inflammatory responses. This highlights that understanding the gut microbiota and metabolite milieu is important to study microbe-host communication and physiology. Future mechanistic studies are needed to determine the role of components of breast milk, microbiota and specific gut-derived metabolites on regulating the developing infant's immune and other physiological systems.

Technical Abstract: Neonatal diet has a large influence on child health and might modulate changes in fecal microbiota and metabolites. The aim is to investigate fecal microbiota and metabo-lites at different ages in infants who were breastfed (BF), received dairy-based milk formula (MF), or received soy-based formula (SF). Methods: Fecal samples were collected at 3 (n = 16, 12, and 14, respectively), 6 (n = 20, 19, and 15, respectively), 9 (n = 12, 11, and12,respectively), and12mo(n = 14, 14, and 15, respectively) for BF, MF, and SF infants. Infants that breastfed until 9 mo and switched to formula were considered as no longer breastfeeding at 12 mo. Microbiota data were obtained using 16S ribosomal RNA sequencing. Untargeted metabolomics was conducted using a Q-Exactive Hybrid Quadrupole-Orbitrap mass spectrometer. The data were analyzed using R (version 3.6.0) within the RStudio (version 1.1.463) platform. At 3, 6, and 9 mo of age BF infants had the lowest a-diversity, SF infants had the highest diversity, and MF was intermediate. Bifidobacterium was 2.6- to 5-fold lower in SF relative toBFinfantsthrough1yoflife. An unidentified genus from Ruminococcaceae higher in the SF (2%) than in the MF (0.4%) and BF (0.08%) infants at 3 mo of age was observed. In BF infants higher levels of butyric acid, d-sphingosine, kynurenic acid, indole-3-lactic acid, indole-3-acetic acid, and betaine were observed than in MF and SF infants. At 3 mo Ruminococcaceae was positively correlated to azelaic, gentisic, isocitric, sebacic, and syringic acids. At 6 mo Oscillospira was negatively correlated with 3-hydroxybutyric-acid, hydroxy-hydrocinnamic acid, and betaine whereas Bifidobacterium was negatively associated with 5-hydroxytryptamine. At 12 mo of age, Lachnospiraceae was negatively associated with hydrox-yphenyllactic acid. Infant diet has a large impact on the fecal microbiome and metabolome in the first year of life.