Date of Award

Spring 5-15-2023

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



Microbes interact with humans in a myriad of ways. They come together in the human gut to form complex communities that collectively transform and individually evolve in response to changing environmental conditions. Individual microbes can also cause human infection and escape antibiotic clearance through acquisition and development of novel resistance mechanisms. In this thesis, I chronicle the relationships between microbes and humans across two axes: from complex communities to single isolates, and from targeted studies of pediatric populations vulnerable to microbiome perturbations and pathogen challenge, to broader human and animal cohorts spanning colonizing and diagnostic environments.

In Chapter 2, I extensively profile individual microbial members of the gut microbiome from birth through early adolescence. This period of early life is essential to stereotypical gut microbiome development, but to date has mainly been characterized at the community level. To dive deeper, I employed deep short- and long-read sequencing of direct and culture-enriched stool to reconstruct thousands of high-quality microbial genomes. I identified hundreds of strain-sharing events within twin pairs, mother-infant dyads, or family triads, and determined Bacteroidales, Oscillospiraceae, and Lachnospiraceae to be vertically transferred from mother to infant, at birth and throughout infancy. I observed over 1,000 strains to persist within ever-changing microbial ecosystems, and catalogued species-level evolutionary rates in a high-throughput manner. Across infant dietary exposures, I identified weaning to be a critical window in which mutation accrual is accelerated among persisting strains, as well as a key inflection point after which the gene families accruing mutations dramatically shift towards those of the maternal state. Taken together, this study offers an extensive catalogue of metagenome-assembled genomes in the infant gut, sharing patterns between cohabitating family members, and within-host evolution across dozens of species during periods of maximum microbiome perturbation.

In Chapter 3, I shift focus from the diverse microbial community in the pediatric gut to a single pathobiont colonizing the nares of NICU-hospitalized infants. Recent atypical trends observed during surveillance for methicillin-resistant Staphylococcus aureus (MRSA) at the St. Louis Children’s Hospital found oxacillin resistance among S. aureus isolates that did not carry the mec cassette, the canonical beta-lactam resistance-conferring operon. To investigate the genomic underpinnings of this resistance, I performed whole genome sequencing on 101 S. aureus isolates that spanned the borderline oxacillin resistance (BORSA), MRSA, and methicillin-susceptible (MSSA) phenotypes. This comparative genomics investigation found BORSA isolates to be phylogenetically diverse, with no common accessory genome that differentiated them from MRSA or MSSA comparators. However, through the creation of a random forest classifier I was able to predict BORSA identity based on beta-lactamase hyperproduction and five substitutions or truncations to key penicillin-binding proteins (PBPs) or the phosphodiesterase GdpP. This work provides evidence against a recent clonal expansion of BORSA and argues against the role of dozens of amino acid substitutions in PBPs previously suggested to contribute to the BORSA phenotype.

In Chapter 4, I direct attention to a close relative of S. aureus, Staphylococcus pseudintermedius. Study of S. pseudintermedius has historically been limited to its role as the dominant skin colonizer of and cause of pyoderma in canines, yet modern clinical diagnostics has revealed the species has long contributed to human morbidity – ironically, while being miscalled as S. aureus. Our expanded understanding beckons key questions regarding the ability of S. pseudintermedius as a species to adapt across environmental niches and host- types. Towards this, I sequenced over 500 S. pseudintermedius isolates captured in and on human and animal patients at the Barnes-Jewish Hospital and Kansas State Veterinary Clinic, as well as on human and pet inhabitants of and abiotic surfaces in households in the St. Louis metropolitan area. Although the whole genome architecture of S. pseudintermedius did not differ significantly by host-species, I found isolates originating from households to share more CRISPR spacers – markers of ancestral phage predation – with each other than with diagnostic isolates. Further, I found diagnostic isolates to harbor extensive resistance gene burden, while isolates from households accrued non-synonymous mutations in defense-related genes amidst MRSA decolonization. Together, this study offers evidence in support of niche adaptation through parallel selection of defense mechanisms among diagnostic and household S. pseudintermedius.

In the Addendum, I discuss antibiotic-mediated microbiome disruption and development of the resistome during infancy. I summarize recent clinical trends of pediatric antibiotic prescriptions, and their associations with long-term pediatric health. I center recent work that interrogates earliest life seeding and development of antibiotic resistance in the gut microbiome, and specifically highlight mobilization and spread of antibiotic resistance between community members.


English (en)

Chair and Committee

Gautam Dantas

Committee Members

Megan T. Baldridge, Carey-Ann D. Burnham, Daniel E. Goldberg, Phillip I. Tarr,