Theses and Dissertations at Montana State University (MSU)
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Item Temporal dynamics of Escherichia coli and the microbiome(Montana State University - Bozeman, College of Letters & Science, 2020) Martinson, Jonathan Nathan Vernon; Chairperson, Graduate Committee: Seth Walk; Seth T. Walk was a co-author of the article, 'Escherichia coli residency in the gut of healthy human adults' submitted to the journal 'EcoSal plus' which is contained within this dissertation.; Nicholas V. Pinkham, Garrett W. Peters, Hanybul Cho, Jeremy Heng, Mychiel Rauch, Susan C. Broadaway and Seth T. Walk were co-authors of the article, 'Rethinking gut microbiome residency and the enterobacteriaceae in healthy human adults' in the journal 'The ISME journal' which is contained within this dissertation.; Nicholas V. Pinkham and Seth T. Walk were co-authors of the article, 'Phenotypic predictors of Escherichia coli residency in the gut of healthy human adults' submitted to the journal 'Applied and environmental microbiology' which is contained within this dissertation.Over the past two decades, our understanding of the gut microbiome has increased dramatically. However, most studies involving healthy adults have relied almost exclusively on cross-sectional design, negating the changes occurring within an individual's microbiome through time. With this, we performed a small longitudinal study over a period of ~2 years with a cohort of 8 healthy adults. By sequencing the DNA encoding the 16S ribosomal RNA gene, we assessed the community level change in this cohort through time. Similar to previous findings, we found that using these methods there was remarkable stability through time with nearly 50% of the microbiome remaining the same throughout the study period in the participants. However, analysis of 16S ribosomal RNA sequences limits taxonomic resolution. By cultivating members of the Enterobacteriaceae, we found that turnover at the clone-level (below the species level) was common. Within the Enterobacteriaceae, Escherichia coli was the most numerically dominant species and most often observed as a long-term member of the gut (i.e. resident). Longitudinal analysis of Escherichia coli revealed that some phylogenetic groups within the species are more often long-term residents than other phylogroups. We next assessed the means by which the resident E. coli were capable of establishing and maintaining themselves in the gut. We found that residents were much more likely to produce antagonism (inhibition of other clones) than the E. coli that did not reside in the gut long-term.Item Examining the potential role of biogenic amines in vaginal microbial ecology and gynecological health(Montana State University - Bozeman, College of Letters & Science, 2019) Borgogna, Joanna-Lynn Claire; Chairperson, Graduate Committee: Carl Yeoman; Carl J. Yeoman was a co-author of the article, 'The application of molecular methods towards an understanding of the role of the vaginal microbiome in health and disease' in the journal 'The human microbiome' which is contained within this thesis.; Michelle D. Shardell, Elisa K. Santori, Tiffanie M. Nelson, Jessica M. Rath, Elbert D. Glover, Jacques Ravel, Patti E. Gravitt, Carl J. Yeoman and Rebecca M. Brotman were co-authors of the article, 'The vaginal metabolome and microbiota of cervical HPV-positive and HPV-negative women: a cross-sectional analysis' in the journal 'British journal of obstetrics and gynecology' which is contained within this thesis.; Michelle D. Shardell, Carl J. Yeoman, Khalil G. Ghanem, Herlin Kadriu, Alexander V. Ulanov, Charlotte A. Gaydos, Justin Hardick, Courtney K. Robinson, Patrik M. Bavoil, Jacques Ravel, Rebecca M. Brotman and Susan Tuddenham were co-authors of the article, 'The association of Chlamydia trachomatis and Mycoplasma genitalium infection with the vaginal metabolome' submitted to the journal 'Scientific reports' which is contained within this thesis.; Savannah Gray, Elisa K. Santori, Ben Americus, Zhong Li, Alexander Ulanov, Jacques Ravel, Rebecca M. Brotman and Carl J. Yeoman were co-authors of the article, 'Biogenic amines affect the growth and lactic acid productin of vaginal Lactobacillus SPP.' which is contained within this thesis.Bacterial vaginosis is the most common vaginal disorder amongst reproductive-aged women affecting nearly 1/3 of all US women. Bacterial vaginosis is associated with an increased risk of adverse sexual and reproductive health outcomes including an increased sexually transmitted infection acquisition risk. Characteristic features of bacterial vaginosis include an increase in vaginal pH (>4.5) that is associated with a depletion of vaginal Lactobacillus spp., and replacement by various strict and facultative anaerobes. The depletion of Lactobacillus spp. is an important feature as the production of lactic acid by vaginal Lactobacillus species is considered the major barrier to infection. Women with bacterial vaginosis have reduced lactic acid and higher concentrations of biogenic amines. Biogenic amines may be important biomolecules bridging important microbiological and clinical characteristics that connect shifts in the vaginal microbiome to common features of bacterial vaginosis. Herein, we utilized 16S rRNA gene amplicon sequencing combined with metabolomics to evaluate the association between biogenic amines and the most prevalent bacterial (Chlamydia trachomatis) and viral (Human papillomavirus) sexually transmitted infection. We further assessed the effect of biogenic amines upon specific growth properties of vaginal lactobacilli. We observed that women who were HPV positive or had Chlamydia trachomatis mono- or Chlamydia trachomatis /Mycoplasma genitalium co-infection had higher concentrations of biogenic amines when compared to women who were uninfected. Growth assays demonstrated that biogenic amines adversely affected the growth of the major vaginal lactobacilli. Putrescine was associated with increased doubling times and longer lag times for all tested species, while cadaverine increased the doubling times of all except L. iners, Exposure to biogenic amines was generally associated with reduced production of lactic acid, Collectively, these data provide valuable evidence that biogenic amines negatively affect the growth of vaginal Lactobacillus species, in vitro, and are associated not only with bacterial vaginosis but also with HPV and C. trachomatis mono- and co-infection. Taken together, these data provide a more refined understanding of the potential impact of biogenic amines upon the vaginal microenvironment and increased susceptibility to bacterial vaginosis, vaginal dysbiosis, and bacterial and viral STIs.Item The microbial community ecology of various systems for the cultivation of algal biodiesel(Montana State University - Bozeman, College of Letters & Science, 2017) Bell, Tisza Ann Szeremy; Chairperson, Graduate Committee: Matthew Fields; Bharath Prithiviraj, Brad D. Wahlen, Matthew W. Fields and Brent M. Peyton were co-authors of the article, 'A lipid-accumulating alga maintains growth in outdoor, alkaliphilic raceway pond with mixed microbial communities' submitted to the journal 'Frontiers in microbiology' which is contained within this thesis.; Emel Sen-Kilic, Tamas Felfoldi, Gabor Vasas, Matthew W. Fields and Brent M. Peyton were co-authors of the article, 'Bacteria and eukarya community during eutrophication and toxic cyanobacterial blooms in the alkaline Lake Velence, Hungary' which is contained within this thesis.; Lakotah Doig, Brent M. Peyton, Robin Gerlach and Matthew W. Fields were co-authors of the article, 'Characterizing the microbial community and its intrinsic ability to produce algal biodiesel in wastewater treatment lagoons' which is contained within this thesis.Algal based biofuel has the potential to aid in offsetting future fossil fuel consumption and demand, and lowering CO 2 emissions. Cultivation strategies are a pivotal component of achieving high biomass yield. Open outdoor pond systems are currently the most economically viable method for large-scale algae cultivation due to less energy for maintenance than closed systems. However, open pond cultivation is subject to microbial colonization, sometimes negatively impacting the algal crop. Thus, large-scale production is hindered by gaps in our fundamental understanding of microbial interactions and ecology. The following research aims to explore the interplay between cultivation methods, nutrient availability, community composition, lipid metabolism, and system ecology and identify cost effective concepts for algal lipid production. Using alkalinity to limit microbial colonization of an open system is investigated in Chapter 2 in which a monoculture of Chlorella vulgaris was successfully cultivated. A putative relationship with a Pseudomonas sp. was identified in which the exchange of key metabolites could have enhanced algal growth and limited contamination. Such interactions may minimize the need for pesticides and fertilizer subsequently reducing pollution and operating costs. Findings suggested that potentially beneficial algal-bacterial relationships occurring in alkaline conditions supported a productive and stable monoculture. Alkalinity, in addition to nutrient abundance, is further explored in a natural freshwater terminal lake system, presented in Chapter 3. Lake eutrophication coupled with temperature increases led to a toxic cyanobacterial bloom that reduced overall eukaryotic diversity. Insight gained on the interplay between alkalinity, nutrients, and community dynamics from this natural system was then applied to a series of artificial wastewater lagoons Chapter 4. Elevated lipid (g/L) was observed in this system partially facilitated by increased water residence time in the lagoons and elevated nitrogen availability. Differing alga community composition were observed during periods of elevated lipid in addition to higher biomass (cells/mL) suggesting that higher lipid volumes were the result of high biomass concentration and not necessarily the lipid productivity of specific alga taxa. The research presented utilizes traditional ecologic concepts like diversity and contributes to a more comprehensive understanding of community interactions helping to minimize cost, reduce pollution, and ultimately contribute to the realization of viable biodiesel.Item The distribution of cultivated and uncultivated cyanobacteria and green non-sulfur bacteria in hot spring microbial mats(Montana State University - Bozeman, College of Agriculture, 1993) Ruff-Roberts, Alyson L.Item A study of the sulphur bacteria of the hot springs of Yellowstone National Park(Montana State University - Bozeman, College of Agriculture, 1948) Howard, Raymond H.Item Selective cloning of 16S rRNA molecules to describe naturally occurring microorganisms(Montana State University - Bozeman, College of Agriculture, 1990) Weller, RolandItem Investigation of microbial population biology during the degradation of organic contaminant mixtures(Montana State University - Bozeman, College of Agriculture, 2001) Kern, Eric AnthonyItem Dipicolinic acid content and heat resistance of spores of Bacillus stearothermophilus and thermophilic bacteria from Yellowstone National Park(Montana State University - Bozeman, College of Agriculture, 1963) Brierley, James AlanItem The microbial dynamics of an epilithic algal-bacterial mat community in an oligotrophic, high alpine stream(Montana State University - Bozeman, College of Agriculture, 1981) Haack, Thomas KennethItem Microbial ecology of nitrifying simulated premises plumbing(Montana State University - Bozeman, College of Letters & Science, 2012) Encarnacion, Gem Deangkinay; Chairperson, Graduate Committee: Anne Camper; Mark D. Burr and Anne K. Camper were co-authors of the article, 'Bacterial communities in nitrifying simulated premises plumbing' in the journal 'Water research' which is contained within this thesis.; Anne K. Camper was a co-author of the article, 'Detection and enrichment of a nitrifying community containing a novel archaeon from simulated premises plumbing' in the journal 'PLoS One' which is contained within this thesis.Because of the Stage 2 Disinfectants and Disinfection Rule limiting then concentration of disinfection by products in drinking water, the use of chloramine as an alternative to chlorine has been increasing. However, the ammonia introduced by chloramination can lead to nitrification which results in the production of nitrite and nitrate, leading to regulatory violations. Nitrification in reactors with copper and polyvinyl chloride (PVC) surfaces was established by indigenous organisms from Bozeman tap water and has been stably maintained for more than 6 years. Statistical analyses of polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) profiles determined that the active bacterial populations were different in the two systems. The assemblage of the organisms was also different from the starting population (BAC influent) suggesting both material and ammonia/carbon source affect the population. No known ammonia oxidizing bacteria were detected suggesting the role of different group for ammonia oxidation. Fluorescence in situ hybridization (FISH) detected archaea in the biofilm from both reactors. Archaeal 16S rRNA gene sequences were found to be phylogenetically affiliated with known archaeal ammonia oxidizers. Two archaeal amoA sequences were amplified from the system as determined by DGGE. We propose to provisionally classify a detected archaeon as Candidatus Nitrosotenuis bozemanii, based on its affinity to Nitrosotenuis uzonensis (Hatzenpichler et al., in preparation). Bacterial abundances were comparable in the two systems but archaeal abundances were higher in the PVC reactor suggesting material effect on the overall microbial population composition and density. Enrichment in modified synthetic Crenarchaeota medium yielded a culture of archaea and bacteria that consistently oxidizes ammonia to nitrate. Attempts to isolate the archaeal component using antibiotics failed, suggesting the disruption of a possible beneficial relationship between the archaea and bacteria. Genes involved in the transformation of nitrogen within the system were also investigated and hao distantly related to that of ammonia oxidizing bacteria was detected but its potential role remains unknown. This study provides evidence of archaea associated with biofilms in drinking water and while further analysis is needed to definitively elucidate their role, results of this study prompts the reevaluation of the current concept of nitrification in drinking water.