Human milk oligosaccharides (HMOs) are thought to influence early intestinal microbiota establishment and may thereby provide benefits to formula-fed infants. We evaluated the effect of infant formula with 2 HMOs (2’Fucosyllactose [2’FL] and Lacto-N-neotetraose [LNnT]) on the establishment of the intestinal microbiota in infants (ClinicalTrials.gov NCT01715246).
Healthy term infants, who were 0–14 days old at enrolment, were randomized to intact protein cow's milk-based infant formula (Control, n 87) or the same formula with 1.0 g/L 2’FL and 0.5 g/L LNnT (Test, n 88). Fully breastfed infants were also studied as a reference group (n 38). Stool samples were collected at 3 months of age for microbiota assessment using 16S rRNA gene sequencing and metagenomics; metabolic signature in stool was assessed using proton NMR.
The global average microbial composition profile was established for infants from whom stool samples were available and who adhered to the protocol. A similar formula-fed pattern for Control (n 65) and Test (n 58) was seen at the genus level, although Test appeared closer to breastfed (n 34) than Control. Calculation of microbial alpha diversity and comparison of the global microbiota composition using random permutations of the redundancy analysis (RDA) confirmed that Test was different from Control at genus level (p < 0.001) and closer to the breastfed group. By statistical analyses we identified several taxa differentially present in Control and Test. These were Bifidobacterium (p = 0.01), Escherichia (p = 0.008), unclassified Coprobacillaceae (p = 0.01), unclassified Peptostreptococcaceae (p = 0.026), Dorea (p = 0.033), and Megamonas (p = 0.035). Correction for False Discovery Rate confirmed the first three taxa. Main discriminants between Test and Control by random forest analysis were Bifidobacterium, Escherichia and Peptostreptococcaceae. Clinically relevant pathogens were very rarely found; however, Clostridium difficile toxin A/B was detected in 14% of Test and 26% Control (OR 0.47, CI 0.17–1.27, p = 0.15). Multivariate stool metabolite analysis identified influential metabolites that discriminate between Test, Control and breastfed group. These were the amino acids phenylalanine, isoleucine, tyrosine, fecal organic acids and fucosylated compounds. Globally, the metabolic signatures observed in Test were more similar to those observed in stool of breastfed infants than Control. The observed profiles may indicate reduced protein fermentation in Test compared to Control.
Together the stool microbiota and metabolic signature show that the addition of 2’FL and LNnT to a starter infant formula shift the stool microbiota towards that observed in breastfed infants, both in composition and function. Further studies are warranted to evaluate whether such a shift in gut ecology towards the breastfed standard leads to health benefits.