Washington University in St. Louis Washington University Open Scholarship Arts & Sciences Electronic Theses and Dissertations Arts & Sciences Winter 12-15-2015 Characterizing the Role of Sialylated Milk Glycans and the Infant Gut Microbiota in Growth and Metabolism Mark Richard Charbonneau Washington University in St. Louis Follow this and additional works at: https://openscholarship.wustl.edu/art_sci_etds Recommended Citation Charbonneau, Mark Richard, "Characterizing the Role of Sialylated Milk Glycans and the Infant Gut Microbiota in Growth and Metabolism" (2015). Arts & Sciences Electronic Theses and Dissertations. 642. https://openscholarship.wustl.edu/art_sci_etds/642 This Dissertation is brought to you for free and open access by the Arts & Sciences at Washington University Open Scholarship. It has been accepted for inclusion in Arts & Sciences Electronic Theses and Dissertations by an authorized administrator of Washington University Open Scholarship. For more information, please contact [email protected]. WASHINGTON UNIVERSITY IN ST. LOUIS Division of Biology and Biomedical Sciences Computational and Systems Biology Dissertation Examination Committee: Jeffrey Gordon, Chair Jeremy Buhler Daniel Goldberg Scott Hultgren Clay Semenkovich Michael Talcott Characterizing the Role of Sialylated Milk Glycans and the Infant Gut Microbiota in Growth and Metabolism by Mark Charbonneau A dissertation presented to the Graduate School of Arts and Sciences of Washington University in requirements for the degree of Doctor of Philosophy December 2015 St. Louis, Missouri © 2015, Mark Charbonneau Table of Contents Acknowledgements ...................................................................................................................... viii ABSTRACT OF THE DISSERTATION ....................................................................................... xi Chapter 1 Introduction Abstract ............................................................................................................................................3 Introduction ......................................................................................................................................3 Defining Human Postnatal Development from a Microbial Perspective .........................................4 Undernutrition and Gut Microbiota Immaturity ..................................................................6 Establishing Microbiota and the Maternal Influence .........................................................13 The Impact of First Foods ..............................................................................................................14 Breast Milk .........................................................................................................................14 Serial Introduction of Complementary Foods in Ways that Promote Maturation of the Gut Microbiota ..........................................................................................................................17 Additional Considerations Regarding the Developmental Biology of the Gut Microbiota ...........18 Obesity ...............................................................................................................................18 Impact of Antibiotics ..........................................................................................................19 Affordable Nutritious Foods: Societal Implications and Challenges.............................................20 Opening the Public Discussion ......................................................................................................22 Science and Technology .....................................................................................................22 Ethics ..................................................................................................................................22 Policy and Governance ......................................................................................................23 Closing Thoughts ...........................................................................................................................23 Acknowledgments ..........................................................................................................................25 References ......................................................................................................................................26 Figure Legends ...............................................................................................................................36 Figures............................................................................................................................................40 ii Chapter 2 Gut bacteria that rescue growth impairments transmitted by immature microbiota from undernourished children Abstract ..........................................................................................................................................45 Main Text .......................................................................................................................................45 A Malawian model of gut microbiota development ..........................................................46 Identification of age-discriminatory taxa that are also growth-discriminatory ..................48 The relationship between age- and growth-discriminatory taxa and femoral phenotypes 51 Effects of gut microbiota immaturity on host metabolism ................................................52 Repairing impaired growth phenotypes with age- and growth-discriminatory strains present in a healthy donor microbiota ................................................................................55 Culturing invasive growth- and age-discriminatory taxa and characterizing their effects on growth ...........................................................................................................................57 Prospectus ......................................................................................................................................59 References and Notes .....................................................................................................................62 Acknowledgements ........................................................................................................................68 Data Deposition .............................................................................................................................68 Declarations ...................................................................................................................................69 Author Contributions .....................................................................................................................69 Figure Legends ...............................................................................................................................70 Figures............................................................................................................................................73 Supplementary Materials ...............................................................................................................78 Materials and Methods ...................................................................................................................78 Human Studies ...................................................................................................................78 Bacterial 16S rRNA sequencing ........................................................................................78 Random Forests-derived Models and Statistical Analysis .................................................79 Gnotobiotic Mouse Studies ................................................................................................79 Preparation of the Malawi-8 (M8) Diet .................................................................80 Generation of clarified stool for gavage into gnotobiotic mice .............................81 Quantitative magnetic resonance (qMR) analysis of body composition ...............81 Sample collection ...................................................................................................82 Micro-computed tomography (micro-CT) .............................................................82 iii Co-housing experiments ........................................................................................82 Targeted mass spectrometry ...............................................................................................82 Culturing and characterization of age- and/or growth- discriminatory bacterial strains from the microbiota of healthy Malawian children ...........................................................83 Genome sequencing of two strains obtained from the healthy infant Malawian donor 8243C .................................................................................................................................84 Supplementary Results ...................................................................................................................84 Genomics-based reconstruction of selected metabolic subsystems in R. gnavus and C. symbiosum strains ..............................................................................................................84 Carbon and energy: central carbon metabolism, carbohydrate utilization, and short chain fatty acid production (Fig. S8A and Table