Saudi Cultural Missions Theses & Dissertations
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Item Restricted THE IMPACTS OF ANTHOCYANINS ON GUT HEALTH: MICROBIOME DYNAMICS AND COLORECTAL CANCER CELL RESPONSES(Utah State University, 2025) Almatani, Mohammed F; Benninghoff, Abby DAnthocyanin (ACN)-rich foods are believed to suppress gut inflammation and may reduce the risk of colitis-associated colorectal cancer (CAC) through direct interactions with the gut epithelium or by modulating the gut microbiome. The overarching goal of this research was to investigate the dynamic changes in gut microbiome composition in response to ACN-rich foods within the context of a Western diet and to assess the direct effects of pure anthocyanins and their aglycones on colon cancer cell lines representing different disease stages. In the first study, male C57BL/6J mice were fed TWD supplemented with freeze- dried, ACN-rich whole food powders. The results demonstrated distinct shifts in gut microbiome composition as early as one day after exposure. However, these changes were not sustained after cessation of the diet, indicating that consistency is critical for persistent effects. Correlation analyses revealed that the unique ACN profiles of each food source were associated with specific microbial shifts, highlighting the differential microbiome-modulating potential of ACNs based on their structural composition. The second study evaluated the cytotoxic effects of purified anthocyanins and their aglycones on human colon cancer cell lines (HT29 and HCT116) at physiologically relevant concentrations. Contrary to expectations, these compounds did not significantly affect cell viability, apoptosis, or cell cycle progression. These findings suggest that the anticancer effects observed with ACN-rich whole foods are unlikely to result from pure anthocyanins alone but may instead depend on synergistic interactions among multiple bioactive compounds and gut microbiome-derived metabolites. Collectively, this research provides an integrative understanding of ACN-rich foods by combining dynamic microbiome analysis with physiologically relevant cancer models. It underscores the importance of whole food matrices and supports the need for further investigation into the role of gut microbial metabolism in mediating the anti-inflammatory and anti-carcinogenic potential of dietary anthocyanins.27 0Item Restricted Palm dates as an additive to improve the nutritional value of ryegrass and brassica-based silages before their use to improve degradability, microbiome and performance of ruminant animals.(Newcastle University, 2025) Alrumaih, Abdullah Amer A; I do not want to include advisor names as its idecated by the Newcastle unversity that ''The person who normally owns copyright for a thesis at Newcastle University is the author.'' please see the highlighted in yellow in the Following ai outcome E-thesis Collection FAQ PDF.Abstract: Ten replicated studies evaluated Seedless Whole Date Palm (SWDP) as an energy rich additive to two contrasting forages to improve the ensiling process, chemical characteristics in vitro dry matter degradability (DMD), the rumen function and the performance and rumen microbiome of growing lambs. This was achieved by conducting a series of in vitro and in vivo experiments where, firstly, five brassica hybrids comprising rape-avon (Avon), stubble turnip (Vollenda), brassica-redstart (Redstart), brassica- swift (Swift) and their mixture (Mixed) were tested for their production potential, nutritive values and DMD. Secondly, the effects of adding four doses (0, 5, 10 and 20%) of SWDP to the 2 selected brassica (Avon and Swift) and Ryegrass forages on their nutritional values after wilting and ensiling were evaluated. Finally, a trial with live lambs was conducted to evaluate the effects of SWDP addition at 0 and 20% in wilted Ryegrass and Swift on the silage quality, feed intake, growth performance, carcass weight, long chain fatty acids, lamb behaviour, IVDMD and rumen microbial profiles. Results confirmed that the addition of SWDP significantly decreased the crude protein (CP) and Oil-A contents (P<0.01 and P<0.01, respectively) of ensiled forages. There was an interaction between silage type and SWDP for their effects on D-value, metabolizable energy (ME), CP, Oil-A (ether extract, EE), neutral detergent fibre (NDF), and lactic acid (P<0.01, P<0.01, P<0.01, P<0.01, P=0.02 and P<0.01, respectively). The addition of SWDP linearly increased D-value and ME contents (P<0.01 and P<0.01, respectively) in the ensiled forages. There was also a significant difference between the five wilted brassica varieties for their mean DMD values (P<0.01). Moreover, the addition of SWDP showed significant differences between the wilted forages for the mean DMD (P<0.01), where the wilted forage x SWDP interaction was significant (P<0.01) for DMD. There was a linear increasing effect of increasing the SWDP addition from 0 to 20% on the DMD of both wilted and ensiled forages (P<0.01). The feed conversion ratio (FCR) (kg DM/kg gain) of 9 was the lowest for lambs fed Swift with SWDP at 0% compared with 13 for Swift with SWDP at 20%. It can be concluded that the ensiled Swift with SWDP at 0 and 20% were better for lamb feeding than Ryegrass at 0 and 20% in term of average daily gain (ADG) and FCR. Based on the in vitro DMD results, it is concluded that the addition of SWDP at 20% did show a positive response when compared with the 0% addition (P<0.01), but Ryegrass responded more to the added SWDP than the Swift to improve DMD. The DMD values of 75.4 and 77.2%, respectively, in Swift at 0 and 20% SWDP were higher than the corresponding values of 47.3 and 57.7%, respectively for Ryegrass at 0 and 20% SWDP. Regarding the microbiome analysis, the Firmicutes and VI Bacteroidetes were the dominant phyla in the rumen fluid (RF) of the trial lambs. Conversely, the Prevotella, Selenomonas, Fibrobacter and Bacteroides genera were abundant in lambs depending upon the ensiled forage type containing the added SWDP. The greater dominance of Bacteroidetes in Ryegrass based RF was perhaps due to its higher NDF content than the Swift based RF. Indeed, the abundances of Firmicutes, Bacteroidetes and Fibrobacteres phyla were increased and those could be used as indicators of increased fibre and protein degrading microbes in the RF of lambs fed Ryegrass-based diets. Keywords: Date palm; Brassica; Ryegrass; Silage; Degradability; Lamb; Microbiome16 0Item Restricted Diversity and vector biology of ectoparasites of small mammals in Saudi Arabia: implications for bacterial zoonoses(University of Liverpool, 2024-06) Alkathiry, Hadil; Makepeace, BenjaminGlobally, rodents are a major reservoir for many vector-borne bacterial diseases that are important for public and veterinary health. Due to their widespread distribution across ecological niches and their capacity to host a vast array of ectoparasites, including ticks, mites, and fleas, rodents are considered important hosts that aid in the persistence and spread of zoonotic illnesses such as scrub typhus (caused by Orientia spp.), Lyme disease and rickettsioses. The objectives of the current study were to (i) investigate the chigger mite fauna and other ectoparasites on rodents in two regions: Asir and Al-Bahah provinces (Saudi Arabia); (ii) determine the identity and prevalence of bacterial pathogens and symbionts in ectoparasites and hosts in these regions, with a special focus of on Orientia; and (iii) analyse the metagenome of the chigger Pentidionis agamae, identified here as a potential vector of Orientia in Saudi Arabia. Small mammals were trapped in southwest Saudi Arabia and in total, 7,392 chiggers, 368 ticks of various stages, 146 mesostigmatid mites, and 53 fleas (Parapulex chephrensis) were collected from 82 hosts. Internal rodent organs were also harvested and stored in 70% ethanol. Chiggers comprised 20 species belonging to nine genera, including a newly described species (Odontacarus thesigeri) and five species that constituted new records for the Arabian Peninsula. The most prevalent chigger species in Asir were Ericotrombidium kazeruni and Ericotrombidium caucasicum, while Schoutedenichia zarudnyi and P. agamae were dominant in Al-Bahah. Phylogenetic analysis of COI fragments of eight chigger species revealed a monophyletic grouping for each chigger genus. Phylogenetic analysis and ASAP (“assemble species by automatic partitioning”) analysis of COI sequences of mesostigmatid mites showed a distinct operational taxonomic unit that may represent a new Dermanyssus spp. The morphology of immature ticks assigned the specimens to Rhipicephalus spp. and Haemaphysalis spp., while phylogenetic trees were constructed based on COI, 12S rRNA, and 16S rRNA sequences, revealing novel clades of Rhipicephalus and Haemaphysalis ticks in Asir. Thirty-two per cent of tested Rhipicephalus spp. and Haemaphysalis spp. were found to be infected with Ehrlichia spp., forming two distinct clades separated by geographical regions. Wolbachia symbiont detection using the wsp gene was conducted on 53 flea samples and 17 chigger pools from Asir and sequences matched supergroups A, B, and V, while two clusters were distinct from known supergroups. The amplification of traD and htrA for Orientia screening was conducted for rodent organs and 165 chigger pools. Seven rodents and two chigger pools of Microtrombicula muhaylensis and P. agamae (sample R9P) were found to be Orientia positive. Phylogenetic analysis of the R9P htrA sequence revealed a single clade shared with Candidatus (Ca.) O. chuto htrA sequences from A. dimidiatus tissues collected in Asir. This is the first time that DNA from Ca. O. chuto has been found in potential vector species from this region, where it is geographically distant from a reported human case in Dubai. Metagenomic assembly and phylogenetic analysis of Wolbachia detected in P. agamae positioned a novel strain, designated as wPaga, within its own distinct clade, namely supergroup X, which segregated with other divergent supergroups. Moreover, the analysis of contigs from all three P. agamae pools identified sequences assigned to Spirochaetes. Based on 16S rRNA and sequence typing genes, these were found to represent a Borrelia clade associated with rodents that has not been detected in arthropods previously. Finally, the metagenomic analysis allowed for the assembly of three mitochondrial genomes from different P. agamae pools, enabling intraspecific comparisons. In summary, these findings highlight the hidden biology of rodent ectoparasites, zoonotic agents, and arthropod symbionts in a highly neglected biogeographical region.20 0Item Restricted Comparison of long-read and short-read bacterial DNA sequencing(King's College London, 2024-08-30) Alqirnas, Mohammed; Carpenter, Guy; Cleaver, LeanneThis study aimed to compare long-read (Oxford Nanopore) and short-read (Illumina) sequencing technologies for characterizing the diversity and composition of in vitro oral biofilms. An oral biofilm model was established using hydroxyapatite discs to mimic the tooth surface. Saliva samples from six healthy participants were pooled and used to inoculate the discs, which underwent aerobic and anaerobic incubation phases. Biofilm formation was assessed using confocal microscopy with LIVE/DEAD staining, revealing heterogeneous growth patterns with coverage ranging from 17% to 47%. DNA extraction was carried out using the GenElute Bacterial Genomic DNA Kit, with yields showing significant variations across experiments (0-5 ng/μL). Interestingly, gel electrophoresis showed no difference in DNA fragment lengths between samples prepared for short-read and long-read sequencing. The experiment also highlighted the potential benefits of CO2-rich environments for early colonizer growth, particularly Streptococcus species. While the biofilm model was successfully established, the results underline the need for protocol optimization, particularly in DNA extraction and biofilm cultivation. This research provides insights into the complexity of oral microbiome analysis and sets the stage for future comparative studies on advanced sequencing technologies in oral microbiome. The findings also emphasize the importance of refining the in vitro experimental protocol, from biofilm cultivation to DNA sequencing and data analysis.13 0Item Restricted Comparison of long-read and short-read bacterial DNA sequencing(King's College London, 2024-08) Alqirnas, Mohammed; Carpenter, Guy; Cleaver, LeanneThis study aimed to compare long-read (Oxford Nanopore) and short-read (Illumina) sequencing technologies for characterizing the diversity and composition of in vitro oral biofilms. An oral biofilm model was established using hydroxyapatite discs to mimic the tooth surface. Saliva samples from six healthy participants were pooled and used to inoculate the discs, which underwent aerobic and anaerobic incubation phases. Biofilm formation was assessed using confocal microscopy with LIVE/DEAD staining, revealing heterogeneous growth patterns with coverage ranging from 17% to 47%. DNA extraction was carried out using the GenElute Bacterial Genomic DNA Kit, with yields showing significant variations across experiments (0-5 ng/μL). Interestingly, gel electrophoresis showed no difference in DNA fragment lengths between samples prepared for short-read and long-read sequencing. The experiment also highlighted the potential benefits of CO2-rich environments for early colonizer growth, particularly Streptococcus species. While the biofilm model was successfully established, the results underline the need for protocol optimization, particularly in DNA extraction and biofilm cultivation. This research provides insights into the complexity of oral microbiome analysis and sets the stage for future comparative studies on advanced sequencing technologies in oral microbiome. The findings also emphasize the importance of refining the in vitro experimental protocol, from biofilm cultivation to DNA sequencing and data analysis.29 0Item Restricted Field Cancerization and Microbiome Effects on Lung Cancer: A Source of Early Detection Biomarkers to Improve Patients’ Outcome(George Mason University, 2024-08-16) Alhammad, Rayan; Luchini, AlessandraLung cancer results in more deaths than any other cancer in the United States and worldwide, with non-small cell lung cancer (NSCLC) accounting for most cases. Diagnosis typically involves chest imaging, molecular testing, and biopsy. However, most patients are diagnosed at advanced stages, with only a 6% chance of a 5-year survival rate. In contrast, early-stage diagnosis and treatment can result in a favorable prognosis, with a high 5-year survival rate of 70-90%. The concept of tumor field cancerization describes a phenomenon where exposure to carcinogens can cause histologic changes in large areas of tissue, creating a field of pre-malignant cells that can eventually develop into tumors. Additionally, microbiota dysbiosis might influence tumor development. Studies have identified several commensal bacteria present in the lower airway tracts, such as Streptococcus, Prevotella, and Veillonella. The high mortality rate of lung cancer is often attributed to i) its late-stage diagnosis, ii) aggressive nature given its ability to metastasize early in the disease process complicating treatment and reducing survival rates, and iii) significant therapeutic challenges despite current treatments such as surgery, chemotherapy, radiation therapy, targeted therapy and immunotherapy. Despite advancements, the survival rate for advanced lung cancer remains low. To address this challenge, our research focuses on identifying risk protein biomarkers that are associated with the earliest molecular changes indicative of an ongoing tumorigenic process, thus offering significant potential for early intervention. Our study investigates the phenotypic molecular changes in the bronchial tree of NSCLC patients in light of the field cancerization theory and correlates these findings with blood biomarkers to support the future development of a non-invasive risk assessment test. Using enhanced liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomic analysis and two independent cohorts of lung cancer patients (N=18, and N=263) with matched plasma and bronchial tree tissue specimens, we identified a set of 6 and 13 candidate risk plasma biomarkers with tissue origin. Additionally, we explored the microbiome proteome composition in NSCLC patient tissue and plasma to support future characterization of its potential role in cancer development. Risk biomarkers will enable the evaluation of individuals at high risk, guiding necessary lifestyle adjustments and facilitating the development of personalized prevention plans and therapies.52 0