Date of Award

Spring 5-15-2021

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



The collection of microbes known as the human microbiome perform vital functions for their host, and when this community becomes unhealthy, its dysbiosis is implicated in a myriad of diseases. The gut microbiota in particular are known to suppress colonization of opportunistic pathogens, regulate the immune system, aid in nutrient breakdown, produce vitamins, and a growing number of other functions. In order to intervene in a dysbiotic microbial ecology, we can try to remove unwanted microbes or try to recolonize the gut with microbes expected to be beneficial. This dissertation provides an overview of the state of medical interventions for the microbiome. Two original research projects are presented detailing 1) the effects of fecal microbiome transplantation (FMT) on the gut microbiota of adults with antibiotic-refractory Clostridioides difficile infection, and 2) the effects of amoxicillin on the gut microbiota of children with uncomplicated severe acute malnutrition. This is accomplished by metagenomic sequencing of the genomes of the bacteria present in the stool of each patient over a study period. The bacterial community proportions, diversity, metabolic potential, and changes over time are assessed with relation to health outcomes. Particular attention is paid to antibiotic resistance (AR), as this represents a growing challenge and a serious obstacle to continued therapeutic use of antibiotics to combat bacterial disease.In the first project, we sequenced and analyzed stool samples from a Phase II clinical trial treating U.S. adults with antimicrobial-refractory C. difficile infections by fecal microbe transplantation of an intact microbial community from healthy donors. We expected to see that remediation of symptoms of C. difficile infection symptoms would correlate with greater engraftment of donor microbiota into the host, and we found this to be true. As in previous studies, we saw that the transplant recipient adopted many individual bacterial taxa from the donor, and their eventual microbiome composition was somewhere between the extremely dysbiotic microbiome from their baseline samples and the healthy community from the donor. We also predicted that successful engraftments would reduce the abundance of antimicrobial resistance genes (ARGs) in the host. We confirmed this, and we also found a dose-response relationship between the completeness of the adoption of the donor configuration and the reduction of ARGs in the host. Additionally, we used selective culture to isolate 38 antimicrobial resistant organisms (AROs) from 5 different bacterial genera and sequenced their genomes. Through tracking their identifying ribosomal 16S sequences throughout the longitudinal study samples, we found that eradication of these strains from the recipient microbiomes was possible and even common. These findings offer both motivation and direction towards the development of rational and defined treatments that could someday be used to control the carriage and spread of dangerous AROs within the gut microbiome. The second project was a collaboration with Doctors Without Borders to evaluate the impact of prophylactic amoxicillin on the gut microbiota of children presenting with severe acute malnutrition (SAM). Even when enrolled in nutritional therapy programs, children with SAM have high probability of relapse and death. The fear and motivation for this randomized controlled trial was that this broad-spectrum antimicrobial could harm the composition of the gut microbiome and select for antimicrobial resistance. Infections with drug resistant pathogens in children who are severely undernourished can be especially concerning. We found that the amoxicillin did indeed have an impact on the gut microbiota with the expected rise in ARGs, but that it resolved even by the next study visit at 4 weeks. We also investigated two mechanism behind the beneficial effects of this prophylactic treatment on recovery from SAM. First, treatment with amoxicillin decreases genes and microbes associated with an age-regressed malnourished community that is not adapted to an adult diet. Secondly, study treatment reduces the incidence of diarrheal illnesses long after cessation of antibiotics. The results of this study strongly support continued prophylactic use of amoxicillin in children with severe acute malnutrition. Together, this body of work forwards our understanding of how the human gut microbiota respond to perturbations and to medical interventions in order to promote human health.


English (en)

Chair and Committee

Gautam Dantas

Committee Members

John Edwards, Chyi Hsieh, Andrew Kau, James Skeath,