Correlating Infant Fecal Microbiota Composition and Human Milk Oligosaccharide Consumption by Microbiota of 1-Month-Old Breastfed Infants

Abstract

Scope: Understanding the biological functions of human milk oligosaccharides (HMOs) in shaping gastrointestinal (GI) tract microbiota during infancy is of great interest. A link between HMOs in maternal milk and infant fecal microbiota composition is examined and the role of microbiota in degrading HMOs within the GI tract of healthy, breastfed, 1-month-old infants is investigated.

Methods and results: Maternal breast milk and infant feces are from the KOALA Birth Cohort. HMOs are quantified in milk and infant fecal samples using liquid chromatography-mass spectrometry. Fecal microbiota composition is characterized using Illumina HiSeq 16S rRNA gene amplicon sequencing. The composition is associated with gender, delivery mode, and milk HMOs: Lacto-N-fucopentaose I and 2'-fucosyllactose. Overall, Bifidobacterium, Bacteroides, Escherichia-Shigella, and Parabacteroides are predominating genera. Three different patterns in infant fecal microbiota structure are detected. GI degradation of HMOs is strongly associated with fecal microbiota composition, and there is a link between utilization of specific HMOs and relative abundance of various phylotypes (operational taxonomic units).

Conclusions: HMOs in maternal milk are among the important factors shaping GI tract microbiota in 1-month-old breastfed infants. An infant's ability to metabolize different HMOs strongly correlates with fecal microbiota composition and specifically with phylotypes within genera Bifidobacterium, Bacteroides, and Lactobacillus.

Keywords: breastfeeding; human milk oligosaccharide; microbial clusters; microbiome.

Figure 1

Constrained analysis (RDA) of different factors and milk HMO levels and their association with the fecal OTU profile of infants. Samples are labeled and enveloped based on the infant assignment to microbial cluster type A, B, or C.

Figure 2

Different utilization patterns of infants defined based on the comparison of HMO profiles in breast milk and infant feces. Peak assignments are as follows: N2‐2′FL, N3‐LNT, N4‐LNnT, N5‐LNFP I, N6‐LNFP II, N7‐LNFP III, N8‐LNFP V, N9‐DFL, N10‐LNDFH I, N11‐LNH, N12‐LNnH; S1‐6′SL, S2‐3′SL, S3‐LSTa, S4‐LSTb, S5‐LSTc.

Figure 3

Association of general HMO consumption patterns with microbial cluster types A, B, C. a) RDA showing the association between HMO consumption patterns and microbial OTUs. Fifteen best fitting OTUs are displayed and samples are color‐coded based on their cluster type assignment; b) segregation of infants based on their HMO consumption pattern in relation to their microbial cluster type classification.

Figure 4

RDA showing the association between the degree of degradation of individual HMOs and microbial OTUs. OTUs which were significantly (p < 0.05) increased in high‐degrading infants for at least one of the HMOs are displayed. Taxa with FDR <0.05 are highlighted in bold. For more information on average relative abundance of the displayed OTUs in the study population and the detailed results of Kruskal–Wallis analyses (see Tables S3 and S6, Supporting Information). Samples are color‐coded based on microbiota cluster type assignment. Red triangles indicate consumption of each HMO, as summarized in red text.

Figure 5

Proportion of infants showing either “high,” “medium,” or “low” HMO consumption levels, within each microbial cluster class A, B, C. Significant differences in distribution as determined by Chi‐square analysis are indicated with an asterisk.

Figure 6

OTUs significantly associated with HMO consumption based on Kruskal–Wallis test including infants classified as high and low consumers for each HMO. Red lines indicate higher OTU relative abundance in relation to low HMO consumption; blue lines indicate higher relative abundance in relation to high consumption. OTU nodes which are connected with the highest number of HMOs are indicated by darker shades of pink. Dotted lines indicate associations with p < 0.05; solid lines indicate associations with FDR <0.05.