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    Genetic diversity of microbes and its impacts on host switching : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Palmerston North, New Zealand
    (Massey University, 2025-08-25) Dos Anjos Almeida, Valter
    Land use around forests, leading to habitat overlap, increases the risk of anthroponotic and zoonotic pathogen/microorganism transmission between humans, livestock, and wildlife. This scenario is exemplified by Buhoma, a village where most residents are primarily subsistence farmers who raise livestock and cultivate crops near the Bwindi Impenetrable National Park (BINP) in Southwestern Uganda, creating an ideal interface for understanding these dynamics. Given the significance of this geographic location and the underrepresentation of African populations in global microbiome research, this project aims to characterise the gut microbiome diversity and potential novel bacterial species, as well as microorganism sharing within a multi-host system in a rural area with documented interactions between humans, livestock, and wildlife. For microbial detection, DNA extracted from 553 faecal samples collected from humans, gorillas, and livestock was processed and sequenced to analyse microbial species communities in different hosts using shotgun high-throughput sequencing and bioinformatics tools. The analysis of 2,411 bacterial metagenome-assembled genomes (MAGs) confirmed the presence of numerous putative novel bacterial species in the gut microbiomes of the Ugandan hosts studied in this project. While many species were host-specific, others were detected across multiple host gut microbiomes from Buhoma and BINP, and in different host samples from other geographic locations (by comparing the MAGs generated in this thesis with other publicly available genomes). Among the bacterial MAGs assembled in this project, genera such as Prevotella and Treponema—considered markers of the gut microbiome in individuals with traditional agricultural lifestyles—and Campylobacter—which comprises species that are leading causes of bacterial gastroenteritis globally—were further investigated. These genera were found to contain numerous putative novel species, contributing to our knowledge of the human and animal gut microbiomes and enhancing our understanding of the species associated with them. The results of this study reveal a high diversity of previously unknown microbes recovered from human, gorilla, and livestock gut microbiomes collected simultaneously at the same wild rural interface. The Treponema genus includes species that inhabit a wide range of hosts and types of microbiotas. In the Ugandan host samples, 75 Treponema MAGs were reconstructed, enabling the identification of sixteen intestinal species, including thirteen putative novel species. Three of the detected species were found in human samples from this study, as well as in publicly available Treponema genomes recovered from animals such as pigs, cattle, wild boars, roe deer, and goats. This detection underscores the potential for interspecies transmission and the establishment of these bacteria in different hosts. Overall, these findings highlight the complex interplay between humans, animals, and their gut microbiomes, emphasising the need for further research to elucidate the implications for public health. Prevotella species are prevalent and abundant components of microbial communities associated with mammals. This bacterial genus influences individual clinical and metabolic responses to dietary changes and overall health conditions. In humans, Prevotella species have been identified in various body sites such as the skin, oral cavity, vagina, and gastrointestinal tract. In the gut microbiome, they are commonly linked with diets abundant in plant-based foods and are particularly prevalent among agriculturalist populations, where they tend to dominate the microbiota. In the investigation of this genus, 37 MAGs were assembled, all belonging to yet-to-be-described species. Phylogenetic analysis revealed that they represented fifteen putative novel intestinal Prevotella species. The nimJ gene, which confers resistance to metronidazole (a nitroimidazole-class drug), was detected in one of the human intestinal Prevotella species. Given the widespread use of antibiotics like metronidazole for treating both humans and animals in regions of Uganda, including Buhoma, the presence of this gene provides evidence that Prevotella species can acquire resistance to commonly used nitroimidazole-class drugs in areas where their use is prevalent. Of the seven putative novel species identified in human gut microbiomes, two were also present in publicly available genomes in the gut microbiomes from pigs and rhesus macaques living in different geographic locations, providing evidence that the same Prevotella intestinal species can inhabit multiple hosts. Overall, these findings expand knowledge of intestinal Prevotella by introducing numerous previously unknown species, offering a species-level perspective for future studies on Prevotella’s impact on health. Campylobacter species are leading causes of bacterial gastroenteritis worldwide, yet their diversity and transmission dynamics at wildlife–livestock–human interfaces remain poorly characterised. I investigated Campylobacter diversity among sympatric mountain gorillas, livestock, and humans in Uganda, assembling 44 Campylobacter MAGs representing seven species—including five putative novel taxa. Three novel species were found in mountain gorillas, livestock harboured C. vicugnae (goats) and C. sp017646085 (cattle), while human gut microbiomes revealed Candidatus Campylobacter infans (not associated with disease) and C. sp900539255, which was significantly enriched in clinical samples (p=0.001) and displayed unique sulfur and nitrogen metabolic pathways. Antimicrobial resistance genes, including blaOXA-471_1, were detected in Ca. C. infans MAGs. Overall, our findings demonstrate high Campylobacter diversity at the human–animal interface in Buhoma and highlight the importance of expanding reference databases for accurate surveillance and effective public health interventions. In summary, this thesis introduces a substantial amount of new information on gut microbiome bacterial species in gorillas, livestock, and humans living at a wild-livestock-human interface. It also provides detailed insights into three bacterial genera present in the gut microbiomes of human populations, as well as other mammals such as gorillas, cattle, and goats.
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    Modelling infectious diseases in multiple species : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Applied Mathematics at Massey University, Albany, New Zealand
    (Massey University, 2019) Babylon, Andrea
    Leptospirosis is an infectious disease caused by bacteria in the genus Leptospira and is considered as the disease of interest in this thesis. It is the highest occurring occupational disease in New Zealand and the country has one of the highest (per capita) incidences of human leptospirosis in the world. Transmission commonly occurs by contact with infectious animals, or materials contaminated by them. The disease is the cause of great financial losses to the country due to both the medical cost of treating infectious individuals, as well as due to production losses in the farming industry. As such, studying the dynamics of infection and possible control measures for the disease in animals, which also minimises exposure to humans, is an important area of research. This thesis aims to develop New Zealand specific models demonstrating the dynamics of leptospirosis infection within and between multiple host species, specifically rats and sheep, thus contributing towards an understanding of not only how ecological exchanges between different host populations influence the spreading of the disease, but also how the incidence of leptospirosis may be diminished. This is achieved with the use of compartmental SI type models of increasing complexity, with simpler models used as building blocks in constructing the more advanced systems. The models presented involving only rats consider an age structure within the population, with different behaviours and infection risks associated with each age class. Models involving only sheep focus on the periodic forcing implemented on the host population by the farmer, and also include an age structure, albeit a somewhat simpler one than the one in the rat models. The seasonal forcing on the livestock population results in a cyclical system which is displayed using limit cycle diagrams. This behaviour is mirrored in the model considering both host species in concert. Each model presents a variety of results, including bifurcation diagrams and quasi-basic reproduction numbers which display the behaviour of the system. The effect of varying various parameter values on the system is explored, and how these may change in relation to climate change is discussed. Parameter values used in numerical results demonstrating analytical ones are New Zealand specific and the model is used to predict conditions under which the infection will persist in the population.
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    Epidemiological, pathological and metabolomic characterisation of an acquired myopathy of dogs in New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Manawatū, New Zealand
    (Massey University, 2018) Hunt, Hayley
    ‘Go Slow’ myopathy (GSM) is an idiopathic myopathy in dogs in New Zealand, characterised by an acute onset of trembling, weakness and collapse, followed by a prolonged period of exercise intolerance. In the first part of this thesis, the epidemiology of the disease was investigated using a telephone survey to obtain information regarding the diet, exercise, and health of affected dogs. Eighty-six confirmed cases were included in this study, and ingestion of wild pig in the week prior to the onset of clinical signs was a consistent finding (76/86 dogs; 88%; 95% confidence interval = 82 – 95%). Cases occurred most commonly in the upper North Island, particularly in Northland. The aim of the second part of this thesis was to characterise the pathology of GSM in the same 86 dogs included in the epidemiological study, using serum biochemistry (78 dogs), histology (20 dogs), and electron microscopy (4 dogs). Acutely, affected dogs had increased serum creatine kinase and aspartate aminotransferase activities, corresponding with the histological finding of skeletal muscle degeneration in the absence of inflammation. Ultrastructural changes in skeletal muscle included mitochondrial hypertrophy, intramitochondrial inclusions and increased sarcoplasmic glycogen. Similar lesions were observed in the skeletal muscle of wild pigs from areas where GSM occurred in dogs. Affected dogs also had increased serum alanine aminotransferase activities due to accumulation of lipid and glycogen in hepatocytes. Overall, the microscopic findings were consistent with a toxic myopathy. To further investigate the pathogenesis of the disease, liver samples were collected from 15 affected dogs and 24 clinically normal dogs for untargeted metabolic profiling using liquid chromatography-mass spectrometry. Comparison of spectra between affected and normal dogs revealed a widespread decrease in phospholipids, and increases in selected dicarboxylic acids and N-acetylated branch chain amino acids in affected dogs. No causative compounds were identified although several candidate mass spectrometric features were identified for future investigation. Taken together, the results of these studies suggest that ‘Go Slow’ myopathy is a toxic mitochondrial myopathy in dogs that is associated with the ingestion of wild pork. The findings reported aid in the prevention, diagnosis, and management of cases, with the primary suggestion being that owners avoid feeding wild pork in areas where the myopathy occurs. Further work is required to elucidate the cause of this disease.