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Using Computational Approaches to Investigate Streptococcal Species from the Food Industry
Title
Using Computational Approaches to Investigate Streptococcal Species from the Food Industry
Creator
Sun, Yukun
Date
2020
Description
Streptococcal species are a major cause of concern in the Food industry. In the swine industry, Streptococcus suis is not only a major...
Show moreStreptococcal species are a major cause of concern in the Food industry. In the swine industry, Streptococcus suis is not only a major pathogen that can cause several systemic issues in pigs, but also an emergent zoonotic agent that can infect workers and consumers alike. However, not all S. suis strains are pathogenic and strain 90-1330, an avirulent Canadian serotype 2/sequence type 28 isolate, was previously found to produce a lantibiotic bacteriocin that kills several pathogenic Streptococcus species. This finding led to the suggestion that S. suis 90-1330 could be used as a probiotic in the swine industry for prophylactic purposes.As part of my thesis (Chapter 2), I sequenced the complete genome of S. suis 90-1330 and used comparative genomic approaches to predict if this strain is indeed avirulent and suitable for probiotic purposes. Results from our comparative analyses suggested that this strain may not be as harmless as initially thought, as its genome was found to code for several virulence factors including a hemolysin that lyses blood cells. The bacteriocin it produces and the products that confer resistance to its effect were found encoded in a functional, mobile integrative and conjugative element (ICE), suggesting that use of this strain as probiotic without further engineering would facilitate the spread of resistance to this bacteriocin. Furthermore, the bacteriocin was found widely distributed across several streptococcal species, indicating that the use of this strain as a probiotic might provide fewer health benefits than originally thought.In Chapter 3, I used the approaches and tools we developed as part of our work on S. suis strains to investigate the genetic diversity pertaining to Streptococcus parasuis and Streptococcus ruminantium. These two streptococcal species were recently removed taxonomically from S. suis based on phenotype assays and on limited genotype data, and the extent of their intra- and interspecific diversity as well as their potential for virulence were unknown. The two novel species were found to be genetically distinct from S. suis in our comparative analyses, as expected from previous studies, but the genetic differences responsible for their phenotypic differences could not be ascertained in large part due to the presence of many unique proteins of unknown functions, highlighting a need for improved methods to infer functions computationally.In Chapter 4, I describe the computer pipeline that we built to facilitate and automate genetic diversity analyses between bacterial species, and which was used extensively for Chapters 2 and 3. Notably, to palliate for data missing from sequencing archives, we implemented a simple solution that generates in silico sequencing datasets from complete and/or draft genomes. I tested and validated our pipeline extensively and describe in this chapter its pros and cons and current limitations.
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Evolution and adaptations to host plants in the beetle genus Diabrotica
Title
Evolution and adaptations to host plants in the beetle genus Diabrotica
Creator
Lata, Dimpal
Date
2022
Description
Corn rootworms (Diabrotica spp.) are among the most destructive pests impacting agriculture in the U.S and are an emerging model for insect...
Show moreCorn rootworms (Diabrotica spp.) are among the most destructive pests impacting agriculture in the U.S and are an emerging model for insect-plant interactions. We have a limited understanding of the genome-scale level difference between specialist and generalist corn rootworm species and their interaction with their host plants. Genome sizesof several species in the genus Diabrotica and an outgroup were estimated using flow cytometry. Results indicated that there has been a recent expansion in genome size in the common ancestor of the virgifera group leading to Diabrotica barberi, Diabrotica virgifera virgifera, and Diabrotica virgifera zeae. Comparative genomic studies between the fucata and virgifera groups of Diabrotica revealed that repeat elements, mostly miniature inverted-transposable elements (MITEs) and gypsy-like long terminal repeat (LTR) retroelements, contributed to genome size expansion. The initial transcriptional profile in western corn rootworm neonates when fed on different potential host plants demonstrated a strong association between western corn rootworm and maize, which was very distinct from other possible hosts and non-host plants. The results also showed presence of several larval development related transcripts unique to host plants and the presence of several muscle development and stress response related transcripts unique to non-host plants. The effect of the maize defensive metabolite DIMBOA on corn rootworms was studied using a novel plant-free system. The survival of both southern and western corn rootworms was not affected at a low concentration of DIMBOA. However, the concentration above the physiological dose found in plants affected the survival of corn rootworms. DIMBOA had no plant independent effect on these corn rootworms weight gain.
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