Date of Award

Winter 12-15-2015

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Computational & Systems Biology)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



Undernutrition is a pressing and pervasive global health problem. The pathogenesis of this disease remains unclear, but epidemiologic studies indicate that it is not due to food insecurity alone. Moreover, current therapeutic interventions have limited efficacy in preventing or ameliorating the long-term sequelae of undernutrition, including stunting and cognitive deficits. Recent culture-independent studies have demonstrated that the normal postnatal pattern of gut microbiota development is disrupted in children with undernutrition, leading to the proposal that perturbations in gut microbiota development impairs healthy growth of the host. Human breast milk contains a diverse repertoire of free and conjugated human milk oligosaccharides (HMOs) frequently decorated with fucose and/or sialic acid moieties. HMOs are not absorbed in the proximal gut and function as prebiotics that promote colonization of the infant gut with bacterial strains associated with numerous benefits (e.g., enhanced gut barrier function, protection from enteropathogen infection, and improved vaccine responses). To date, the relationships between the overall abundance of breast milk HMOs, development of a healthy gut microbiota, and the growth phenotypes of infants and children have not been well characterized. The central hypotheses of my thesis are that (i) the gut microbiota plays a key role in supporting healthy growth and metabolism in infants and children, (ii) perturbations in microbiota function are causally related to undernutrition in infants and children, (iii) the representation of HMO species in mothers’ milk is significantly correlated with the nutritional status and growth outcomes of their offspring (as defined by anthropometry), and (iv) HMOs promote growth and modulate metabolism through microbiota-dependent mechanisms and may yield new therapeutic agents for treating and ultimately preventing undernutrition. My thesis is presented in four chapters.

The first chapter is presented as a perspective, describing the relationship between perturbations in postnatal development/maturation of the gut microbiota and childhood undernutrition. This chapter describes hypotheses and experimental models for performing proof-of-concept experiments that test the causal role of the gut microbiota, milk glycans, and interactions between these components in modulating host metabolism and growth.

Chapter two describes a set of experiments that involve transplanting fecal microbiota from Malawian infants and children (manifesting healthy growth or varying degrees of undernutrition) into young germ-free mice fed a representative Malawian diet. These studies revealed that immature microbiota from severely stunted/underweight donors transmit impaired growth phenotypes as compared to microbiota from healthy donors. The representation of several taxa in the microbiota of recipient animals correlated with lean body mass gain, bone morphology, and metabolic phenotypes in liver, muscle, and brain. Furthermore, co-housing these ‘humanized’ gnotobiotic mice shortly after colonization revealed that invasion of bacterial taxa from mice harboring a healthy infant’s microbiota to cagemates harboring an immature microbiota from a stunted/underweight donor ameliorated growth faltering. These results indicate that gut microbiota immaturity is causally related to undernutrition.

The third chapter begins by defining the relationship between infant growth outcomes and breast milk HMO content in two independent Malawian birth cohorts. Analysis of human milk oligosaccharides from 6-month postpartum Malawian mothers revealed that sialylated HMOs are significantly less abundant in milk from mothers with severely stunted infants. This chapter then describes the effects of sialylated milk oligosaccharides on growth and metabolism using young gnotobiotic mice and newborn gnotobiotic piglets. In both cases, animals were colonized with a sequenced bacterial culture collection generated from a severely stunted Malawian infant, and fed a prototypic Malawian diet with and without supplementation using a purified preparation of sialylated bovine milk oligosaccharides (S-BMO). S-BMO produced a microbiota-dependent augmentation of body weight and lean body mass gain, changed bone morphology, and altered liver, muscle, and brain metabolism in ways indicative of a greater ability to utilize nutrients for anabolism. These two preclinical models establish a causal microbiota-dependent relationship between S-BMO and growth promotion.

Chapter four details future research directions, including experimental approaches for determining the microbial dependencies of S-BMO mediated growth and identifying bioactive structures present in S-BMO. Finally, this chapter describes the potential for and challenges facing the use of dietary milk oligosaccharide supplements to treat childhood undernutrition.


English (en)

Chair and Committee

JeffreyI Gordon

Committee Members

Daniel Goldberg, Scott Hultgren, Clay Semenkovich, Jeremy Buhler, Michael Talcott


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