Browsing by Author "Kim, Caroline Chae-hyun"

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    Identification of rumen methanogens, characterization of substrate requirements and measurement of hydrogen thresholds : a thesis presented in partial fulfilment of the requirements for the degree of Master 's in Microbiology
    (Massey University, 2012) Kim, Caroline Chae-hyun
    In New Zealand, exported farmed commodities derived from ruminants make up about one-third of the nation’s economy. However, farming ruminants creates a significant environmental impact by emitting methane which is a by-product of the microbial fermentation occurring in the rumen. Accumulated methane in the atmosphere is considered to be an important contributing factor to global warming and climate change. Methanogenic archaea, collectively called methanogens, inhabiting the rumen are responsible for the production of ruminal methane. These organisms are capable of anaerobically reducing CO2 to CH4, using H2, formate, methanol, a range of methyl-compounds, or acetate as electron-donors. Currently, all known methanogens that have been isolated from a diverse range of habitats are classified into 28 genera and 113 species based on the study of pure cultures and analysis of small subunit rRNA gene sequence data. Less than 10% of these species were isolated from the rumen and these reflect only a small portion of the true rumen methanogen diversity that has been determined by cultivation-independent methods. This project has been derived from the necessity to characterise genome sequences of a greater diversity of rumen methanogens than is currently covered in public culture collections. 14 methanogen strains were isolated as pure cultures and identified based on 16S rRNA and mcrA gene sequences in order to create a comprehensive phylogenetic tree comparing the genetic distances between the newly identified strains and the few named species. Strains 229/11, AbM4, M1, SM9, G16, D5, BRM9, YCM1, ISO3-F5, and A4 were then selected to be characterised for their substrate requirements for growth, by systematically omitting single or multiple components from the growth medium. Finally, the threshold levels of hydrogen, below which the methanogens fail to use it as a substrate, were measured for these strains by gas chromatography. Overall, the H2 thresholds of rumen methanogens fell within the range between 0.5 and 5.8 Pa. Methanobrevibacter, the most predominant group of methanogens occurring in the rumen, had relatively higher H2 thresholds compared to the genus Methanosphaera, a group of methanogens frequently isolated from New Zealand ruminants, and the genus Methanobacterium.
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    Pectin degradation and metabolism in Monoglobus pectinilyticus 14T from human faeces : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Microbiology at Massey University, Manawatu, New Zealand
    (Massey University, 2017) Kim, Caroline Chae-hyun
    Pectin is a conspicuous plant polysaccharide, comprising one third of the dry weight of dietary fibre in common vegetables and fruit. Although pectin is almost completely digested by the human gut microbiota, few bacterial species are known to possess a comprehensive glycobiome to challenge the structurally complex pectin. The current understanding of the colonic degradation of pectin is incomplete, as the knowledge has almost exclusively derived from studying the sequestration system of Bacteroides spp. Here I report the isolation and characterization of Monoglobus pectinilyticus, and the sequencing of its genome which so far encodes the most pectin-specialized repertoire of carbohydrate active enzymes (CAZymes) found from the human gut. M. pectinilyticus also possesses an extracellular pectin degradation system consisting of novel protein constituents which did not find significant sequence homology and functional matches using the most up-to-date nucleotide and protein sequence databases. Proteome analysis of M. pectinilyticus using iTRAQ quantification revealed that pectin-degrading CAZymes and the potential constituents of the novel pectin degradation system were differentially up-regulated in response to the availability of pectin. Finally, using quantitative PCR, a positive correlation was observed between the prevalence of M. pectinilyticus and the consumption of fibre, vegetables, and pectin in individuals living in NZ. The discovery of M. pectinilyticus may add a new layer of complexity onto our interpretation of the colonic pectin degradation by presenting a system highly relevant to the pectin-rich diet of humans, and by suggesting a possibility outside the established paradigms of microbial polysaccharide degradation. The presence of M. pectinilyticus and the related uncultured bacteria in the gastrointestinal systems of humans and animals indicated that the organisms of this lineage are frequent terrestrial gut commensals, prompting an investigation into the genomic and molecular properties underlying their carbohydrate degradation potentials.