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Improvement of Microbial Detection and Analysis Techniques in Complex Biological Environments


Porter, Michael Koizumi (2024) Improvement of Microbial Detection and Analysis Techniques in Complex Biological Environments. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/7chb-wk98.


Human bodies are home to a vast assortment of microbes, including bacteria, fungi, and viruses. These microbes live within their human hosts, interacting with each other and influencing states of health and disease. Despite their prevalence and importance, studying host-microbe interactions has been limited by the dearth of appropriate tools and approaches, and an underappreciation for the role of biophysics. This thesis describes the development and application of novel tools and approaches for studying bacteria, fungi, and viruses to uncover their potential roles in human health and disease.

In my first project, we investigated bacterial aggregation, a phenomenon related to important host-microbe interactions such as biofilm formation and the clearance of pathogens from the gastrointestinal tract. We found that bacteria aggregate in the presence of polymers (such as dietary fiber) via a mechanism that is qualitatively consistent with depletion-type forces under gut-like conditions. Surprisingly, motile bacteria aggregate more than nonmotile bacteria in viscous, high-polymer concentrations due to the higher effective diffusivity and inter-bacterial collisions enabled by motility. These two results give insight on how the foods (such as fiber) that we consume can physically affect the structure of microbes and other matter in the gut.

In my next projects, we investigated viral-load kinetics to understand the best testing modality for early detection of SARS-CoV-2 via a large community-based household transmission study. By collecting longitudinal, paired saliva and nasal-swab specimens from SARS-CoV-2 patients starting from the incident of infection, we quantified the viral-load trajectories of COVID-19-positive participants in each specimen type over time. Our results revealed that viral loads increased quickly and reached a higher peak in nasal-swab specimens, whereas viral loads were detectable earlier but reached a lower maximum in saliva. Both specimen types exhibited a temporal trend whereby viral loads were higher in specimens collected in the morning compared with the evening. In samples where infectious viral titer was measured, we found that the ratio of N gene viral load and infectious viral titer did not remain consistent throughout the course of infection. These three results help us understand the heterogeneity of SARS-CoV-2 disease progression in different individuals, and how the analytical sensitivity of a diagnostic, the specimen type, and time of sampling can be crucial in conducting community surveillance programs during a pandemic. Finally, we extended and co-validated for fungi a novel sample-preparation method that enriches fungal cells in host-rich samples to enable the first demonstration of deep metagenomic sequencing of fungal communities directly from clinical samples (without a culture step). Our results show that this method depletes host DNA by over 1000-fold by mass, improving taxonomic classification and gene calling, as well as enabling de novo metagenome assembled genome (MAG) assembly in samples dominated by human biomass.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:microbiome, mycobiome, SARS-CoV-2, viral load, nucleic acid
Degree Grantor:California Institute of Technology
Division:Chemistry and Chemical Engineering
Major Option:Chemical Engineering
Thesis Availability:Restricted to Caltech community only
Research Advisor(s):
  • Ismagilov, Rustem F.
Thesis Committee:
  • Wang, Zhen-Gang (chair)
  • Tirrell, David A.
  • Leadbetter, Jared R.
  • Ismagilov, Rustem F.
Defense Date:23 May 2024
Funding AgencyGrant Number
Bill and Melinda Gates FoundationINV023124
Jacobs Institute for Molecular Engineering for Medicine at CaltechUNSPECIFIED
Rosen Biotechnology Leadership ProgramUNSPECIFIED
Kenneth Rainin Foundation2018-1207
Caltech Space-Health Innovation FundTRISH
Merkin Institute for Translational ResearchUNSPECIFIED
Defense Advanced Research Projects Agency (DARPA)HR0011-17-2-0037
Record Number:CaltechTHESIS:05292024-020036252
Persistent URL:
Related URLs:
URLURL TypeDescription material corresponding to chapter 2 material corresponding to chapter 3 material corresponding to chapter 4 material corresponding to chapter 5
Porter, Michael Koizumi0000-0002-0777-7563
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:16432
Deposited By: Michael Porter
Deposited On:29 May 2024 18:57
Last Modified:30 May 2024 23:37

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