Differences in the Fecal Metabolome and Microbiome Between Exclusive and Partial Breastfed Infants are More Pronounced at 2 Months Compared to 5 Months

Abstract Objectives This study aimed to characterize the impact of feeding practices on the infant fecal metabolome and microbiome at 2 months and 5 months of age in exclusive breastfeeding (EBF) and partial breastfeeding (PBF) infants. Methods Fecal samples were collected from infants at 2 months and 5 months of age from Bandung, Indonesia. Exclusive breastfeeding was determined using the stable isotope deuterium dose-to-mother (DTM) technique. Fecal metabolites were extracted using Dulbecco's phosphate-buffered saline, and analyzed using NMR spectroscopy. Fecal microbial DNA was extracted at the same time using the MoBio PowerLyzer PowerSoil DNA isolation kit (MoBio, Carlsbad, CA). The V4 region of 16SrRNA was targeted. The DNA library sample was analyzed via 300-bp paired-end sequencing on the Illumina MiSeq platform. Results Fecal samples from EBF infants at 2 months of age revealed significantly higher human milk oligosaccharides (HMOs), short-chain fatty acids and related metabolites compared to PBF infants. However, fecal samples from infants at 5 months of age revealed no differences in metabolome between EBF and PBF after p-value adjustment for multiple comparisons. Gut microbes, especially Bifidobacterium were higher in EBF infants at age 2 months even though not statistically significant. However, this difference was eliminated at age 5 months. Conclusions In the present study, infant feeding practices had a stronger influence on the infant fecal metabolome and microbiome at the age of 2 months as compared to 5 months. Funding Sources 2014 Bill & Melinda Gates Foundation. CS would also like to acknowledge funding from the Kinsella endowed chair in Food, Nutrition, and health as well as USDA-NIFA Hatch project 1,021,411.