Tandon, Disha (2023). A Microbiota-Dependent Auxotrophic Salmonella Typhimurium Vaccine: Bacterial Adaptation and Mucosal Transcriptomic Response in Gnotobiotic Mice. (Thesis). Universität Bern, Bern
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Abstract
For all organisms, evolution is an ongoing process. Enteric commensal bacteria and pathogens are no exception. With increasing focus on gut microbiota and enteric diseases, it has become paramount to study the adaptation of gut bacteria/pathogens to their host. In the context of commensals, these adaptations can render the concerned bacteria better at utilizing and exchanging the available nutrients, hence optimizing their metabolic niche. In the context of pathogens, adaptations can make them better colonizers, aiding their transmission and/or affecting their virulence capability, thus altering their state of pathogenicity. However, pathogenic adaptations come at the cost of trade-offs between their virulence and fitness. These adaptations depend on many factors including the pathogen's association to host gut microbiota, host immune status, and stage of infection. At the expense of partial/full virulence loss, most pathogens succeed in surviving and replicating through efficient transmission. This characteristic can be utilized in the development of live vaccines against pathogens. However, studying the evolution of the live vaccines is equally important given the constant risk of such vaccines gaining back the factors that made them genetically or phenotypically attenuated. Here, we studied the long-term evolution of a cell-wall auxotrophic potential live vaccine against the model organism Salmonella enterica supsp. enterica serovar Typhimurium (S. Typhimurium) through omics approach and subsequent phenotypic validation in low-complexity microbiota associated gnotobiotic mouse models. The auxotrophic nature of this live vaccine renders it metabolically dependent on the surrounding bacterial community. We described the temporal genomic adaptation of this live vaccine in the context of its virulence, auxotrophy, and metabolic transport. We also showed that the reversal of auxotrophy is not apparent in this live vaccine as expected over long-term colonization through means of genetic material transmission. We revealed that the virulence adaptation over time is dynamic and dependent on regulatory genetic determinants. Finally, in our first step to genetically validate the observed genomic evolutionary changes, we characterized the cellular invasiveness of genomic representative reisolates of the live vaccine from different time points. These initial findings demonstrate that the long-term evolution of vaccine candidates is important in terms of their dynamic virulence capacity and metabolic adaptation, hence affecting their continued efficacy and safety in the host. In addition to the long-term evolution, we also studied the gastrointestinal mucosal transcriptomic response conferred by the auxotrophic S. Typhimurium live vaccine in gnotobiotic mouse models. We explored the mucosal immune response after auxotrophic S. Typhimurium has stably colonized the murine gut and characterized it in the context of differentially regulated genes and gene-clusters. Finally, we hypothesized a plausible interplay of immune and metabolic mechanisms instrumental in protecting against pathogenic S. Typhimurium. Following a deviation from the omics analysis of long-term evolution and mucosal transcriptomics, we established a robust 'bench-to-laptop' pipeline to analyze the lowcomplexity bacterial composition of a gnotobiotic murine gastrointestinal microbiome using long-read sequencing. We showed the efficiency of this pipeline in terms of detecting low-abundance bacteria. Finally, we demonstrated the accuracy of this pipeline using an optimal mock community.
| Item Type: | Thesis |
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| Dissertation Type: | Cumulative |
| Date of Defense: | 26 January 2023 |
| Subjects: | 600 Technology > 610 Medicine & health |
| Institute / Center: | 04 Faculty of Medicine |
| Depositing User: | Hammer Igor |
| Date Deposited: | 05 Dec 2025 09:43 |
| Last Modified: | 05 Dec 2025 23:25 |
| URI: | https://boristheses.unibe.ch/id/eprint/6935 |
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