142 research outputs found
Presence of Archaea in the Indoor Environment and Their Relationships with Housing Characteristics
No full textArchaea are widespread and abundant in soils, oceans, or human and animal gastrointestinal (GI) tracts. However, very little is known about the presence of Archaea in indoor environments and factors that can regulate their abundances. Using a quantitative PCR approach, and targeting the archaeal and bacterial 16S rRNA genes in floor dust samples, we found that Archaea are a common part of the indoor microbiota, 5.01 ± 0.14 (log 16S rRNA gene copies/g dust, mean ± SE) in bedrooms and 5.58 ± 0.13 in common rooms, such as living rooms. Their abundance, however, was lower than bacteria: 9.20 ± 0.32 and 9.17 ± 0.32 in bedrooms and common rooms, respectively. In addition, by measuring a broad array of environmental factors, we obtained preliminary insights into how the abundance of total archaeal 16S rRNA gene copies in indoor environment would be associated with building characteristics and occupants’ activities. Based on the results, Archaea are not equally distributed within houses, and the areas with greater input of outdoor microbiome and higher traffic and material heterogeneity tend to have a higher abundance of Archaea. Nevertheless, more research is needed to better understand causes and consequences of this microbial group in indoor environments.Natural Sciences and Engineering Research Council of Canada (Discovery Grants)CHILD Stud
Exploring the role of cholesterol and coprostanol in clostridioides difficile physiological fitness : from association with fecal microbiota transplantation (FMT) success to causality studies
No full textThe full abstract for this thesis is available in the body of the thesis, and will be available when the embargo expires.Applied Science, Faculty ofEngineering, School of (Okanagan)Graduat
Long-term outcomes of antibiotic treatments in fecal microbiota transplantation donors on microbiota composition, function, and antibiotic resistance genes
No full textThe full abstract for this thesis is available in the body of the thesis, and will be available when the embargo expires.Applied Science, Faculty ofEngineering, School of (Okanagan)Graduat
Investigating the human microbiome : dynamic interactions and therapeutic potentials in health and disease states
No full textThe intricate nexus between humans, environmental factors, and the gut microbiota plays a pivotal role in determining the overall health of the host. Our gut microbiota's composition is a dynamic tapestry woven from threads of both early-life events and adult experiences, each contributing uniquely to our overall health and well-being. Thus, the overall aim of this thesis was to investigate the role of the gut microbiome in health and disease states. The gut microbiota’s role in cholesterol metabolism (cholesterol to coprostanol conversion), is not fully understood. Therefore, I first aimed to explore the gut’s environment, encompassing mucus, microbiome, and metabolites to explore its relationship with cholesterol metabolism among healthy participants. High-converters had increased Akkermansia muciniphila. Importantly, the causal role of A. muciniphila in conversion was confirmed. Non-converters showed reduced mucus glycan sialylation and fecal bile acid desulfation, similar to trends observed in inflammatory bowel disease (IBD). Next, I aimed to gain a holistic understanding of the impact of adverse childhood experiences (ACEs) on gut microbiota. ACEs can impact physical and mental health outcomes in adulthood; however, studies assessing how ACEs may impact gut microbiota are lacking. High ACE individuals displayed distinct gut microbiota differences potentially impacting intestinal tissue integrity. They also experienced a higher prevalence of diarrhea, possibly linked to stress on the gastrointestinal system. Lastly, I aimed to better understand the underlying mechanisms for fecal microbiota transplantation (FMT) and optimize microbial therapeutics for recurrent Clostridioides difficile infections (rCDI). Studies often have a uni-kingdom focus and few studies have examined the role of gut mycobiome and virome on FMT efficacy. Thus, I aimed to investigate whether FMT super-donors exist or whether the gut microbiomes of both donors and recipients are implicated in FMT success. Our results suggested that FMT outcome is not only dependent on the ecological structure of the recipients but also on the interactions between the donor and recipient microbiomes. In summary, our integrated studies underscore the multi-faceted factors involved in microbiome-mediated mechanisms in health and disease states. Insights gathered can pave the way for innovative therapeutic interventions against diseases and microbiota-related conditions.Applied Science, Faculty ofEngineering, School of (Okanagan)Graduat
Synthesis and characterizations of antimicrobial coating by atomic layer deposition technique for personal protective equipment applications
No full textThe outbreak of COVID-19 has led to significant demand for Personal Protective Equipment (PPE), such as masks and face shields. While these PPEs can protect people from many infectious agents, they usually are one-time use and non-degradable after disposal, causing a shortage of supply and environmental issues. While many reusable substitutes, such as reusable cloth masks, were developed, their prevention capability might be compromised after prolonged usage. As such, self-disinfecting coatings have been applied to PPEs to improve antibacterial and antiviral properties. However, commercial coating methods, such as spraying and physical vapor deposition, have several limitations for PPE applications, including poor coverage, loose adhesion, and high coating temperature.
This thesis work adopted an advanced atomic layer deposition (ALD) technique to fabricate nanoscale self-disinfecting coatings that overcome the above mentioned coating approaches limitations. This work investigated the ALD fabrication, material characterizations, and antimicrobial performance of titanium oxide (TiO₂) and zinc oxide (ZnO), two typical UV-activated self-disinfecting materials. The ALD-deposited TiO₂ and ZnO thin films on the glass substrate had thickness of 81.6 ± 6.6 nm and 312.8 ± 41.3 nm, respectively. Structural analysis by X-ray diffraction, Raman spectroscopy, and X-ray photoelectron microscopy confirmed the successful deposition of TiO₂ and ZnO, most of which were amorphous. The antimicrobial properties of the ALD-TiO₂ and ZnO were evaluated against E. coli, under modified AATCC-100 standard, with commercial TiO₂ and ZnO powders as references. Data indicated that ALD-ZnO could eliminate E. coli during a 12-hour test. All the data were verified through P value test with alpha set to 0.05, and statistically proved the antimicrobial performance of the ALD-ZnO. Moreover, the nanoscale ALD-ZnO exhibited antimicrobial properties similar to commercial ZnO.
On the other hand, P-value tests indicated ALD-TiO₂ coating and commercial TiO₂ powders did not generate statistically significant data that suggests antimicrobial activity toward E. coli. The different antimicrobial properties of ALD-ZnO and TiO₂ could be caused by more substantial UV absorption capability of the former than the latter, as revealed by the UV absorption test. It is expected that this work could stimulate the application of the ALD technique for applying self-disinfecting ZnO coatings for PPE.Applied Science, Faculty ofEngineering, School of (Okanagan)Graduat
The effect of indoor daylight on indoor microbiome under a controlled mini-living lab and a natural hospital setting : towards better healthy building designs
No full textThe COVID-19 pandemic started in 2019 have brought increasing public attentions to the built environment quality and human health. The negative impacts of infectious agents in buildings have long been recognized by health professionals before the occurrence of the recent global pandemic, and extensive efforts have been made to remove “harmful” substances from the buildings that we spent 90% of the time in today. However, current buildings are far from being truly healthful for the occupants evidenced by growing risks of hospital associated infections, seasonal epidemic outbreaks, and recent global pandemic. The root of the problem is to reduce the pathogens inside the buildings yet indoor microbiome is highly dynamic which interacts with numerous building factors simultaneously thus brings tremendous challenges to cleaning and disinfections. In recent years, scientists and researchers have starting to realize that improving building design can provide extensive benefits to occupant’s health meanwhile reduce the building’s environmental impact. Indoor daylight, an important healthy building foundation, plays a crucial role in affecting the occupant’s mental health and well-beings, albeit its effect on indoor microbiome has rarely been explored.
The goal of this study is to explore the interactions between indoor daylight and indoor microbiome and provide important insights for the future healthy building design. To achieve this, a literature review was first provided in chapter 2, and two experiments were conducted: the first experiment (chapter 3) was performed in a controlled laboratory environment, where bacterial and fungal pathogens were exposed to different indoor daylight conditions on different surface materials. The second experiment was performed in a hospital (chapter 4), where indoor environment and patient samples were collected in patient rooms with electrochromic windows (N=5), and with regular windows and blinds (N=5) over the five-day of patient stay. Results of this study showed that indoor daylight can be a promising intervention to reduce pathogen growth and minimize risks of infections in all built environments. Green building design such as the use of electrochromic window which brings more daylight into the buildings can be a critical step to maintain a healthy indoor microbiome and achieve a truly healthy building.Applied Science, Faculty ofEngineering, School of (Okanagan)Graduat
Effect of fungal deterioration on physical and mechanical properties of hemp and flax natural fiber composites
No full textThe development and application of bio-sourced composites have been gaining wide attention, yet their deterioration due to the growth of ubiquitous microorganisms during storage/manufacturing/in-service phases is still not fully understood for optimum material selection and design purposes. In this study, samples of non-woven flax fibers, hemp fibers, and mats made of co-mingled randomly-oriented flax or hemp fiber (50%) and polypropylene fiber (50%) were subjected to 28 days of exposure to (i) no water-no fungi, (ii) water only and (iii) water along with the Chaetomium globosum fungus. Biocomposite samples were measured for weight loss over time, to observe the rate of fungal growth and the respiration of cellulose components in the fibers. Tensile testing was conducted to measure mechanical properties of the composite samples under different configurations. Scanning electron microscopy was employed to visualize fungal hyphal growth on the natural fibers, as well as to observe the fracture planes and failure modes of the biocomposite samples. Results showed that fungal growth significantly affects the dry mass as well as the tensile elastic modulus of the tested natural fiber mats and composites, and the effect depends on both the type and the length scale of fibers, as well as the exposure condition and time.Peer reviewed: YesNRC publication: Ye
Detection of antibiotic resistance in swine production
No full textSince antibiotics have been added to animal feed for decades, foodanimals and their wastes constitute a reservoir of antibiotic-resistant bacteria. Atthe Swine Complex of McGill University, the addition of antibiotics to swine feedfor subtherapeutic applications has been discontinued since January 2007. Theobjective of this work was to assess the prevalence and short-term evolution ofantibiotic resistance among bacterial populations in swine production 2.5 yearsafter this discontinuation. Feces from ten healthy pigs (6 males and 4 females)born at the Swine Complex of McGill from the same sow and administered feedwithout antibiotics were sampled during suckling, weanling, growing andfinishing. The percentage of chlortetracycline-resistant anaerobic bacterialpopulations (TetR) was higher than that of tylosin-resistant anaerobic bacterialpopulations (TylR) at weanling, growing and finishing, with generally largerdifferences in males than in females. At the finishing stage, i.e. prior to thetransportation of animals to the slaughterhouse, resistant populations variedbetween 3.1x10^6 and 2.5x10^9 CFU g^-1. In all pigs, tet(L), tet(O) and erm(B) weredetected by PCR at suckling and weanling, whereas only tet(O) was detected atgrowing and finishing. Quantification of tet(O) by real-time PCR showed that atsuckling, the abundance of this gene was 18 times higher in females than inmales, was similar between the two genders at weanling and growing, andreached 5.1x10^5 and 5.6x10^5 copies of tet(O)/g of total DNA in the feces ofmales and females, respectively, at finishing. In this study, the high abundanceand proportion of antibiotic-resistant populations, as well as the occurrence ofresistance genes within these populations despite the discontinuation of antibioticaddition to feeds imply either that more time would be required for antibioticresistance to decrease to lower levels, and/or that factors such as the presence ofmetals in feed impose a selective pressure that maintains antibiotic resistancegenes among these bacterial populations.Puisque des antibiotiques sont ajoutés aux moulées des animaux de fermedepuis des décennies, ces animaux et leurs déjections constituent un réservoir debactéries résistantes aux antibiotiques. Au Complexe porcin de l'UniversitéMcGill, l'ajout d'antibiotiques dans les aliments pour porcs pour les applicationssous-thérapeutiques a été interrompu en janvier 2007. L'objectif de ce travail étaitd'évaluer la prévalence et l'évolution à court terme de la résistance auxantibiotiques chez les populations bactériennes en production porcine 2,5 ansaprès cette interruption. Les matières fécales de dix porcs sains (6 mâles et 4femelles) nés au Complexe porcin de McGill de la même truie et nourris avec desmoulées sans antibiotiques ont été échantillonnées durant les phases d'allaitement,sevrage, croissance et finition. Le pourcentage de bactéries anaérobies résistantesà la chlortétracycline (TetR) était généralement plus élevé que le pourcentage debactéries anaérobies résistantes à la tylosine (TylR) lors des phases de sevrage,croissance et finition, avec des différences plus grandes chez les mâles que chezles femelles. Au stade de la finition, c'est à dire avant le transport des animauxvers l'abattoir, les populations résistantes variaient entre 3.1x10^6 et 2.5x10^9 UFCg^-1. Chez tous les porcs, les gènes tet(L), tet(O) et erm(B) ont été détectés parPCR lors des phases d'allaitement et de sevrage, alors que seulement tet(O) a étédétecté en croissance et finition. La quantification de tet(O) par PCR en tempsréel a montré que, à l'allaitement, l'abondance de ce gène était de 18 fois plusélevé chez les femelles que chez les mâles, était similaire entre les deux sexes ensevrage et en croissance, et a atteint 5.1x10^5 et 5.6x10^5 copies de tet(O)/gd'ADN total dans les excréments des males et des femelles, respectivement, à laphase de finition. La forte abondance et la proportion élevée de populationsrésistantes aux antibiotiques, ainsi que la présence de gènes de résistance au seinde ces populations malgré l'interruption de l'ajout d'antibiotiques aux mouléesimpliquent soit que plus de temps serait nécessaire pour que la résistance auxantibiotiques décroisse à des niveaux inférieurs, et/ou que des facteurs tel laXII présence de métaux dans les moulées impose une pression sélective qui maintientles gènes de résistance aux antibiotiques parmi ces populations bactériennes
The factors that influence prokaryotic and eukaryotic community structure in indoor dust
No full textBuildings are complex ecological systems that support a high diversity of prokaryotic and
eukaryotic communities. Since many of these organisms interact with humans and their
activities, and adding the considerable amount of time modern humans spend indoors, it is critical to understand the taxonomic composition of indoor biota as well as the ecological processes and environmental factors that may influence their diversity and composition. In this thesis, I report on studies where I employed a Next-Generation DNA Sequencing technique, monitored 668 environmental factors and occupants’ activities, conducted advanced multivariate statistical analyses, and demonstrated that community composition of different organisms in indoor environments, including Fungi, Bacteria, and Animals may be influenced by different building characteristics, furnishings, type of occupants as well as their activities. In addition, this is the first study reporting the presence of Archaea in household dust as a common part of the indoor microbiota; however, the archaeal abundance in indoor environment was considerably lower than Bacteria, perhaps because of less available sources contributing to indoor Archaea or more environmental filtering preventing archaeal establishment in indoor environments. This also can be interpreted that the indoor archaeal assemblages are probably allochthonous for the most part (passive entrants of archaeal traces from different sources), in contrast, to those of the Bacteria which are a mixture of allochthonous and autochthonous (live and active inhabitants of dust). Finally, in a separate study with samples collected over a 20-year period, I found that the total airborne fungal spore count in outdoor air would likely increase significantly in future years as a result of climate change, indicating a likely rise in indoor fungal spore abundance as well. Overall, this study as one of the first to look for members of all domains of life in a single cohort study, has advanced our understanding of biological components of residential houses
and illustrated how community composition of different organisms in the indoor environment may be influenced by different building characteristics, furnishing, and its
occupants. I believe such comprehension of indoor ecology can help researchers design
intervention studies to provide public health policy decision makers with new tools to
improve the built environment.Arts and Sciences, Irving K. Barber School of (Okanagan)Biology, Department of (Okanagan)Graduat
Fast Genetic Algorithm For Feature Selection — A Qualitative Approximation Approach
No full textWe propose a two-stage surrogate-assisted evolutionary approach to address the computational issues arising from using Genetic Algorithm (GA) for feature selection in a wrapper setting for large datasets. The proposed approach involves constructing a lightweight qualitative meta-model by sub-sampling data instances and then using this meta-model to carry out the feature selection task. We define "Approximation Usefulness" to capture the necessary conditions that allow the meta-model to lead the evolutionary computations to the correct maximum of the fitness function. Based on our procedure we create CHCQX a Qualitative approXimations variant of the GA-based algorithm CHC (Cross generational elitist selection, Heterogeneous recombination and Cataclysmic mutation). We show that CHCQX converges faster to feature subset solutions of significantly higher accuracy, particularly for large datasets with over 100K instances. We also demonstrate the applicability of our approach to Swarm Intelligence (SI), with results of PSOQX, a qualitative approximation adaptation of the Particle Swarm Optimization (PSO) method. A GitHub repository with the complete implementation is available2. This paper for the Hot-off-the-Press track at GECCO 2023 summarizes the original work published at [3].References[1] Mohammed Ghaith Altarabichi, Yuantao Fan, Sepideh Pashami, Peyman Sheikholharam Mashhadi, and Sławomir Nowaczyk. 2021. Extracting invariant features for predicting state of health of batteries in hybrid energy buses. In 2021 ieee 8th international conference on data science and advanced analytics (dsaa). IEEE, 1–6.[2] Mohammed Ghaith Altarabichi, Sławomir Nowaczyk, Sepideh Pashami, and Peyman Sheikholharam Mashhadi. 2021. Surrogate-assisted genetic algorithm for wrapper feature selection. In 2021 IEEE Congress on Evolutionary Computation (CEC). IEEE, 776–785.[3] Mohammed Ghaith Altarabichi, Sławomir Nowaczyk, Sepideh Pashami, and Peyman Sheikholharam Mashhadi. 2023. Fast Genetic Algorithm for feature selection—A qualitative approximation approach. Expert systems with applications 211 (2023), 118528.© 2023 Copyright held by the owner/author(s).</p
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