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Diverse HMOs in Breast Milk Help Gut Microbiota Flourish

    A mother breastfeeds her baby to represent effects studied between breastmilk and infant formula, which is often supplemented with synthetic HMOs like 2-fucosyllactose (2’FL).

    Written by: Alla Katsnelson, Ph.D | Issue # 126 | 2025

    • Researchers cultured stool samples from seven toddlers,  then added either a pool of multiple HMOs or synthetic 2’FL, a commercially available HMO often added to infant formula. 
    • Bacteria were able to utilize a wide variety of HMOs in the pooled sample.
    • The pooled HMOs drove a large change in metabolic activity of the cultured bacteria, while 2’FL alone had a much smaller effect on the cultures. 

    A combination of human milk oligosaccharides (HMOs) may significantly modulate the microbiome, according to a recent study of gut bacteria collected from young children and grown in a dish [1]. However, adding just one synthetic HMO – specifically, 2-fucosyllactose (2’FL), which is most often added to infant formula today [2] – has a substantially smaller effect on the microbiome. 

    Human milk contains more than 200 types of different HMOs. Human cells cannot digest HMOs, and researchers believe they primarily support the infant’s gut microbiome [3].

    Scientists studying how bacteria in the microbiome utilize HMOs have generally focused on a group of bacteria called bifidobacteria, which are known to be probiotic [4]. But here, the team set out to explore HMOs’ effects on a much larger swathe of gut bacteria. “No one has really thought much about other microbes in the gut, because they are kind of hard to culture,” says Emma Allen-Vercoe, a simicrobiologist and microbiome researcher at the University of Guelph who led the work. “But the paper actually found that there is an enormous diversity of microbes that can utilize human milk oligosaccharides – and that they all do it in slightly different ways.” 

    The researchers studied stool samples from 7 children 18-24 months old who were part of the DIABIMMUNE birth cohort. The cohort follows children from infancy through adolescence to determine how exposure to microorganisms in early childhood affects the risk of developing Type 1 diabetes. Although Allen-Vercoe and her colleagues initially aimed to explore the link between HMOs and diabetes, they ended up focusing more narrowly on how HMOs affect bacteria cultured from the children’s stool samples. 

    The first step was to culture a diverse population of bacteria from each sample. Because bacterial species from the gut microbiome tend to be finicky, they used a specialized bioreactor called the RoboGut, which is designed to mimic conditions that the bacteria would experience naturally [5]. They were able to culture more than 400 species, says Simone Renwick, a postdoctoral researcher at the Mother-Milk-Infant Center of Research Excellence at the University of California, Davis and the study’s first author. 

    Next, the researchers added either a single HMO, synthetic 2’FL, or a mixture of 150-200 pooled HMOs, taken from milk samples of several women, to the bacterial cultures that were derived from the children’s stool. They compared the changes they observed to control cultures to which nothing was added.

    Cultures to which they added the pooled HMOs quickly changed their microbial composition. Several types of bacteria expanded in number while others shrank. In contrast, cultures to which they added 2’FL barely changed, remaining similar to the control cultures. 

    In subsequent experiments, the team profiled the metabolic activity that occurred in response to adding either the pooled HMOs or the 2’FL, measuring how bacteria under each set of conditions broke down the HMOs, which are complex sugars. They quantified 47 different metabolites – some of which were upregulated and some of which were suppressed – when the pooled HMOs were added. However, they observed almost no change in metabolite composition after adding 2’FL. Only the bacterial community of one child noticeably shifted its metabolic activity after the single HMO was added. 

    The researchers tested how the cultures metabolized 19 of the most common and abundant HMOs produced by women and found that the cultured bacteria could make metabolic use of all of them. 

    Finally, the researchers probed how each of 330 different strains of bacteria in the samples, which belonged to 157 different species, changed its growth pattern in response to the addition of HMOs. Overall, many different types of bacteria utilized HMOs and there was a high degree of individual differences among infants in which species were able to do so. 

    The study used microbiome samples from a just small number of children, and the researchers only added the HMOs to the cultures once.  Nonetheless, the findings suggest that HMOs likely have an enormous effect on shaping a young child’s microbiome in still largely unknown ways, says Renwick. They also point to the need for exploring a wide range of HMOs beyond 2’FL.  

    “Our research really underscores the importance of providing infants with a diversity of HMO structures,” says Renwick. “And I think there’s more research on this now, and more interest, than ever before.”

     

    References

    1. Renwick S, Furst A, Knip M; DIABIMMUNE Study Group; Bode L, Danska JS, Allen-Vercoe E. Modulating the developing gut microbiota with 2′-fucosyllactose and pooled human milk oligosaccharides. Microbiome. 2025. 13(1):44. 
    2. Vandenplas Y, Berger B, Carnielli VP, Ksiazyk J, Lagström H, Sanchez Luna M, Migacheva N, Mosselmans JM, Picaud JC, Possner M, Singhal A, Wabitsch M. Human Milk Oligosaccharides: 2′-Fucosyllactose (2′-FL) and Lacto-N-Neotetraose (LNnT) in Infant Formula. Nutrients. 2018;10(9):1161.  
    3. Walsh C, Lane JA, van Sinderen D, Hickey RM. Human milk oligosaccharides: Shaping the infant gut microbiota and supporting health. J Funct Foods.2020. 72:104074. 
    4. 1: O’Callaghan A, van Sinderen D. Bifidobacteria and Their Role as Members of the Human Gut Microbiota. Front Microbiol. 2016;7:925.
    5. Gianetto-Hill CM, Vancuren SJ, Daisley B, Renwick S, Wilde J, Schroeter K, Daigneault MC, Allen-Vercoe E. The Robogut: A Bioreactor Model of the Human Colon for Evaluation of Gut Microbial Community Ecology and Function. Curr Protoc. 2023;3(4):e737.