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

Abstract

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. 𝘱𝘦𝘤𝘵𝘪𝘯𝘪𝘭𝘺𝘵𝘪𝘤𝘶𝘴and 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.