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Adaptation of a Single-Stage Chemostat System to Model Functional Aspects of the Human Distal Gut Microbiota

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Title: Adaptation of a Single-Stage Chemostat System to Model Functional Aspects of the Human Distal Gut Microbiota
Author: Schroeter, Kathleen Frances Betty
Department: Department of Molecular and Cellular Biology
Program: Molecular and Cellular Biology
Advisor: Allen-Vercoe, EmmaKhursigara, Cezar
Abstract: The human gastrointestinal (GI) microbiota plays an important role in health and disease; in particular, commensal colonic biofilms have become a key focus of modern research efforts. However, in vitro models of the distal gut that also investigate colonic biofilm formation are still in their infancy. In this study we modified an in vitro single-stage chemostat model to successfully capture and sample the early colonizer biofilm communities associated with the healthy human distal gut. Mucin and sIgA, host-derived macromolecules used by the gut microbiota as binding sites for biofilm formation, were used to condition biofilm sampling sections. Fecal communities and defined microbial populations were used to validate the biofilm capture model and were analyzed with 16S-DGGE (a molecular fingerprinting technique) and community 16S rRNA gene sequencing. More diverse biofilm growth was captured on biologically relevant substrata compared to controls for all tested communities. We also identified members of the Enterobacteriaceae, Gammaproteobacteria incertae sedis, and to a lesser extent, the Streptococcaceae, Bifidobacteriaceae and Lactobacillaceae families as contributing to early biofilm formation. In addition, defined microbial communities were able to successfully simplify the fecal community from which they were isolated while still retaining considerable complexity in the planktonic (steady state) and biofilm forms. We were also able to create reproducible, defined microbial communities derived from feces that achieved the same ecological and functional steady state as one another in the chemostat model, despite the inclusion of isolate inocula with different starting biomass proportions. Overall, the research presented in this thesis has helped to advance our current understanding of the structure of healthy biofilm communities in the distal colon. This information may help to guide researchers and clinicians who aim to modulate the microbiota of patients with acute or chronic GI diseases, including the use of, for example, microbial ecosystem therapeutics to treat and cure Clostridium difficile infections. In the future, our experimental approach could also be applied to the investigation of different types of distal gut communities in a state of health and disease, in addition to other niches of the human microbiome, including vaginal, oral, skin and nasopharyngeal microbiotas.
Date: 2014-08
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