Date: 2021-04-22
Time: 05:48:44 UTC
Title: Dissertation defense, April 20, 2021
After so many years, it ended so quick, and so well. My microbiology PhD
began at Emory University in the fall of 2016, but I only really chose a
thesis topic in the spring 2017 when I joined Timothy Read's laboratory.
While I worked on many collaborative projects there, it was his S.
aureus phage host range R21 submission that came to be my own. Tim had
submitted a grant proposal to discover the basis of phage host range in
the whole, diverse Staphylococcus aureus bacterial species. For
reference, bacteriophages, or "phages", are viruses that infect and kill
bacteria. Host range is the maximum number of strains a phage can infect
and kill amongst all possible strains. The goal of this research is to
predict host range from the genome sequence of the host. In that way,
you could personalize phage therapies to S. aureus strains causing
infection in particular patients.
In my dissertation research, I conducted two major studies regarding the
host determinants of S. aureus phage host ranges. In the first study, I
conducted a phage host range genome wide association study on diverse
strains capturing a snapshot of S. aureus species diversity. I developed
a high-throughout spot assay to rapidly collect host range phenotypes
for these strains against eight different S. aureus phages. The goal of
the GWAS was to identify the most important species-wide determinants of
phage host range in a hypothesis-free, unbiased manner. Quite
strikingly, unlike previous studies, I did not find phage receptor genes
or other obvious gene candidates for perfect phage infection barriers.
Instead, the GWAS uncovered determinants with more subtle phenotypic
effects, like helping bacteria grow well even during successful phage
infection. At least several genes showed causative roles upon
experimentation, as opposed to just strong correlations, and much
remains to be discovered as far as the causes of S. aureus phage host
range, with only 60-70% of phenotypic variability explained by
significant GWAS hits.
The second study, unlike the first, looked backwards in time at
previously identified phage resistance genes in the S. aureus species. I
instead looked at evolutionary patterns of these genes and evaluated how
well they could predict phage resistance phenotypes in the first study
or levels of horizontal gene transfer. I found genes involved in forming
the phage receptor, a surface carbohydrate called wall teichoic acid, to
be the most conserved in the species by far, being encoded by 100% of
strains in our database of 40,000+ S. aureus strain genomes. Phage
resistance genes with similar functions were more likely to be encoded
together on genomes, which makes sense both given bacterial genes are
often operonic (encoded next to each other, so that they are transcribed
from DNA to RNA all in one molecule) and phage defense genes are often
encoded near each other in so-called phage defense islands. Finally I
approached the relationship between phage resistance genes and either
resistance phenotypes measured in the lab or horizontal gene transfer
measured by accessory genome content. Only superinfection immunity gene
presence correlated with increased temperate phage resistance or
accessory genome content, which follows from its indelible tie to
prophages. Prophages encode transcription repressors that prevent
infection of a superinfecting phage of the same type. These repressors,
or superinfection immunity genes, thus cause resistance to temperate
phages of the same type in the lab, and correlate with increased
accessory genome (not found in all strains) either due to being
hallmarks of prophage genes, other non-prophage genes (e.g., antibiotic
resistance) carried along with prophages, or just increased levels of
horizontal gene transfer (transduction by phages) that may increase
chances for prophage integration.
Despite a sudden and jarring zoom bombing at the end of the defense,
just after I had answered the first question, it went incredibly well.
It was such a relief to complete. As my advisor said was universally
true but also universally paradoxical, I didn't feel any different after
getting the PhD.
I posted the practice talk here for posterity:
Dissertation practice talk
https://youtu.be/mvMIwtnsm7M
