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Quantitative Sequencing and its Application to Studies of the Human Small-Intestine Microbiota


Barlow, Jacob T. (2022) Quantitative Sequencing and its Application to Studies of the Human Small-Intestine Microbiota. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/ca28-fk21.


Our understanding of the interplay between microbial species and the hosts they live on and in is continually expanding. New insights have focused not only microorganisms that drive specific disease states but also those that help maintain human health. As research drives towards mechanistic understanding of host-microbe relationships new quantitative tools are needed to help interrogate these complex interactions. Chapter I of this thesis discusses formulation of a method for rapid detection of antibiotic resistance in Neisseria gonorrhoeae. Our approach identified RNA signatures from transcriptional profiling of Neisseria gonorrhoeae after 10-minute antibiotic exposure. Utilization of these RNA markers allowed for rapid identification of antibiotic susceptibility or resistance to the antibiotic ciprofloxacin. Chapter II shifts focus to the development of a quantitative sequencing technique for the measurement of absolute taxon abundances in complex microbial communities. Combining the precision of digital PCR with the high-throughput nature of 16S rRNA gene amplicon sequencing allowed for simultaneous quantitative profiling of all bacterial taxa in host-associated microbial communities. We extensively characterized our quantitative sequencing methodology in the presence of high host nucleic acid levels and low microbial loads to understand the limits of quantification and detection in complex sample types. Last, Chapter III applies the quantitative sequencing technology from Chapter II to investigate the microbial community of the human small intestine, specifically the duodenum. Data from the duodenum of 250 individuals revealed a wide range of total microbial loads and a distinct subset of microbes, termed disruptor taxa, that were associated with small intestinal bacterial overgrowth (SIBO) and GI symptom severity.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:microbiome, 16S rRNA gene, sequencing, human health, small intestine, digital PCR
Degree Grantor:California Institute of Technology
Division:Biology and Biological Engineering
Major Option:Bioengineering
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Ismagilov, Rustem F.
Thesis Committee:
  • Mazmanian, Sarkis K. (chair)
  • Thomson, Matthew
  • Cai, Long
  • Ismagilov, Rustem F.
Defense Date:26 August 2021
Non-Caltech Author Email:jtbarlow3 (AT)
Funding AgencyGrant Number
Kenneth Rainin Foundation Innovator Award2018–1207
NIH Training Grant5T32GM112592-03
ARO MURIW911NF-17-1-0402
Record Number:CaltechTHESIS:10282021-191743624
Persistent URL:
Related URLs:
URLURL TypeDescription adapted for Chapter 1 adapted for Chapter 2 adapted for Chapter 3
Barlow, Jacob T.0000-0002-1842-4835
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:14409
Deposited By: Jacob Barlow
Deposited On:05 Nov 2021 16:22
Last Modified:12 Nov 2021 20:49

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