Date of Award

Spring 5-15-2016

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Molecular Genetics & Genomics)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



Immediately following birth, there is a rapid and dynamic succession of microbes that colonize the human gut; this developmental program is largely completed within the first 24-30 months of postnatal life. This consortium of microbes, known as the gut microbiota, impacts metabolism of dietary components, maturation of the immune system including the gut mucosal barrier, and the ability of enteropathogens to establish themselves. Much remains unknown about this patterned bacterial progression within infants and children, and the extent to which gut microbiota maturation is directly related to healthy growth.

Childhood undernutrition is a devastating global health problem. Not only is it a leading cause of childhood mortality, undernutrition has many long-term consequences, including stunting, neurodevelopmental abnormalities and immune dysfunction. Furthermore, current therapeutic interventions have limited efficacy in mitigating these sequelae. Recent studies have demonstrated that gut microbiota maturation is disrupted in undernourished children. My thesis tests the hypothesis that gut microbiota maturation not only serves as a biomarker of health status but is causally related to the growth and development of infants and children.

Chapter one provides an overview of the human gut microbiota in the developing infant. Chapter two initially describes a bacterial V4-16S rRNA analysis of the fecal microbiota of healthy infants and children enrolled in a Malawian cohort; Random Forests-based modeling of the result- ing datasets yielded a sparse 25-taxa model of normal gut microbiota development. This model of gut microbiota maturation demonstrated that undernourished children have significantly immature, i.e., younger-looking, microbiota compared to their healthy chronologically age-matched counterparts. Moreover, the state of gut microbiota maturation at 12 months of age in members of a Malawian birth cohort was predictive of growth phenotypes (as de ned by anthropometry) at 18 months. Transplanting 19 microbiota from age-matched healthy or undernourished Malawian infants and children into recently weaned gnotobiotic mice fed a representative Malawian diet revealed that immature microbiota from undernourished children conferred impaired growth phenotypes (de ned by serial measurements of total weight and lean body mass) relative to mice colonized with mature microbiota from healthy donors. These differences were not associated with significant differences in food consumption. These transplantations also demonstrated differences in bone morphology and altered metabolic profiles in serum, liver, muscle, and brain. Random Forests modeling of V4-16S rRNA datasets generated from the fecal microbiota of recipient mice established that a subset of age-discriminatory taxa were growth-discriminatory. Furthermore, co-housing mice shortly after they had been colonized with either a mature microbiota from a healthy (H) 6-month-old Malawian infant or an immature microbiota from an 6-month-old severely stunt- ed/underweight (Un) infant revealed invasion of taxa from the mature microbiota into the immature microbiota with a concomitant prevention of impaired growth in Un cagemates. The principal invaders were age- and growth-discriminatory bacterial strains. Five of these invading strains were cultured and added to the Un microbiota prior to its transplantation to young germ-free mice. Two members of the consortium were able to establish themselves in mice harboring the Un microbiota; their presence ameliorated the growth faltering and metabolic phenotypes produced by the Un microbiota. The results of Chapter 2 provide evidence that gut microbiota composition is causally related to undernutrition.

Chapter three addresses interactions between human milk oligosaccharides (HMOs) and the gut microbiota as related to host growth and metabolism. In the breast milk of 6-month postpartum mothers with severely stunted infants, sialylated HMOs were significantly less abundant than in the milk of mothers with healthy infants. To investigate this observation, germ-free mice were fed the representative Malawian diet, with or without purified sialylated bovine milk oligosaccharides (S-BMO), and colonized with a microbial consortium cultured from the fecal microbiota of a 6-month-old severely stunted Malawian infant. S-BMO supplementation conferred a microbiota-dependent increase in lean mass gain, altered bone morphology, and altered liver, muscle, and brain metabolic profiles that indicated an enhanced capacity for nutrient anabolism. These results were also observed in gnotobiotic pigs harboring the same microbes and fed the Malawian diet.

The fourth and final chapter discusses future experiments designed to characterize the mechanisms by which microbiota immaturity could impact growth and metabolism, and how findings and concepts obtained from preclinical gnotobiotic animal models could be directly tested in clinical studies.


English (en)

Chair and Committee

Jeffrey I. Gordon

Committee Members

Daniel Goldberg, Scott Hultgren, Karen Seibert, Clay Semenkovich,


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