Human Milk Oligosaccharide (HMO) Metabolizing Gene Abundances in Human Infant Fecal Samples

Abstract

ObjectivesTo benefit from the complex oligosaccharides found in human milk, an infant relies on microbial metabolism of these compounds. The main objective of this study was to determine the abundance of Bifidobacterium infantis human milk oligosaccharide (HMO) metabolizing genes in infant fecal samples. MethodsFecal samples from 40 6-mos-old infants were collected. Genomic DNA was extracted, and quantitative real-time PCR was used to determine the abundance of several genes in B. infantis. B infantis specific primer sets were used to target 5 HMO metabolizing genes as well as the 16S rRNA gene. Additional 16S rRNA primer sets were used to target overall bacteria, overall Bifidobacterium, B. breve and B. longum. Abundances of each qPCR reaction were compared by infant human milk exposure, solid food intake, and mode of delivery. ResultsMode of delivery was not associated with any PCR targets. Two HMO genes, a sialidase and a glycoside hydrolase, as well as a B. infantis 16S rRNA gene were more abundant in the feces of human milk fed infants (p < 0.05). The sialidase and a B. infantis 16S rRNA gene tended to be less abundant when a larger percentage of an infant’s diet consisted of solids (p < 0.10). When accounting for solid food intake, human milk exposure continued to be positively associated with the sialidase and a B. infantis 16S rRNA gene abundance (p < 0.05) and tended to be related to the abundance of the glycoside hydrolase (p < 0.10). An assessment of 5 B. infantis specific primer sets targeting HMO metabolizing genes demonstrated that the stools of human milk fed infants harbored a more diverse set of these genes than those of non-human milk fed infants (p = 0.02). ConclusionsHerein, we have identified a qPCR primer set targeting a sialidase that is consistently associated with human milk exposure even in the presence of solid food intake. With further development and validation in additional populations of infants, these assays could be used to group samples by dietary exposure even where no record of dietary intake exists. Thus, this assay would provide a method by which infant human milk intake proximal to sample collection can be assessed quickly in any well-equipped molecular biology lab. Funding SourcesThis research was partially supported by the MSU College of Agriculture and Natural Resources Undergraduate Research Program as well as the Max Gonzenbach Research Scholarship.