Date of Award
1-18-2022
Degree Name
Doctor of Philosophy (PhD)
Degree Type
Dissertation
Abstract
Worldwide, malnutrition (undernutrition) is the leading cause of death in children under 5. Studies of healthy members of birth cohorts from low- and middle-income countries have identified a program of gut microbial community development that is disrupted in children with severe acute malnutrition (SAM) and moderate acute malnutrition (MAM). This perturbed gut microbiome development has been linked to the pathogenesis of malnutrition. Repair of this gut microbial dysbiosis in children with MAM with microbiota-directed complementary foods (MDCFs) designed to increase the fitness and expressed beneficial functions of underrepresented bacterial community members restores healthy growth, including improvements in mediators of metabolic and immune function. These findings provide evidence that the gut microbiota is causally linked to postnatal development and represent a substantial development in microbiota directed therapies. However, the durability (and generalizability) of the microbial community and host responses to this MDCF (and whether the intervention prevents the long-term sequelae associated with malnutrition) are not known. This dissertation represents an approach to understanding metabolic mechanisms governing host-microbe interactions in the gut of healthy infants and children and the relationship between these mechanisms and malnutrition. To design more effective therapies, we must understand how microbial community assembly (succession) is regulated in the human gut, as well as mechanisms that mediate interactions between microbes and the host. In this thesis, I employ a systems level approach to characterize a novel class of gut bacterial enzymes involved in NAD metabolism encoded by Toll/interleukin-1 receptor (TIR) domains and their relationship to malnutrition in the fecal microbiomes of Bangladeshi infants and children. NAD is an essential co-factor in myriad metabolic reactions with far-reaching effects on human physiology. In silico analyses were performed to identify and categorize TIR domains in bacterial proteomes. The NADase activities of 152 bacterial TIRs were then characterized in vitro. A consortium of 26 cultured, genome-sequenced human gut bacterial strains representing the diversity of TIRs observed in the microbiome and NADase activities documented in vitro, were introduced into germ-free mice fed defined diets. Mass spectrometry of cecal metabolites disclosed that a product unique to TIR NADase activity, variant cyclic-ADPR-x (v-cADPR-x), distinguished colonized from germ-free animals. Mass spectrometry and microbial RNA- Seq of gnotobiotic mice colonized with one, two and all members of the bacterial consortium, identified Bacteroides xylanisolvens as the principal in vivo source of v-cADPR-x. Guided by bioinformatic analyses of biochemically validated TIR domains, we determined that compared to age-matched healthy Bangladeshi children, those with acute malnutrition had significantly lower fecal levels of TIRs known or predicted to generate v-cADPR-x, and of this metabolite. There was not a statistically significant correlation between the level of TIR domains predicted to produce ADPR and the level of v-cADPR-x. Together, these results indicate that v-cADPR-x may be an informative biomarker of healthy gut microbiome development. This work represents an extension of the recent discovery of TIR enzymatic activity in a human protein to a characterization of this activity in the gut microbiome. The approach described in this thesis provides a broad description of this system, laying a foundation for future work. These future studies may include more refined analysis of bacterial TIR enzymology, analyses relating the context in which TIR domains are found to their functions, and an exploration of the role of TIR domains, and their NADase activity, in transkingdom interactions including intestinal development of their mammalian hosts.
Language
English (en)
Chair and Committee
Jeffrey Gordon
Recommended Citation
Weagley, James Stephen, "Characterizing Human Gut Bacterial TIR Domains In Vitro, in Gnotobiotic Mice and Malnourished Children" (2022). Arts & Sciences Electronic Theses and Dissertations. 3246.
https://openscholarship.wustl.edu/art_sci_etds/3246