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Analysis of microbial communities in three diverse commodity systems

Capouya, Rachel Danielle, Capouya
http://rave.ohiolink.edu/etdc/view?acc_num=osu1543510790291037

Abstract Details

2018, Doctor of Philosophy, Ohio State University, Plant Pathology.
The importance of microbial communities has been demonstrated in countless systems to date and the development of next-generation high throughput sequencing technology has dramatically increased our ability to assess the microbial communities while overcoming the challenges of traditional culture-based assays. This collection of projects in microbiome sequencing analysis is comprised of work in vastly different systems with a central theme: investigating the composition of microbial communities in each system and analyzing how changes in that composition may be associated with different variables. We chose to investigate the microbes present in green coffee beans, specifically comparing the communities across different geographic origins and beans of different defect statuses. We drew a general profile of the associated fungal and bacterial species residing in these beans post-processing, as well as assessed differences between beans having any of five economically significant defects and between beans from three coffee-producing regions across the globe. This set the stage for further applied experiments to determine if some of the identified microbes can be manipulated to impact coffee quality by pre-roasting treatments. Our next project served to identify potentially critical changes in the community composition throughout checkpoints in a multistep procedure designed to complete fungal pre-treatment of switchgrass, or Miscanthus (Miscanthus x giganteus), with the wood decay fungus Ceriporiopsis subvermispora for biofuel production. A collaborator developed a protocol to introduce the unsterilized Miscanthus feedstock into a system containing only sterilized Miscanthus and the degradative fungus. However, it was found that the efficacy of lignin degradation in the system was reduced following the stepwise introduction of unsterilized material. The objective of our project was to assess the changes in the microbial community at each step to determine if the reduced efficacy was result of a contaminating factor or the outcolonization of the feedstock by the native microbes harbored in the unsterilized Miscanthus. We determined that the population of C. subvermispora was decimated throughout the process and the indigenous microbes were quickly able to colonize the system and return the community to a state similar to that found in untreated, unsterilized Miscanthus. This demonstrated the necessity of retaining the sterilization step the fungal pretreatment process. We were approached with a proposal from Certified Angus Beef to explore the microbial communities on dry-aged beef. It was noted that aged beef from multiple locations, while using similar condition and starting material, had differing sensory qualities depending on the facility in which it was aged. We investigated the communities identified on samples from five aging facilities in tandem with sensory evaluation studies conducted on the same meats. We examined the results together to establish a microbial profile of dry aged beef, and to assess potential microbial associations correlated with notable sensory differences in the final product. We additionally determined an even distribution of the microbes across the surface of the loin and to a depth of 1 cm into the meat. Taken together, these studies demonstrate the importance of microbiomes in plant seed quality, biofuel production, and the crafting of gourmet food.
Thomas Mitchell (Advisor)
Francesca Peduto-Hand (Committee Member)
Pierce Paul (Committee Member)
Kristin Mercer (Committee Member)
228 p.
Plant Pathology
microbial communities; coffee; dry aged beef; microbiome; Miscanthus

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Citations

  • Capouya, Capouya, R. D. (2018). Analysis of microbial communities in three diverse commodity systems [Doctoral dissertation, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1543510790291037

    APA Style (7th edition)

  • Capouya, Capouya, Rachel. Analysis of microbial communities in three diverse commodity systems. 2018. Ohio State University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1543510790291037.

    MLA Style (8th edition)

  • Capouya, Capouya, Rachel. "Analysis of microbial communities in three diverse commodity systems." Doctoral dissertation, Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu1543510790291037

    Chicago Manual of Style (17th edition)

osu1543510790291037
566
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This open access ETD is published by The Ohio State University and OhioLINK.