Prokaryotic systematics has changed astonishingly during recent several decades, from phylogeny relied on morphology and chemotaxonomy to genome-driven phylogeny. This research provided several cases of species identification and delineation where genome-based phylogenetics can be applied. Chapter 2 claimed that biochemical trait-based taxonomy is not trustable whereas genome-based taxonomy is more robust. In this chapter, it is showed that chemotaxonomic characteristics are altered by the loss of a single gene or single operon. Therefore the existence of certain phenotypic trait cannot be a phylogenetic marker by itself.
Instead, genome-wide phylogenetic analysis using universal core genes enables consistent and more reasonable result. Although the gene set of core genes changed, it rarely affects the phylogenetic reconstruction result. In chapter 3 and 4, the genomic data solely charged in changing the misidentified taxonomy.
Chapter 3 proven the ANI value between genomes was charged as an identifier to define the novelty of the isolated strain, and proposed them as the novel species. This chapter also conclude that the newly identified genera in Burkholderia sensu lato are monophyletic confirmed by the phylogenomic analysis.
However, the fixation of nomenclature was not done for the species whose genome is not sequenced yet.
Chapter 4 showed that the B. cereus and B. thuringiensis are tentatively not separated species, proven by phylogenomic analysis and genomic screening.
Distinguishing B. cereus and B. thuringiensis is impossible by biochemical kit such as API. Therefore the productivity of Bt toxin is a marker for identifying B.
thuringiensis from B. cereus. However, this study showed that the food poisoning toxin is ubiquitous among B. cereus and B. thuringiensis and Bt toxin-containing
ANI values between the member strains exceed species delineation cutoff (95~96%) and gene content dissimilarity is lower than species delineation cutoff (0.2).
All themes in this study identify the novelty of species based on genomic relatedness data, by newly defining and redefining the border between them. The achieved results for those researches are meaningful for abolishing the confusion of identification and proposing genome-based taxonomy instead of phenotype-based taxonomy. Also, the newly identified boundary of B. cereus in this study (Chapter 4) can be applied to fast and accurate identification from food poisoning outbreak.
Also, this study revealed the containing Bt toxin gene in B. cereus strains and can be implemented into specific treatment from the plant pest.
Not only the case of B. cereus and B. thuringiensis shown in this study, re- clustering and demarcating microbial species utilized in this study can be applicable in the diagnosis of the pathogens and forensic investigation. The correct identification of the isolated strains is crucial in fast and exact diagnosis of certain disease.
Also, the boundary of species and strain can be issued in the field of patent.
The boundary of patents is regarded as the most important issue in the field of intellectual property rights. Nevertheless, it is true that the range of patent microbial strain is somewhat vaguely defined, based on its phenotype. The accumulated researches of bacterial species delineation including this study could also be taken to delimit the intellectual property rights of the patent strains of microorganisms.
The concept of microbial species and the criteria for separating species have continuously altered. In fact, these changes can occur because the species itself is a
unit of artificial cluster for the research and practical convenience. Since the evolutionary history of the genomes of microorganisms does not change, and the trace of history remains in the genome. Therefore, classification based on the core gene at the genomic level is consistent systematics.
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