Document Type

Dissertation - Open Access

Award Date


Degree Name

Doctor of Philosophy (PhD)


Veterinary and Biomedical Sciences

First Advisor

Joy Scaria


Clostridium difficile, Colonization resistance, Culturomics, Human gut microbiome, Minibioreactor

Library of Congress Subject Headings

Human gut microbiota is comprised of thousands of species which fall into two major categories or “enterotypes” based on dominating bacteria: “Bacteroides” and “Prevotella”. Bacteroides enterotype dominates the microbiota of the western population because of a high protein and fat diet, whereas Prevotella enterotype is dominate in the gut of the eastern population because of a high carbohydrate diet. While most of the microbiota studies focused on the Bacteroides enterotype using both metagenomics and culturomics, Prevotella enterotype is understudied, especially in the field of culturomics. The structure of the Prevotella dominated gut microbiome is revealed by metagenomic studies, but the individual bacterial species and their characteristics require culturomics and phenotypic characterization studies. To understand how microbes assemble into communities and provide colonization resistance against pathogens, we used the culturomics approach to capture the bacterial diversity of the Prevotella dominated community. We cultured 1590 isolates belonging to 102 bacterial species and characterized them for their substrate utilization, short chain fatty acid production and inhibition of Clostridium difficile. We found that 66 bacterial species were able to inhibit C. difficile in vitro. Furthermore, using a combinatorial community assembly approach, we identified the minimum number of bacteria required to resist C. difficile in vitro is twelve. During this culturomics, we also isolated two novel bacterial species from the Prevotella dominated microbiome. Furthermore, to understand how the Prevotella dominated community is shaped by certain prebiotic substrates, we combined rice bran and quercetin to analyze their effect on microbiome composition in minibioreactors. The combination of these prebiotics significantly reduces potential pathogenic bacteria by alleviating propionate levels. Also, there are studies suggesting inhibition of C. difficile may occur by conversion of bile acids by C. scindens. We analyzed the genetic differences of five C. scindens strains and tested their ability to inhibit C. difficile in vitro. We found a variation in C. scindens genomes and their ability to inhibit C. difficile in the presence and absence of bile. This research improves our understanding of gut microbiota using culturomics and identifies mechanisms utilized by gut microbes to inhibit C. difficile in vitro, which is valuable step in the development of biotherapeutics for gut diseases in future.



Number of Pages



South Dakota State University


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Available for download on Tuesday, June 15, 2021

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Microbiology Commons