Environmental Microbiology and Microbial Ecology Commons^™

Investigating Soil Microbiome Changes During Panax Quinquefolius Cultivation In New Gardens, Pok Man Paul Wan

Electronic Thesis and Dissertation Repository

Ginseng (Panax quinquefolius) is susceptible to ginseng replant disease (GRD), resulting in root rot and decreased yield when ginseng is grown in soils previously used for ginseng crops. Although fungal and oomycete pathogens are implicated, GRD is a complex disease and the changes in the soil when initially cultivating ginseng that lead to GRD remain unclear. This thesis reported changes in the soil microbiome from three new gardens in Norfolk County, Ontario over three years starting from seeding with ginseng. Over this period of cultivation, metabarcoding of the V4 region of the 16S ribosomal RNA gene clearly showed …

Towards More Complete Metagenomic Analyses Through Circularized Genomes And Conjugative Elements, Benjamin R. Joris

Electronic Thesis and Dissertation Repository

Advancements in sequencing technologies have revolutionized biological sciences and led to the emergence of a number of fields of research. One such field of research is metagenomics, which is the study of the genomic content of complex communities of bacteria. The goal of this thesis was to contribute computational methodology that can maximize the data generated in these studies and to apply these protocols human and environmental metagenomic samples.

Standard metagenomic analyses include a step for binning of assembled contigs, which has previously been shown to exclude mobile genetic elements, and I demonstrated that this phenomenon extends to all conjugative …

Characterizing The Diversity Of The Eukaryotic Microbiome In Marine Crustacean Zooplankton., Rose-Lynne Savage

Electronic Thesis and Dissertation Repository

Understanding zooplankton productivity is critical for modeling marine food web function, of which one poorly known factor is the influence of zooplankton symbionts. Zooplankton protist symbiont diversity is underestimated due to the limited surveys and techniques previously used. Using 18S V4 metabarcoding, I characterized the eukaryotic microbiomes associated with crustacean zooplankton from the northern Strait of Georgia, BC. Apostome ciliates were most abundant in all hosts except for cyclopoid copepods, which were dominated by Syndiniales. Most symbiont lineages were more abundant in one or two hosts, suggesting some degree of host preference. Microbiome data also provided information on diet, confirming …

Clinical And Mechanistic Insights Into Novel Probiotic Functions And Formulations, Jordan Bisanz

Electronic Thesis and Dissertation Repository

Using a combination of hypothesis and discovery based approaches, the goal of this thesis was to better describe novel probiotic functions and their mechanisms while striving to better understand the effect of formulation on Bifidobacterium animalis subsp. lactis, Lactobacillus paracasei and L. rhamnosus.

Using RNA-Seq, a bacterial metatranscriptome analysis of a commonly consumed probiotic yogurt showed that the organisms adapted to storage time and flavor additions. This led to the discovery that in addition to the probiotic health benefits, members of the L. casei group (L. rhamnosus and L. paracasei) produce volatile sulfur compounds mediated by a novel …