Date of Award

Winter 12-15-2021

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Molecular Microbiology & Microbial Pathogenesis)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



In 1973, Theodosius Dobzhansky famously wrote that nothing in biology makes sense except in the light of evolution. Today, nearly 50 years later, little in microbiology – or in biology, for that matter – makes sense except in the light of genomics. Microbial genomics populates the field with innumerable testable hypotheses for evaluation in vitro and in vivo, allows us to monitor microbial populations in real time and at a massive scale, and underpins our approach to entire domains of microbiology, including microbial evolution. In this Thesis, I present three studies from my graduate research united by their common theme of translational microbial genomics.

In Chapter 1, I discuss the comparative genomics of the Mycobacterium avium complex (MAC), a diverse group of emerging pathogens. MAC is now more prevalent than M. tuberculosis in many countries, including the United States, but our understanding of these organisms’ genomics has lagged behind their clinical impact. I found that different MAC species encode distinct suites of biomedically relevant genes, including antibiotic resistance genes and virulence factors. Moreover, M. avium isolates from different sources – human pulmonary infections, human disseminated infections, animals, and natural environments – have different core and accessory genomes, distinct patterns of horizontal gene transfer, and other identifying genomic features. Finally, I identified highly similar MAC strains from distinct patients separated by nearly 10 years and hundreds of miles, suggesting that MAC strains are not only temporally stable within environmental reservoirs but also geographically dispersed across reservoirs. This work provides valuable insight into the genomes of these versatile pathogens and will facilitate future exploration of MAC ecology, evolution, and pathogenesis.

In Chapter 2, I report a clinical case study of a patient who received fecal microbiota transplant (FMT) as an experimental treatment for recurrent antibiotic-resistant urinary tract infection (UTI). Because UTIs are frequently re-seeded from intestinal reservoirs, FMT is being explored as a treatment modality, but key safety and efficacy questions remain unanswered. I found that FMT product RBX2660 increased the patient’s gut microbiome diversity but did not eliminate gut uropathogen carriage, and multidrug-resistant UTI recurred after subsequent antibiotic exposure. Therefore, restoring microbiome diversity is insufficient to prevent disease recurrence by residual multidrug-resistant pathogens. Instead, complete uropathogen eradication via niche competition may be required for FMT to adequately resolve this condition.

Finally, in Chapter 3, I present a multi-center, multi-omics analysis of necrotizing enterocolitis (NEC), a devastating neonatal gastrointestinal disease associated with microbiome dysbiosis. NEC is a major threat to preterm neonates, but its incidence, mortality, and standard treatment have remained largely unchanged for decades. However, recent technological advances, particularly massively high-throughput metagenome and metatranscriptome sequencing, offer appealing new opportunities to resolve long-standing questions in neonatal microbiology generally and NEC specifically. In this study, I leveraged an extensive prospective cohort with dense longitudinal sampling (>2000 stool samples from >100 infants), rich metadata (dozens of clinical variables per patient), and robust multi-omic analysis to interrogate this landscape in unprecedented detail. I found that NEC lacked strong microbiome and metadata signatures in aggregate. However, parsing NEC cases by age at onset revealed divergent associations. Early-onset NEC (onsetlife; DOL) lacked a microbiome signature but was strongly associated with clinical features, including high frequency of ventilation. Conversely, late-onset NEC (onset >40 DOL) had few metadata associations but displayed a strong microbiome signature, including stunted microbiome maturation, a near-absence of commensals, and massive enrichment of Klebsiella and other Enterobacteriaceae. Collectively, these findings provide key insights into NEC etiologies and pathogenesis and may inspire a new era of personalized risk assessment, early diagnosis, and timely intervention for this devastating pediatric disease.


English (en)

Chair and Committee

Gautam Dantas

Committee Members

Gautam Dantas

Available for download on Saturday, March 23, 2024