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Development of Analytical Tools and Animal Models for Studies of Small-Intestine Dysbiosis


Bogatyrev, Said R. (2020) Development of Analytical Tools and Animal Models for Studies of Small-Intestine Dysbiosis. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/VJDZ-7B52.


Our appreciation of the role of human-associated microbial communities in the context of human health and disease has grown dramatically in the past two decades, with modern research tools enabling deeper insights into the mechanisms of host-microbial interactions. The elusive notion of dysbiosis, a state of microbial imbalance related to a disease, has achieved widespread distribution across popular, scientific, and medical literature (on September 16, 2019 PubMed search yielded 6,064 records of scientific and medical publications containing this keyword). The conventional wisdom further narrows down the definition and understanding of dysbiosis towards a compositional "imbalance" of the microbiota (a community of all microorganisms inhabiting human body). There exists an additional and frequently overlooked aspect of microbial imbalance in the context of the human gastrointestinal system, something that we can define as a "spatial imbalance": a state of the microbial community in the host gastrointestinal system where even a "healthy" and "balanced" microbiota may be associated with or causative of a disease by being present in sections of the gastrointestinal tract where it is not "supposed" to be, with the most prominent example being small intestinal bacterial overgrowth (SIBO). This thesis describes the progress in the development of analytical tools (quantitative microbiome profiling described in Chapter I) and refinement of animal mouse models (non-coprophagic mouse model described in Chapter II) for exploring the normal function of small-intestine microbiota in health and for dissecting the mechanisms of emergence and the persistence of the small-intestine dysbiosis (SIBO) in the future.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Microbial quantification, 16S rRNA gene amplicon sequencing, metabolomics analyses, mouse models, small-intestine microbiota, bile acids, deconjugation, coprophagy, microbial colonization
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:
  • Elowitz, Michael B. (chair)
  • Ismagilov, Rustem F.
  • Mazmanian, Sarkis K.
  • Sternberg, Paul W.
Defense Date:20 September 2019
Funding AgencyGrant Number
Army Research Office (ARO) Multidisciplinary University Research Initiative (MURI)W911NF-17-1-0402
Kenneth Rainin FoundationInnovator Award
Jacobs Institute for Molecular Engineering for MedicineUNSPECIFIED
Record Number:CaltechTHESIS:10012019-095132591
Persistent URL:
Related URLs:
URLURL TypeDescription 2 supplementary 16S rRNA gene amplicon sequencing data.
Bogatyrev, Said R.0000-0003-0486-9451
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:11805
Deposited By: Said Bogatyrev
Deposited On:05 Nov 2019 19:24
Last Modified:04 Nov 2021 21:12

Thesis Files

PDF (Thesis Full Text) - Final Version
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[img] Archive (ZIP) (Thesis Chapter 2 Supplementary Data and Analytical Scripts) - Supplemental Material
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