Breast milk-derived human milk oligosaccharides promote Bifidobacterium interactions within a single ecosystem

Melissa A.E. Lawson, Ian J. O’Neill, Magdalena Kujawska, Sree Gowrinadh Javvadi, Anisha Wijeyesekera, Zak Flegg, Lisa Chalklen, Lindsay J. Hall*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

167 Citations (Scopus)


Diet-microbe interactions play an important role in modulating the early-life microbiota, with Bifidobacterium strains and species dominating the gut of breast-fed infants. Here, we sought to explore how infant diet drives distinct bifidobacterial community composition and dynamics within individual infant ecosystems. Genomic characterisation of 19 strains isolated from breast-fed infants revealed a diverse genomic architecture enriched in carbohydrate metabolism genes, which was distinct to each strain, but collectively formed a pangenome across infants. Presence of gene clusters implicated in digestion of human milk oligosaccharides (HMOs) varied between species, with growth studies indicating that within single infants there were differences in the ability to utilise 2′FL and LNnT HMOs between strains. Cross-feeding experiments were performed with HMO degraders and non-HMO users (using spent or ‘conditioned’ media and direct co-culture). Further 1H-NMR analysis identified fucose, galactose, acetate, and N-acetylglucosamine as key by-products of HMO metabolism; as demonstrated by modest growth of non-HMO users on spend media from HMO metabolism. These experiments indicate how HMO metabolism permits the sharing of resources to maximise nutrient consumption from the diet and highlights the cooperative nature of bifidobacterial strains and their role as ‘foundation’ species in the infant ecosystem. The intra- and inter-infant bifidobacterial community behaviour may contribute to the diversity and dominance of Bifidobacterium in early life and suggests avenues for future development of new diet and microbiota-based therapies to promote infant health.

Original languageEnglish
Pages (from-to)635-648
Number of pages14
JournalISME Journal
Issue number2
Publication statusPublished - 1 Feb 2020

Bibliographical note

Funding Information:
Funding This work was funded by a Wellcome Trust Investigator Award (100/974/C/13/Z), and the BBSRC Norwich Research Park Bioscience Doctoral Training Grant (BB/M011216/1, supervisor LJH, student MK); Institute Strategic Programme Gut Microbes and Health BB/R012490/1, and its constituent project(s) BBS/E/F/000PR10353 and BBS/E/F/000PR10356, and Institute Strategic Programme Gut Health and Food Safety BB/J004529/1 to LJH. MAEL was funded by the Marie Sklodowska-Curie Individual Fellowship (Project 661594).

Publisher Copyright:
© 2019, The Author(s).

ASJC Scopus subject areas

  • Microbiology
  • Ecology, Evolution, Behavior and Systematics


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