Mountain Scholar :: Browsing by Author "Weir, Tiffany, committee member"

Browsing by Author "Weir, Tiffany, committee member"

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Open Access
Comparison of five oral cannabidiol preparations in adult humans: pharmacokinetics, body composition, and heart rate variability
(Colorado State University. Libraries, 2021) Williams, Natasha N. Bondareva, author; Bell, Christopher, advisor; Weir, Tiffany, committee member; LaRocca, Tom, committee member
Data supporting the physiological effects of cannabidiol (CBD) ingestion in humans are conflicting. Differences between CBD preparations and bioavailability may contribute to these discrepancies. Further, an influence of body composition on CBD bioavailability is feasible, but currently undocumented. The aims of this study were to: (1) compare the pharmacokinetics of five oral CBD preparations over 4 hours; (2) examine the relationship between body composition and CBD pharmacokinetics; and, (3) explore the influence of CBD on heart rate variability. In total, five preparations of CBD, standardized to 30 mg, were administered orally to 15 healthy men and women (21–62 years) in a randomized, crossover design. Prior to and 60 min following CBD ingestion, heart rate variability was determined. Body composition was assessed using dual energy X-ray absorptiometry. Peak circulating CBD concentration, time to peak concentration, and area under the curve was superior in a preparation comprising 5% CBD concentration liquid. Fat free mass was a significant predictor (R2 = 0.365, p = 0.017) of time to peak concentration for this preparation. Several heart rate variability parameters, including peak frequency of the high frequency band, were favorably, but modestly modified following CBD ingestion. These data confirm an influence of CBD preparation and body composition on CBD bioavailability, and suggest that acute CBD ingestion may have a modest influence on autonomic regulation of heart rate.
Open Access
Cyanobacteria biofertilizer solubilizes soil phosphorus and alters soil microbial communities
(Colorado State University. Libraries, 2022) Afkairin, Antisar, author; Davis, Jessica G., advisor; Stromberger, Mary E., committee member; Storteboom, Heather, committee member; Weir, Tiffany, committee member
To view the abstract, please see the full text of the document.
Open Access
Development of a high-throughput phenotyping method for measuring sorghum carotenoids
(Colorado State University. Libraries, 2024) Zapata Carvajal, Nelson David, author; Rhodes, Davina, advisor; Prenni, Jessica, committee member; Weir, Tiffany, committee member
Vitamin A deficiency is the leading cause of preventable blindness in young children, and also leads to infertility and decreased immune function. Humans cannot synthesize vitamin A, so it must be consumed in the diet, either as preformed vitamin A or as provitamin carotenoid (PVACs) in plant foods. Access to PVACs is limited in sub-Saharan Africa where many diets are less diverse and primarily consist of cereals, such as sorghum, with intrinsically low concentrations of PVACs. Therefore, biofortification breeding efforts aim to increase PVACs to biologically relevant levels to reduce global vitamin A deficiency. In order to select and breed high carotenoid varieties, thousands of progeny in a breeding program must be phenotyped. High-performance liquid chromatography (HPLC) is the gold standard carotenoid phenotyping method; however, it is expensive and time-consuming, making it impractical for large-scale screening. We hypothesized that a high-throughput phenotyping (HTP) method using UV-VIS spectrophotometry can identify high carotenoid sorghum lines for selection during breeding. In this study, a simple and rapid method for carotenoid extraction and UV-VIS spectrophotometric detection in a 96-well plate format was developed and validated. To develop the HTP method, we measured 60 samples using both HPLC and UV-VIS, identifying a strong correlation (R2=0.62, p-value<4.51x10-14) between total carotenoid concentrations measured with the HTP method and the gold standard HPLC method. To validate the HTP method, we measured carotenoids in 249 lines in a biparental breeding family, using both HPLC and UV-VIS, and again identified a strong correlation (R2=0.61, p-value<2.2x10-16). We also compared the predictability of the UV-VIS method to that of a simple visual inspection of grain color and found that the UV-VIS method performed significantly better. This promising HTP method will enable rapid screening of a large number of samples, helping breeders more efficiently make selections for carotenoid biofortification.
Open Access
Development of advanced microbial communities for enhancing waste hydrolysis processes: insights from the application of molecular biology tools
(Colorado State University. Libraries, 2016) Wilson, Laura Paige, author; De Long, Susan K., advisor; Sharvelle, Sybil, committee member; Bareither, Christopher, committee member; Weir, Tiffany, committee member
Anaerobic digestion (AD) is an environmentally attractive technology for conversion of various solid wastes to energy. However, despite numerous benefits, AD applications to OFMSW remain limited in North America due to economic barriers with existing technologies. Suboptimal conditions in anaerobic digesters (e.g., presence of common inhibitors ammonia and salinity) limit waste hydrolysis in AD and lead to unstable performance and process failures compromising economic viability. To guide development of microbial management strategies to avoid process upsets and failures due to inhibitors, hydrolysis rates were determined in batch, single-stage digesters seeded with unacclimated or acclimated inocula under a range of ammonia and salinity concentrations for two model feedstocks (food waste and manure). Using unacclimated inocula, hydrolysis was found to be severely inhibited for elevated ammonia (decrease of nearly 4-fold relative to baseline) and salinity (decrease of up to 10-fold relative to baseline). However, for inocula acclimated over 2 to 4 months, statistically significant inhibition was not detectable except in the case of food waste subjected to elevated ammonia concentrations (p-value = 0.01). Inhibitors and feedstock were found to have a major influence on bacterial community structure. Next, a more detailed analysis of the acclimation process revealed that microbial communities under stressed conditions (elevated ammonia) adapt more slowly (weeks) to feedstock changes (from wastewater sludge to manure or filter paper) than under non-stressed conditions (days). Molecular tools were utilized to separate temporal effects on hydrolyzers from temporal effects on methanogens. Bacterial and archaeal sequencing results identified multiple organisms (e.g., Clostridiales vadinBB60, Ruminococcaceae, Marinilabiaceae, Methanobacterium, and Thermoplasmatales Incertae Sedis) that were selected for in microbial communities in stressed reactors under perturbed conditions (feedstock changes). Collectively, results from these studies suggested that weeks of acclimation are required to build up sufficient quantities of desired hydrolyzing microbes; thus, hydrolysis processes operated in batch mode should be inoculated with each new batch, and desired microorganisms should be maintained in the system via properly developed inoculation strategies. To identify improved methods of maintaining such communities in multi-stage reactor systems, reactor performance under elevated ammonia and salinity was compared for leach bed reactors (LBRs) seeded with unacclimated inoculum and different ratios of acclimated inoculum (0-60% by mass) at start-up. Additionally, the effect of seeding methods was examined by identifying the optimal ratio of fresh waste to previously digested waste in multi-stage systems incorporating leachate recycle during long-term operation. Results demonstrated that high quantities of inoculum (~60%) increase waste hydrolysis and are beneficial at start-up or when inhibitors are increasing. After start-up (~112 days) with high inoculum quantities, leachate recirculation leads to accumulation of inhibitor-tolerant hydrolyzing bacteria in leachate. During long-term operation, low inoculum quantities (~10%) effectively increase waste hydrolysis relative to without solids-derived inoculum. Additionally, molecular analyses indicated that combining digested solids with leachate-based inoculum doubles quantities of Bacteria contacting waste over a batch and supplies additional desirable phylotypes Bacteriodes and Clostridia. To provide detailed insight into microbial community activity during degradation, metatranscriptomic analyses were conducted on reactors fed food waste and manure under low ammonia, and several common active (e.g., Methanomicrobia, Methanosaeta concilii, and Clostridia) and unique active (e.g., Enterobacteriaceae, Clostridium thermocellum, and Clostridium celluloyticum) phylotypes between the reactors were identified. Functional classification of the active microbial communities generally revealed several similarities between the reactors despite the differences in feedstock. However, similarities or differences in transcript abundance for specific gene categories (e.g. one-carbon metabolism or fermentation) might indicate some potentially useful biomarkers for monitoring process health. Additionally, data from this experiment expanded the gene sequence database for assay development, which is particularly key for improving current functional gene-targeted assays to more accurately characterize microbial communities. Overall, results from this study have provided operational guidance for establishing and maintaining desired microbial communities as inocula to enhance waste hydrolysis for a variety of feedstocks.
Open Access
From BCG vaccination routes to lung and gut microbiota: avenues to tackle Mycobacterium tuberculosis infection
(Colorado State University. Libraries, 2021) Silva-Angulo, Fabiola, author; Henao-Tamayo, Marcela, advisor; Weir, Tiffany, committee member; Abdo, Zaid, committee member; Izzo, Angelo, committee member
Tuberculosis is an infectious lung disease responsible for approximately 1.4 million human deaths, world-wide every year. The causal agent of tuberculosis, Mycobacterium tuberculosis (M. tuberculosis), has been estimated to latently infect one-third of the human population. Currently, the BCG vaccine, a live attenuated strain of Mycobacterium bovis, is the only vaccine available to control the disease. Although the BCG vaccine has been the most widely administered worldwide and has been used for more than 100 years, tuberculosis dissemination remains uncontrolled and highly prevalent, especially in developing countries. Several questions about the effect that local microbiota and the administration route of BCG vaccination make on tuberculosis immunopathogenesis remain unanswered. These questions are critical for developing new approaches to control the disease. BCG vaccination is administered intradermally, however, some studies have suggested that BCG vaccination efficacy may be dependent on the administration route. Vaccination through the natural route of M. tuberculosis infection and a combination of other routes have been studied in animal models with varying results. Currently, the analysis of vaccination through the natural infection site is an attractive approach to priming innate immunity. The first study of this thesis examined the immune response induced after BCG vaccination using different routes (aerosol, subcutaneous, intravenous, and intranasal) in C57BL/6 mic and their response to pulmonary M. tuberculosis infection. The study was focused on specific markers of both CD4+ and CD8+ T cells. Our data suggested differences in the adaptive immune response based on the route of BCG vaccination and mainly elicited by CD4+ T cell immune response, with the intranasal delivery the most effective in decreasing the growth of M. tuberculosis in lungs. Another crucial question is the effect of M. tuberculosis infection and BCG vaccination on the structure, diversity, and potential function of the host lung and gut microbiota. Thus, the objective for the second study of this thesis was to characterize the effect of BCG vaccination and M. tuberculosis infection on the lung and gut micro- and mycobiota of C57BL/6 mice. Results indicated that BCG vaccination and M. tuberculosis infection in mice altered the relative lung abundance of Firmicutes and Bacteroidetes phyla compared to the control non-vaccinated, non-infected group. Lung diversity was most affected after M. tuberculosis infection. A multivariate regression approach was used to compare the profile evolution of gut and lung microbiota. More genera had modified relative abundances associated with BCG vaccination status at the gut level compared with lung. Conversely, genera with modified relative abundances associated with M. tuberculosis infection were numerous at lung level, and indicated that the local host response against infection impacted the whole microbial flora while the immune response after vaccination modified mainly the gut microbiota. This study demonstrated that parenteral vaccination with a live attenuated microorganism induced both lung and gut dysbiosis, which may play a crucial role in the immune response to M. tuberculosis infection.
Open Access
From computation to communication: unveiling Salmonella metabolic plasticity and public perceptions of the microbial world using multi-omics and thematic analysis
(Colorado State University. Libraries, 2024) Kokkinias, Katherine, author; Wrighton, Kelly C., advisor; Kelp, Nicole, committee member; Borlee, Brad, committee member; Weir, Tiffany, committee member
Research and communication on microorganisms and microbiomes has become increasingly important in recent decades due to evolving threats posed by infectious diseases and microbial contributions to ecological systems. Antibiotic resistance presents a significant challenge to global health equity, with nontyphoidal Salmonella infections being a prominent concern. Despite its prevalence and impact, Salmonella infections lack effective vaccines, posing a serious threat to vulnerable populations. Concurrently, misconceptions and misinformation about microorganisms and microbiomes can arise given the dynamic nature of scientific research which can hinder effective science communication and health outcomes. Despite this, little is known about public perceptions of microorganisms and microbiomes, impeding our ability to create effective, tailored science messaging. Both basic pathogen research and science communication research are essential to identify targeted prevention strategies and to understand public perceptions of microorganism and microbiomes. This dissertation spans microbiome and science communication research, employing both qualitative and quantitative methods. The overarching research goals of this dissertation are to 1) lay the groundwork for therapeutics by studying Salmonella metabolism and metabolic plasticity, 2) develop a multi-omics repository to expand the usability of our omics datasets, and 3) understand public perceptions of microorganisms and microbiomes to improve future microbial science communication efforts. Chapter 1 as the introductory chapter reviews the current state of Salmonella and science communication research, providing a context for the new research presented in this dissertation. Through a multi-omics approach, Chapter 2 explores the metabolic strategies of Salmonella under different diet backgrounds and over time, offering insights into potential therapeutic targets. Chapter 3 introduces the CBA_DREAMM database, facilitating centralized storage and sharing of multi-omics datasets to enhance communication of our research and collaboration in microbiome research. Chapter 4 investigates public perceptions of microbes and microbiomes in the United States, revealing a need for tailored science communication efforts. Additionally, the study emphasizes the importance of clear communication, trust, and emotions, like apathy, in science communication. Chapter 5 is the conclusion, summarizing findings from Chapter 2, 3, and 4 and describing future directions. By bridging natural and social sciences, this dissertation aims to inform strategies for tackling global issues by advancing microbiome and science communication research.
Open Access
Genetic diversity of ACC-deaminase positive bacteria in Colorado soil under winter wheat cultivars (Triticum aestivum L.)
(Colorado State University. Libraries, 2018) Elamari, Asma A., author; Stromberger, Mary E., advisor; Weir, Tiffany, committee member; Byrne, Patrick, committee member; Newman, Steven, committee member
ACC-deaminase positive bacteria (ACC+) promote plant growth and development by lowering abiotic stress ethylene levels through deamination of 1-aminocyclopropane-1-carboxylic acid (ACC), the immediate precursor of ethylene. During drought stress, ACC+ bacteria can help plants better tolerate drought stress in arid and semi-arid areas such as Colorado. The purpose of this study was to assess the capability of ACC+ bacteria to support winter wheat cultivar growth and production under drought stress conditions. In a field study, the relative abundance and genetic diversity of ACC+ bacteria associated with four winter wheat cultivars (Baca, Hatcher, Ripper, and RonL) were assessed under dryland, limited irrigation, and fully irrigated conditions in Colorado. The abundance of ACC deaminase positive bacteria was relatively high, with numbers ranging between 1.69 × 107 and 3.28 × 109 CFU's g-1 soil. At anthesis, the abundance and relative percent of ACC+ bacteria were greater under dryland and limited irrigation compared to full irrigation, and greater under RonL than other cultivars. The composition of rhizosphere ACC+ bacteria was distinct under RonL compared to Ripper. The majority of ACC+ bacteria enriched from these soils were Proteobacteria, specifically Pseudomonas spp. These results suggest that cultivar was a stronger driver of community composition of ACC+ bacteria than irrigation practice. The second study was conducted using a total of 55 bacterial isolates from the original experimental soils (RonL, Ripper, and Hatcher), which were selected to assay for Plant-Growth Promoting (PGP) traits: ACC-deaminase activity, Indole Acetic Acid (IAA) production, osmotic stress tolerance, phosphorus solubilization, and siderophore production. Most isolates were identified as species of Pseudomonas, but other species such as Arthrobacter, Variovorax, Agrobacterium, Rhizobium, Ochrobacterium, Micrococcus, Rahnella, and Bacillus were represented as well. Out of 55 isolates, 47 bacterial isolates tolerated osmotic stress when tested at an osmotic stress of -0.73 MPa water potential, 42 isolates demonstrated ACC-deaminase activity (potential ACC-deaminase activity ranged from 0.012 to 4.36 nmoles mg-1 protein h-1), 16 isolates were capable of solubilizing rock phosphate, one isolate produced IAA in the presence of 200 µg mL-1 tryptophan, and none of the isolates produced siderophores in vitro. Seven bacterial isolates that exhibit multiple PGPRs traits were selected for a root elongation assay using winter wheat seeds. The isolates selected were three Pseudomonas sp. isolated from RonL rhizospheres in fully irrigated plots (RLF6, RLF9, and RLF12); one Variovorax sp. isolated from Ripper rhizosphere in a dryland plot (RD12), one Pseudomonas sp. from Ripper rhizosphere of a fully irrigated plot (RF12), and two Pseudomonas sp. isolated from Hatcher rhizospheres (HD8 and HF1). The results showed that 6 days after seeds were inoculated, Ripper seedlings had the longest roots. In addition, isolates RLF6 and RF12, both Pseudomonas sp., were found to be the most effective in increasing root length as compared to sterile inoculum (control). The effect of inoculation on root length, however, was dependent on cultivar type. A subsequent field plot study was conducted to test the effectiveness of Pseudomonas sp. RLF9 to improve wheat growth and productivity under drought stress. Inoculum was prepared in the form of alginate bead and distributed in trenches next to winter wheat plants (at stem elongation growth phase), in replicated field plots under irrigated and non-irrigated treatments. Six weeks after inoculation, numbers of culturable Pseudomonas sp. were greater (P ≤ 0.05) in soil inoculated with RLF9 than sterile inoculant, except for the RonL/Ripper bioculture treatment. Overall, soil under RonL accumulated the highest ACC-deaminase positive bacterial populations (1.8×105 CFUs g-1 soil) compared to other cultivar treatments. Soil ACC deaminase activity was highly variable but tended to be greatest in soil planted to monocultures of RonL and Ripper, and bicultures of RonL and Ripper. There was no significant correlation between inoculant abundance in soil and soil ACC-deaminase activity, perhaps because of ACC deaminase activity of indigenous soil bacteria. The field season was marked with abundant rainfall during the spring, followed by outbreaks of pathogens, including stripe rust, that affected all field treatments and confounded late season drought and heat stress. As a result, there were no irrigation treatment effects or inoculation effects on wheat yield indices. The findings of this study are very attractive for further field studies, which would be helpful in extending isolate use as PGP inocula for wheat production, especially in Colorado and perhaps other semi-arid regions. Specifically, inoculation of winter wheat cultivars with PGPR's containing ACC-deaminase and other PGP traits could be an effective approach for successful crop production. Selection of PGPR inoculants and wheat cultivar combinations for obtaining optimum responses should be considered in future studies. The ability of potential inoculants to survive in the rhizosphere, compete with indigenous microbial communities, and colonize roots should also be studied. Based on laboratory studies of potential PGPR activities, Pseudomonas sp. RLF9 and possibly Pseudomonas sp. RLF6 could be good inocula selection to improve wheat growth and productivity under drought stress. Further research is needed to demonstrate the effectiveness of RLF6 and RLF9 as effective inoculants in the field.
Open Access
Internalizing symptoms, medication adherence, and perceived social support in individuals with inflammatory bowel disease
(Colorado State University. Libraries, 2017) Bascom, Elise, author; Borrayo, Evelinn, advisor; Rickard, Kathryn M., committee member; Weir, Tiffany, committee member
The present study examines perceived social support for individuals with inflammatory bowel disease (IBD). Patients were recruited for this study from online forums consisting of Facebook support groups, Twitter followers, and email. This study investigated sociodemographic and disease-related predictors of disease severity for individuals with IBD, as well as whether or not perceived social support moderates the relationship between disease severity, internalizing symptoms, quality of life, and medication adherence. A sample size of 155 individuals self-reporting with inflammatory bowel disease (ulcerative colitis or Crohn's disease) completed questionnaires related to disease severity, disease type, disease duration, quality of life, depression, anxiety, stress, perceived social support, and medication adherence. The study findings suggest that anxiety and stress are potential predictors of scores on disease severity for this population. Results also suggests that perceived social support is likely to have (or had in this sample) a significant, moderating relationship between disease severity and anxiety, disease severity and stress, and disease severity and the full depression, anxiety and stress scale (DASS). Anxiety was also found to moderate the relationship between disease severity and adjusted quality of life (QoL) scale. Perceived social support did not moderate the relationship between disease severity and the abbreviated medication adherence rating scale (MARS) generated by principle component analysis. It is important to note that future research should include a more randomized, representative sample, allowing for more conclusive findings. Understanding the psychological impact associated with this disease provides continued evidence for the need support individuals coping with IBD.
Open Access
Investigating the impact of the microbiome on beef steak color stability
(Colorado State University. Libraries, 2022) Smith, Colton Levi, author; Nair, Mahesh N., advisor; Morgan, J. Brad, committee member; Geornaras, Ifigenia, committee member; Weir, Tiffany, committee member; Metcalf, Jessica L., committee member; Clark, Daniel L., committee member
Meat color is the most influential characteristic for consumer purchasing decisions. In fact, consumer discrimination of discolored beef results in approximately $3.73 billion/year lost in revenue in the US. Interestingly, most often these products are not yet microbially spoiled, leading to unnecessary food waste. Complicating matters, different muscles originating from the same carcass discolor at different rates. Several studies have investigated the physiochemical, enzymatic, and intrinsic muscle properties of muscles with differing color stabilities such as color stabile beef longissimus lumborum (LL) and color labile psoas major (PM). However, the impact of microbial growth on the meat color stability has not been investigated yet. Therefore, the objective of this study was to characterize the microbial populations and their biochemical parameters of color labile and color stabile beef muscle cuts during aerobic retail display. Paired USDA Select LL and PM (n = 5) were collected from a local abattoir and aged for 14 days in darkness under vacuum at 3°C. After aging, the muscles were fabricated into 2.54-cm thick steaks and packaged aerobically in a foam tray wrapped with polyvinyl chloride film. Steaks were then placed into an open faced multi-decked retail display case for 7 days at 4°C ± 1°C. Each day, beginning day of fabrication, steaks were evaluated for visual color, percentage discoloration, instrumental color, water activity, pH, metmyoglobin reducing activity, microbial levels as determined by using culture-dependent methods (aerobic plate counts, lactic acid bacteria plate counts, Pseudomonas spp. plate counts and Enterobacteriaceae plate counts), and 16S rRNA bacterial gene sequencing (microbiome). Visual color was darker (P < 0.05) for PM than LL for all days, and percentage discoloration was greater (P < 0.05) for PM than LL from the second daif retail display. Color stability (determined by MRA) was greater (P > 0.05) in LL compared to PM for all days. The pH was greater (P < 0.05) for PM for the first 5 days of display compared to LL. However, water activity was the same (P > 0.05) for both muscles across all display days. Microbiological analyses revealed that aerobic plate counts, and lactic acid bacteria plate count were greater (P < 0.05) for PM starting on day 1 of display compared to LL. The Pseudomonas spp. plate counts were similar (P > 0.05) until day 2, after which PM was greater (P < 0.05) than LL and remained greater for the remaining days. Moreover, the 16S rRNA gene sequencing showed no differences (P > 0.05) in the alpha or beta diversities of the microbial communities between muscles. The results indicated that PM has less color stability and a greater amount of microbial growth than LL during retail display. Despite the increased number of bacteria on PM earlier during display, the microbiome analyses showed no major differences in the microbial communities between the muscles on the same display day. These data may suggest that microbial metabolic pathways, evidenced by faster microbial growth on PM compared to LL, may be a bigger contributor to color stability differences than the microbial community composition. Further work establishing these metabolic differences is needed to understand the biochemical interaction between the microbiota and the beef steaks.
Open Access
Investigation of dietary rice bran for protection against Salmonella enterica Typhimurium infection in mice
(Colorado State University. Libraries, 2014) Kumar, Ajay, author; Ryan, Elizabeth P., advisor; Dow, Steven, committee member; Leach, Jan, committee member; Schenkel, Alan, committee member; Weir, Tiffany, committee member
Rice bran is a byproduct of rice milling for white rice. Rice bran is a rich source of nutrients such as vitamins, minerals, soluble and insoluble fibers, fatty acids, polyphenols and proteins. Research has shown the beneficial health effects of rice bran in hyperlipidemia, diabetes, immune modulation, allergies and cancer. This dissertation focuses on evaluation of rice bran for protection against Salmonella using a mouse model of oral infection. Salmonella is a food and water borne pathogen that affects a variety of hosts including plants, animals and humans. Salmonella infections are a major public health challenge around the globe. Currently, salmonellosis is treated using high doses of synthetic antimicrobials and the problem of drug resistance has increased. In this scenario, alternative and sustainable interventions are needed to control Salmonella infections. Several dietary agents have been studied for protective effects in Salmonella infection models. We tested the prophylactic effects of dietary rice bran in a Salmonella model of infection using female 129S6/SvEvTac mouse model with infection of Salmonella enterica Typhimurium 14028s strain. Feeding of 10% dietary rice bran for one week prior to infection significantly (p<0.05) reduced fecal excretion of Salmonella in orally infected mice. Salmonella-infected, rice bran fed mice also showed a significant decrease in systemic inflammatory cytokines such as TNF-α, IFN-γ and IL-12 as compared to control diet fed animals. The colonization resistance against enteric pathogens is highly influenced by composition of gut microflora. Supplementation of dietary rice bran increased the number of Lactobacillus spp. in feces of mice as compared to mice that were fed control diet. Research has shown that oral administration of some species of Lactobacillus reduces the colonization of Salmonella. We hypothesized that rice bran components also enhance mucosal protection by preventing Salmonella entry into the epithelial cells. Methanolic rice bran extracts were assessed in mouse small intestinal epithelial (MSIE) cells for blocking Salmonella entry and intracellular replication. Rice bran extract significantly reduced Salmonella entry and intracellular replication into MSIE cells. These results suggest the potential mechanisms for dietary rice bran induced improvement of colonization resistance against Salmonella. Given that rice crops have a large variation in genotype and phenotype such as in yield, disease and pest resistance, drought resistance, and nutrient quality, we hypothesized that variation in rice bran across cultivars induces differential protection against Salmonella infection due to differences in their phytochemical profile. A panel of six varieties namely IAC 600, Jasmine 85, IL 121-1-1, Wells, Red Wells and SHU 121 were tested in the in vitro and in vivo model of Salmonella infection. We found that rice bran extracts across varieties inhibited Salmonella entry into the MSIE and Caco-2 cells to different extents. IAC 600 fed animals significantly (p<0.05) reduced Salmonella fecal excretion as compared to the control diet fed animals. IAC 600 fed animals also reduced Salmonella fecal shedding significantly (p<0.05) as compared to SHU 121 diet fed animals at 2 and 6 days post Salmonella infection. Histopathological analysis revealed that IAC 600 diet fed animals had better ileal pathological scores as compared to SHU 121 and the control diet fed animals post Salmonella infection. SHU 121 and the control diet fed groups showed higher ulceration and inflammatory changes in ileum as compared to IAC 600 fed animals. Next we analyzed the fatty acid profile, mineral profile and total phenolic contents of rice bran. Stearic acid, lignoceric acid, boron and total phenol content were significantly correlated with Salmonella fecal shedding in mice across varieties. However, further studies are required to confirm the role of these nutrients from rice bran in protection against Salmonella. These results suggest that the variety of rice plays an important role in bran-induced protection against Salmonella infection and this difference in protection across the varieties could be attributed to a combination of bioactive components. Our studies suggest that dietary rice bran improves colonization resistance against Salmonella in mice. Rice bran could have important role in prevention of enteric infections in resource scarce populations and further human clinical studies are required. Rice bran may also be evaluated for supplementing diets of food animals to prevent Salmonella infections and therefore could have a potential role in food safety.
Open Access
Mechanisms of vascular dysfunction in obesity and type 2 diabetes: role of the gut microbiota and endoplasmic reticulum stress
(Colorado State University. Libraries, 2018) Battson, Micah Lee, author; Gentile, Christopher, advisor; Cox-York, Kimberly, advisor; Weir, Tiffany, committee member; Pagliassotti, Michael, committee member; Chicco, Adam, committee member
Vascular dysfunction, characterized by arterial stiffness and endothelial dysfunction, is a key antecedent to overt cardiovascular disease in obesity and type 2 diabetes. Although the mechanisms underlying the development of vascular dysfunction in obese and type 2 diabetic individuals are not fully known, a growing body of evidence suggest that adverse cellular processes, including endoplasmic reticulum (ER) stress, inflammation and oxidative stress, are primarily responsible for the disruption of normal vascular function in these two metabolic diseases. Therefore, identifying effective strategies to mitigate one or more of these adverse processes may lead to novel therapies for the treatment of vascular dysfunction in obesity and/or type 2 diabetes. In addition, ascertaining the initial triggering factor(s) that promote these adverse processes will inform innovative ways to prevent or control the progression of vascular dysfunction. The goals of this dissertation research were to 1) examine the underlying causes of vascular dysfunction in obesity and type 2 diabetes and 2) identify potential strategies to mitigate vascular dysfunction in these metabolic diseases. To this end, we conducted three separate studies in murine models of obesity and/or type 2 diabetes aimed to modulate key factors that can affect vascular function. In all three studies, we measured aortic pulse wave velocity and endothelium-dependent dilation as clinically relevant indices of arterial stiffness and endothelial dysfunction, respectively. We also conducted various biochemical analyses to explore the potential mechanisms by which our experimental interventions altered vascular function. In our first study (Chapter 2), we examined the role of ER stress in diabetic vascular dysfunction. In type 2 diabetic (db/db) mice, we found that chronic administration of the ER stress inhibitor, tauroursodeoxycholic acid (TUDCA), significantly reduced arterial stiffness and endothelial dysfunction. These vascular improvements were associated with reduced expression of ER stress-related genes within the aorta and surrounding perivascular adipose tissue (PVAT). Next (Chapter 3), we examined the role of the gut microbiota in the development of vascular dysfunction in obesity. We found that Western diet (WD)-induced obesity increased arterial stiffness, impaired endothelial function, and promoted endotoxemia-related inflammation. Antibiotic treatment to suppress the gut microbiota in WD-fed mice reduced arterial stiffness, improved endothelial function, and attenuated systemic and vascular inflammation. In our final study (Chapter 4), we examined whether gut dysbiosis represents a causal factor in the development of obesity-related vascular dysfunction. We found that transplant of gut microbiota from obese (ob/ob) to control mice promoted the development of arterial stiffness, and this was associated with reduced abundance of a symbiotic bacterium, Akkermansia muciniphila, decreased short-chain fatty acid levels, and increased gut permeability. In contrast, transplant of control microbiota to obese mice did not attenuate arterial stiffness. Collectively, these studies in mice provided evidence that 1) mitigation of ER stress improves vascular function in type 2 diabetes, 2) gut dysbiosis contributes to vascular dysfunction in WD-induced obesity, and 3) an obese-type microbiota can promote arterial stiffening independent of body weight. Future clinical trials and mechanistic studies are needed to translate our findings to humans and to further examine the molecular mechanisms linking gut dysbiosis to vascular dysfunction.
Embargo
Molecular and sociocultural exploration of sourdough: impacts on gluten sensitivity and bread characteristics
(Colorado State University. Libraries, 2023) Clark, Caitlin, author; Van Buiten, Charlene, advisor; Stone, Martha, committee member; Weir, Tiffany, committee member; Gentile, Chris, committee member; Prenni, Jessica, committee member
Sourdough is a bread product fermented by communities of wild bacteria and fungi known as a starter culture. Previous work has examined the effects of specific starter organisms on bread quality, but the relationships between whole microbiomes and dough/bread physicochemical properties are currently unknown. The objective of this study was to investigate the relationship between physicochemical properties of sourdough breads and the microbiomes of their starter cultures. Twenty sourdough starters with characterized microbiomes were used to produce wheat-based dough and bread. The chemical properties (pH, titratable acidity, free amino acids, Aw) of dough and physical properties (loaf volume, crust color, texture) of the breads were compared to a control fermented with baker's yeast. The degradation and toxicity of gliadin resulting from fermentation with the sourdough samples was also studied in vitro. Results indicate that sourdough-fermented breads produced under real-world conditions are distinct from yeast-fermented bread in terms of physicochemical parameters and proteolysis, which may exert downstream effects on the inflammatory capacity of gluten. We also investigated the beliefs and behaviors of gluten-sensitive sourdough consumers and professional sourdough bakers. We found that commercial sourdough is not reported to relieve gluten-mediated symptoms for consumers diagnosed with celiac disease (CD) or non-celiac gluten sensitivity (NCGS), but undiagnosed (UD) gluten-sensitive consumers may benefit from it. We also determined that sourdough bakers act as brokers of health advice in the gluten-sensitive community.
Open Access
Multi-omics investigation of interactions between persistent bacteria and Salmonella in the inflamed gut
(Colorado State University. Libraries, 2023) Leleiwi, Ikaia, author; Wrighton, Kelly C., advisor; Prenni, Jessica, committee member; Szymanski, Erika, committee member; Weir, Tiffany, committee member
Salmonella is a globally relevant enteric pathogen responsible for numerous outbreaks and debilitating illness yearly. Expansive tropism allows Salmonella to find bastion in zoonotic reservoirs including prominent food animals. Continued prophylactic antibiotic use in livestock and therapeutic antibiotic use in humans has increased selection for multi-drug resistant Salmonella varieties. Most of the current research on Salmonella enteric disease is performed absent complete native gut microbiota. Further, common murine models that could facilitate study of Salmonella in a robust community setting lack model-specific microbiome resources to accomplish the feat. Presented in this dissertation is a comprehensive catalogue of CBA/J mouse gut microbial genomes created as a resource for the research community. The genome database was used to recruit various omics data types to expand the current knowledge of Salmonella infection in a complex community setting, identifying community members robust to inflammation and with potential to further explore as probiotics. In Chapter 1, I review the current state of Salmonella pathogenesis in the context of the gut microbiome. The focus here is to survey the literature for prominent Salmonella mechanisms of infection and how they relate to both host and commensal microbes. I explore host responses to Salmonella and microbial metabolites capable of affecting Salmonella pathogenesis. This microbiome-centric take on Salmonella infection implies a need for comprehensive methods to examine microbes and their processes in vivo, including queries of genes and gene products. A special emphasis on multi-omics approaches is mentioned in this section as powerful tools to holistically study the complete Salmonella-included gut microbiome and to address deficiencies in prior work, ultimately providing more translatable results impacting human health. Chapter 2 outlines the creation of the CBAJ-DB – a first of its kind bacteria and virus genome collection produced from the gut communities of Salmonella infected and uninfected CBA/J mice. Relevance of this work to Salmonella research is explained, emphasizing the CBA/J model advantages to study enteric infection in unperturbed gut communities. Robust genome recovery from deep sequencing yielded over 2,000 bacterial metagenome-assembled genomes including novel bacteria strains and taxa with implications for other mouse breeds and human microbiomes. Viral genomes reconstructed from metagenomic sequencing were linked to bacteria hosts and mined for genes germane to bacteria function. The complete functional potential of the CBA/J gut community in infected and uninfected mice was also explored, detailing a decrease in immune-modulatory functional potential following Salmonella infection, and implying a potentially important role of Alistipes sp. in butyrate production. Importantly, work from this chapter provides the infrastructure for genome-resolved multi-omics investigations detailed in Chapter 3 that are critical to determine functional links between Salmonella and the commensal microbiota. In Chapter 3 additional metagenomic sequencing is combined with the CBAJ-DB and used to recruit metatranscriptomic and metabolomic data from infected and uninfected CBA/J mice. We reveal expression and metabolites that implicate numerous commensal bacteria with the flow of sulfur in the inflamed intestine, making it available for host oxidation to tetrathionate in support of Salmonella anaerobic respiration. Current dogma surrounding Salmonella lactate utilization from the host is also confronted by our data, which implies potential cross feeding on microbially derived D-lactate by Salmonella during peak infection. These expression data are supported by random forest and logistic regression modeling which determined genes for D-lactate production or utilization are important to Salmonella-association of other bacteria in the inflamed gut. Relatively abundant bacteria observed in Chapter 2 were confirmed to be active in infected communities and to be expressing genes relevant to Salmonella processes like chitinase, lactate dehydrogenase, and sulfatase. Not only does this chapter illustrate the utility of the CBAJ-DB but it highlights how multi-omics investigation in complete ecosystems can unveil results that may be different than claims made based on in vitro or reduced community in vivo studies. The final chapter presented here summarizes the key findings from Chapters 2 and 3 and offers avenues for future research including specific strain isolation from infected communities and subsequent Salmonella competition experiments to determine probiotic therapeutic potential. This dissertation aims to (1) Examine the diversity of the CBA/J mouse gut and provide a genomic resource to the microbiome community, (2) using various omics techniques, discover interactions between Salmonella and commensal bacteria that could impact pathogenesis, and (3) identify members of the inflamed community with probiotic potential that are indifferent to Salmonella or that display niche overlap for substrate competition with Salmonella. Ultimately, this dissertation provides a comprehensive examination of Salmonella infection amidst a whole and robust microbiome identifying important membership in the inflamed community and linking autochthonous processes with pathogenic ones to better understand Salmonella enteric disease.
Open Access
Novel transcriptomic mechanisms of brain aging
(Colorado State University. Libraries, 2023) Cavalier, Alyssa Nicole, author; LaRocca, Thomas, advisor; Lark, Daniel, committee member; Hamilton, Karyn, committee member; Weir, Tiffany, committee member
As the world ages, the incidence of age-related diseases like dementia is expected to increase. Brain aging is characterized by declines in cognitive function that may develop into mild cognitive impairment, which increases the risk for dementia. In fact, age is the primary risk factor for late-onset Alzheimer's disease, which is the most common age-related dementia. The adverse cellular and molecular processes that underlie cognitive decline with aging in the brain are known collectively as the "hallmarks of brain aging." Advances in next-generation sequencing (e.g., transcriptomics/RNA-seq) have made it possible to investigate age- and disease-related changes in the brain at the broad gene expression level, and to identify potential therapeutic targets. With the support of my committee and mentoring team, I completed three studies using transcriptomics that characterize novel mechanisms that underlie brain aging. My findings include: (1) doxorubicin chemotherapy accelerates brain aging at the gene expression level, (2) apigenin nutraceutical supplementation targets age-related inflammation in the brain and rescues cognitive impairment in old mice, and (3) epigenetic dysregulation of transposable elements (remnants of viral infection in the genome) with aging contributes to age-related inflammation in Alzheimer's disease. Together, my work provides insight into transcripts and cellular/molecular pathways that are modifiable and may be therapeutic targets to delay or prevent consequences of brain aging.
Open Access
Pharmacokinetic investigation of commercially available edible marijuana products in humans: potential influence of body composition and influence on glucose control
(Colorado State University. Libraries, 2021) Ewell, Taylor, author; Bell, Christopher, advisor; Hickey, Matthew, committee member; Hamilton, Karyn, committee member; Weir, Tiffany, committee member
Our investigation of five commercially available edible marijuana products containing 10mg of delta-9-tetrahydrocannabinol (THC) aimed to describe the pharmacokinetics of these products, investigate the potential influence of body composition on THC bioavailability, and, based on epidemiological research completed in the last decade, determine if acute marijuana ingestion influences glucose tolerance when compared to a THC-free gummy. We studied seven regular marijuana users. We utilized a single-blind randomized controlled crossover study design in which participants self-administered edible marijuana or a THC-free gummy. Thirty minutes following marijuana ingestion a standard oral glucose tolerance test was initiated via consumption of a 75g glucose drink. There was, at minimum, a four-day washout period between trials. Average time to peak plasma THC concentration ranged from 35 to 90 minutes, and average peak THC concentrations ranged from 3.2 to 5.5 ng/ml. Significant differences between products were identified twenty- and thirty-minutes post-ingestion. Several measures of body composition had significant correlations with plasma THC, although none of these correlations persisted across all products. There were no differences in indices of glycemic control between marijuana products or the THC-free gummy. Following acute edible marijuana ingestion in habitual users, significant differences in THC pharmacokinetics existed between similar products, possibly due to body composition, although glucose control was not impacted. In summary, these data may inform recreational users to the proper dose for marijuana ingestion to achieve the desired outcome and to avoid overdose.
Open Access
Quality and nutritional aspects of conventional and novel food proteins
(Colorado State University. Libraries, 2020) Thompson, Tyler Warren, author; Nair, Mahesh Narayanan, advisor; Belk, Keith E., advisor; Geornaras, Ifigenia, committee member; Weir, Tiffany, committee member
Cattle weights have increased during the last couple of decades and have not always been accompanied by improvements in facility capabilities and management. Alongside quality issues of color, tenderness, and water holding capacity, issues such as sour muscles and bone taints are now appearing with high frequency in the meat industry. Development of off-flavor/sourness in deep muscles such as knuckles (vastus femoris, vastus lateralis, vastus medialis, and rectus femoris) has been a long-standing issue in the beef industry, however, has not been well characterized. Therefore, the objective of this study was to investigate the potential cause and to characterize the sour odor associated with beef knuckles using microbial, odor panel, and gas chromatography-mass spectrometric (GC-MS) analyses. Knuckles (n = 10) identified as having no sour odor (control), slight sour odor (SLI-SO), or severe sour odor (SVR-SO) were collected from the fabrication line of a commercial beef processing plant. Upon collection of knuckles, synovial fluid and the femur surface were swabbed to determine psychrotrophic anaerobic sporeformer presence. The collected knuckles were transported on ice to the laboratory where they were aseptically separated into two halves, with one half destined for microbial, odor, and GC-MS analyses on the day of collection (day 0) and the other half for the same analyses (excluding GC-MS) after 35 days of vacuum packaged storage at 0 - 2°C (day 35). For microbial analysis, 15 g of tissue was excised from the muscle surface and was analyzed for aerobic plate counts (Petrifilm Aerobic Count plates) and lactic acid bacteria counts (Lactobacilli MRS agar). Samples (5 g) for GC-MS were held at -80°C until analysis. The remainder of the sample was diced and used for trained odor panels. Odor panelists identified differences (P < 0.05) for all tested attributes (off odor, oxidation, putrid, and sour notes) between control and sour knuckles (SLI-SO and SVR-SO) on day 0. Similarly, on day 35, differences (P < 0.05) were observed between control, SLI-SO, and SVR-SO knuckles for all attributes, with SVR-SO samples receiving the highest score for all categories. However, the microbiological analysis found no differences between aerobic plate counts and lactic acid bacteria counts of control, SLI-SO, and SVR-SO knuckles on day 0 or day 35. In addition, GC-MS analysis did not indicate a difference (P > 0.05) in the abundance of volatiles between the treatments (probably due to high variations within treatment groups). Overall, compounds such as acetic, acetoin, propionic, butyric, and isobutyric acid were trending towards having greater abundance in sour samples. Although animal proteins have been the primary source of protein in the human diet, plant-based proteins have gained popularity in recent years. While some studies have indicated lesser environmental impacts, the nutritional composition of plant-proteins has not been readily investigated. Therefore, the objectives were to evaluate the nutritional composition of Morning Star Farms spicy black bean burger (VB), Beyond Meat's Beyond Burger (BB), Impossible Food's Impossible Burger (IB), a boneless top loin pork chop (PC), and 80% lean 20% fat ground pork (GP). Six different cities were selected for product collection to give a representative view of the products (Seattle, WA; Peyton, CO; Memphis, TN; Newburgh, IN; Houston, TX; and Brooklyn, NY). Following collection, products were brought back to Colorado State University. Half of the products sampled from each city were cooked, and the remaining half were left in their raw state. All ground products were cooked to an internal temperature of 71°C while the PC was cooked to 63°C. Samples (both raw and cooked) were then homogenized individually and stored under vacuum-packaged conditions at -80°C until further analysis. Methodologies for proximate analysis, amino acids, fatty acids, minerals, vitamins, organic acids, and allergens were conducted following the Association of Official Analytical Chemist (AOAC) guidelines. Overall, the product state (raw or cooked) had little effect on the nutritional composition. Analysis indicated that the PC contained the highest (P < 0.05) amounts of protein, essential amino acids, and B-vitamins. Cholesterol was found highest (P < 0.05) in the pork products (PC and GP) with no cholesterol being identified in the plant-based products (VB, BB, and IB). However, when evaluating mineral make-up, the plant-based products contained the highest (P < 0.05) amounts, especially in sodium and iron levels. Sodium levels were about ten times higher, along with iron levels being 3 to 4 times higher in plant-based products. Overall, the pork products were found to contain the greatest amounts of amino acids, and B-vitamins needed in a diet. While the plant-based products were generally lower in nutrients, the IB was found at nutritional levels close to the GP and PC.
Open Access
Rice bran supplementation modulates environmental enteric dysfunction markers and serum metabolites in weaning Nicaraguan infants
(Colorado State University. Libraries, 2018) Zambrana Gutiérrez, Luis Enrique, author; Ryan, Elizabeth, advisor; Legare, Marie, committee member; Weir, Tiffany, committee member
Rice bran (RB) is an agricultural byproduct from whole grain rice processing. It is an accessible, underutilized food ingredient that merits global health research attention to improve nutritional security, reduce childhood malnutrition, and mitigate environmental enteric dysfunction (EED). The objective was to analyze the effects of dietary RB supplementation on growth, EED biomarkers, and serum metabolites in healthy, weaning infants from six-to-twelve months old residing in León, Nicaragua. Effects of dietary RB supplementation on growth and EED biomarkers were examined after a six-month feeding period. Five-month-old infants (n=71) were screened for eligibility and 62 infants were randomized, for a prospective clinical trial (NCT02615886). The randomization was done within the health sector where each child belongs and by sex to either be allocated to RB dietary group or control group without RB consumption. Weight and length measurements and stool samples were collected at 6 (baseline), 8 and 12 months of age. Blood was collected at 12 months only. Stool and serum EED biomarkers were compared between study groups. Two-sample t-tests were used to compare weight and length between the two groups, and a non-parametric Wilcoxon Rank-Sum test was used to test differences for EED biomarkers. Targeted and non-targeted serum metabolite profiling was completed by using liquid chromatography tandem-mass spectroscopy. The RB group had significantly increased length-for-age Z-score (LAZ) from 6 to 8 months, and 6 to 12 months compared to control (p<0.01). RB participants showed decreased intestinal permeability and inflammation in the stool marker Alpha-1-Antitrypsin (p=0.02) and beneficial effects on gut function in the serum Glucagon-like-peptide-2 (p<0.04). Fifty-four serum metabolites were significantly different following RB supplementations versus control. These results support multiple favorable outcomes from RB supplementation in weaning infants. Findings from this pilot study support that RB intake during weaning is safe, promotes healthy intestinal functions, and enhances growth outcomes.
Open Access
Soil bacterial influence on alfalfa growth and health
(Colorado State University. Libraries, 2013) Sheflin, Amy M., author; Vivanco, Jorge, advisor; Weir, Tiffany, committee member; Badri, Dayakar, committee member; Manter, Dan, committee member; Paschke, Mark, committee member
Soil microbial communities have demonstrated enormous potential for promotion of plant health and productivity. In particular, the diversity of the soil community may play an important role for increased plant growth. However, previous research has focused on soil fungal diversity and neglected the role that diversity of soil bacteria may play in influencing plant growth. Therefore, a greenhouse study was conducted to determine if soil bacterial community structure influences alfalfa productivity. Prior to setup, nine soils with varying physico-chemical and microbiological profiles were chemically and biologically characterized. Soil physico-chemical factors for experimental soils were quantified via standard methods of soil nutrient testing. In addition, soil microbiology was characterized using 454 pyrosequencing to determine soil diversity indices and taxonomic classification of the soil bacterial community. These microbial communities were extracted into soil suspensions and transplanted to alfalfa plants growing in a sterile substrate. Filtered (soil microorganisms removed) and non-filtered (soil microorganisms retained) soil suspensions were applied to separate soil chemical and microbiological effects. Alfalfa plants were grown in a greenhouse for 60 days post germination; then roots and shoots were harvested, dried and weighed. This experimental setup was used to answer two distinct research questions. In the first study, alfalfa biomass was correlated with both soil physico-chemical and bacterial measures to determine which soil factors influenced plant productivity. For four soils, a biologically inactive (filtered) extract included unidentified chemical factors that had a negative effect on plant biomass production. However, in two of these cases inclusion of soil microbes counteracted this negative effect and restored plant growth to a level equal to the non-amended control. Among bacterial classes, the relative abundance of Deltaproteobacteria in soils was significantly correlated with plant productivity. Correlations between plant productivity and soil bacterial richness, diversity and evenness were marginally significant and more highly correlated than soil physico-chemical factors. Results suggest that soil microbiology can compensate for negative effects on plant growth due to soil chemistry, potentially due to microbial remediation of organic soil chemical residues such as herbicides. Also, in this study, relative abundance of specific bacterial taxa was more highly correlated than bacterial diversity indices with improved plant productivity. Many species of bacteria, referred to collectively as plant growth promoting rhizobacteria (PGPR), are known to be particularly beneficial to plant health and yield. However, inconsistency in establishment of PGPR inoculants has limited their practical use in the field. While PGPR inoculation failures have been partially attributed to competition with the indigenous soil community, studies focusing on the role that indigenous soil bacteria play on the establishment of PGPR inoculants are rare. Soil bacterial diversity is known to prevent establishment of fungal pathogens and may inhibit PGPR establishment as well. Therefore a second study was conducted using four of the nine original experimental soils, which were selected to represent the largest variety of US locale and management types from collected soils. Including four soils allowed for expansion beyond previous bacterial diversity research, which utilized only one soil type, while simultaneously including inoculation treatments of two different organisms. The same experimental setup was utilized except that either a PGPR (Pseudomonas putida) or a pathogenic microorganism (Phytophthora medicaginis) was introduced for comparison to non-amended controls. Subsequently, effects on alfalfa biomass production and disease were measured. In addition, PGPR colonization by P. putida KT2440 was quantified using qPCR via detection of the gfp gene carried on the KT2440 plasmid. Results from the second study showed increases in alfalfa productivity with added PGPR were significantly larger in soils with higher soil microbial diversity. However, no differences in PGPR root colonization were observed among non-filtered treatment groups. These results suggest that the increased effectiveness of the PGPR in high diversity communities was due to increased effectiveness of other beneficial soil microorganisms. Indeed, several native PGPR and N cycling species were correlated with shoot biomass increases when adding PGPR. Conversely, disease incidence and severity caused by "P. medicaginis" was not significantly associated with soil bacterial diversity. These results emphasize the role of soil microbial community composition and its functional relationship with the invading organism in predicting effects of an introduced PGPR inoculant or soil pathogen. In conclusion, both soil chemical and biological qualities were evaluated to lend confidence that observed effects on alfalfa biomass and microbial invasion were due to biological rather than chemical influences. Soil bacteria were found to influence plant productivity by counteracting other soil factors with negative effects on plant growth. In addition, soil community diversity played a less consequential role in these experiments than the specific taxonomical and functional bacterial members. Furthermore, soil bacterial diversity significantly improved the beneficial effects of PGPR inoculants, but was not shown to significantly reduce disease incidence or severity.
Open Access
The abundance of ACC deaminase-positive bacteria and their interaction with winter wheat in a Colorado soil
(Colorado State University. Libraries, 2012) Abduelafez, Ibrahem, author; Stromberger, Mary, advisor; Weir, Tiffany, committee member; Moragues Canela, Marc, committee member
Plant growth-promoting rhizobacteria (PGPRs) are known as beneficial bacteria for plant growth and yield. One PGPR group are the ACC deaminase-positive (ACC+) bacteria which degrade 1-aminocyclopropane-1-carboxylic acid (ACC), the plant-produced precursor to ethylene. Plants produce ethylene in elevated quantities under environmental stress ("stress ethylene"), and studies have shown that ACC+ bacteria, in association with plant roots, can improve plant growth under abiotic stress (e.g., drought, salinity, heavy metals) by reducing concentrations of stress ethylene. There are few studies that have examined the natural abundance and distribution of these bacteria as affected by plant genotype, plant growth stage, and agricultural management practice; and no studies have been conducted in the western United States. The objectives of my research were to determine the influence of winter wheat genotype and irrigation practice on the abundance of culturable ACC+ bacteria in a Colorado soil, and to determine the plant-growth-promoting effect of selected ACC+ on winter wheat varieties ranging in drought sensitivities under greenhouse conditions. A field study was conducted at the Limited Irrigation Research Farm (LIRF) in Greeley, Colorado. Roots and root-associated soil (0-20 cm depth) were collected with a shovel under four winter wheat varieties (Triticum aestivum L. "Baca", "Hatcher", "Ripper" and "RonL") managed by three different irrigation regimes: full irrigation, limited irrigation (irrigation commencing at the anthesis stage), and dryland. Samples were collected at four physiological growth stages during the 2010-2011 growing season: emergence (November 2010), green-up (March 2011), anthesis (May 2011) and mid-grain filling (June 2011). Total culturable bacteria were enumerated on TSB agar, and culturable ACC+ bacteria were enumerated on DF minimal salts agar media containing ACC as the sole N source. The abundance of ACC+ bacteria was relatively high in the Colorado soil (1.69 × 107- 3.28 × 109 CFU's g-1) and varied according by an interaction between sampling date and irrigation practice (P < 0.0001). Abundance of ACC+ bacteria in the fully irrigated plots peaked in March and declined throughout the rest of the growing season, whereas ACC+ bacterial numbers increased significantly in the late growth stages for the dryland and limited irrigation treatments. The percentage of ACC+ bacteria, relative to total culturable bacteria, was significantly affected by the three-way interaction between wheat variety × irrigation treatment × sampling date (P= 0.0095). Whereas few differences in % ACC+ bacteria were observed among treatments in November and March, % ACC+ bacteria in May and June were generally greater under dryland or limited irrigation compared to full irrigation management. Wheat variety had no effect on % ACC bacteria under full irrigation, whereas % ACC bacteria generally was lowest under Baca and greatest under RonL under limited irrigation or dryland. A greenhouse study was conducted to determine how interactions among specific ACC+ bacterial strains, winter wheat genotype, and water stress affect winter wheat productivity. Two strains of Pseudomonas brassicacearum (HD6 and HF1) were selected for inocula because of their high ACC-deaminase activity and numerical dominance in a Colorado soil. Two winter wheat varieties (Ripper and RonL) were grown under non-stressed (soil maintained at 80-100% water holding capacity) or water-stressed (soil maintained at 40-60% water holding capacity) conditions, with different ACC+ bacterial inoculum treatments (HD6, HF1, or a combination of HD6 + HF1). Inoculation with ACC+ bacteria increased stem height of both wheat varieties, and increased the biomass, number of seeds, and number of fertile heads of RonL. There was a negative effect of the strain HD6 on Ripper productivity under non-stressed conditions in the greenhouse study. In conclusion, these studies demonstrate that the abundance of ACC+ bacteria and the potential effects of these bacteria on winter wheat productivity are dependent on winter wheat genotype and irrigation practice. Certain wheat varieties are able to accumulate more numbers of ACC+ bacteria in their rhizospheres under water stress, and certain strains of ACC+ bacteria can positively (RonL) or negatively (Ripper) impact winter wheat depending on the level of water stress.
Open Access
The effect of tylosin exposure or exclusion on liver abscess prevalence, fecal pathogen populations, and the microflora of finished beef products from feedlot cattle
(Colorado State University. Libraries, 2018) Weissend, Carla Jane, author; Martin, Jennifer, advisor; Belk, Keith, committee member; Bryant, Tony, committee member; Metcalf, Jessica, committee member; Weir, Tiffany, committee member
There is great pressure to reduce use of, and find alternatives to, antibiotics in animal production. More than 70% of feedlot cattle in 1000+ head lots are currently exposed to tylosin phosphate, a macrolide antibiotic used for the reduction and prevention of liver abscesses. As such, its potential removal from cattle feeding strategies could have a marked impact on both the economics of the beef industry and food safety. Additionally, little is known about the effect of tylosin exposure or exclusion on the microbiome of finished beef products. In light of these facts, a blinded, randomized, controlled field trial was conducted to evaluate the impact on the prevalence of liver abscesses and the characterization of the microbiome of feces, liver abscesses, carcasses, and finished beef products through 16S rRNA gene sequencing and shotgun sequencing from feedlot cattle with and without exposure to tylosin. Overall, liver abscess rates were lower among cattle exposed to tylosin. However, there were no differences among treatment groups for any of the sample types, suggesting that removal of tylosin from current feeding strategies will not upend the safety of the beef supply. The information gained in this study will provide valuable insight as the search for alternative feeding strategies to antibiotics continues.