APC Microbiome Ireland - Doctoral Theses

Permanent URI for this collection

https://hdl.handle.net/10468/1244

Browse

Now showing 1 - 5 of 108

Impact of food, environmental and pharmaceutical antimicrobials on the gut microbiome
(University College Cork, 2024) Walsh, Lauren; Ross, R. Paul; Hill, Colin; Science Foundation Ireland
This thesis is concerned with antimicrobials (both protein, peptide and chemical based) and their role in the gut microbiome from a functional and compositional perspective, as well as the isolation and development of new bacteriocins against pathogenic bacteria of interest. Pharmaceutical antimicrobials such as antibiotics, bacteriocins, phages and their endolysins are discussed in chapters 1, 3, 4 and 5. Chapter 1 describes antibiotic alternatives that could potentially be used to treat nosocomial methicillin resistant Staphylococcus aureus (MRSA) infection. Some alternative options include bacteriocins, phages and phage lysins. In Chapter 5, the antibiotics fidaxomicin and vancomycin were compared with the two bacteriocins, thuricin CD and nisin, as potential therapeutics to combat CDI and to assess their overall impact on the gut microbiome. Chapters 3 and 4 specifically discuss the isolation of novel bacteriocin producing bacteria. Chapter 3 describes the isolation of two bacteriocin producing strains termed AS1 and AS2. Chapter 4 outlines the isolation of Paenibacillus ottowii FAA_942_34, which demonstrated activity against IBD-associated bacteria. Environmental antimicrobials and food antimicrobials were examined in chapters 2, 6 and 7. Chapter 2 is a review focusing on the herbicide glyphosateTM, specifically focusing on the compositional and functional changes that glyphosate elicits in the gut microbiome. In chapter 6, glyphosate and four food preservatives were analysed for their effect on the gut microbiome. In Chapter 7, the heavy metal cadmium was used as a selective agent to identify transformants acquiring pJOS01. Following electroporation of pJOS01 into Staphylococcus aureus RN4220, a smaller 21 Kb plasmid termed pJOS02 was recovered in transformants. Formation of pJOS02 from pJOS01 is thought to result from the presence of inverted repeat regions at either end of pJOS02. Overall, the results of this thesis outline a variety of antimicrobials and their effect on the gut microbiome and their potential as therapeutics. This research builds on the growing amount of knowledge around the antimicrobials, the gut microbiome and the effect antimicrobials have on the composition and functionality of the gut microbiome.
Unravelling the role of circadian rhythmicity in microbiota-gut-brain axis signalling
(University College Cork, 2023) Tofani Sousa e Silva, Gabriel; Cryan, John; Saks-Kavanaugh Foundation; Science Foundation Ireland
Modern habits are becoming more and more disruptive to health. Our days are often filled with circadian disruption and stress exposure. We need to understand how our responses to these external stimuli are shaped and how they can be targeted to promote health. A growing body of research demonstrates the role of the gut microbiota in influencing brain function and behavior. The stress and circadian systems, which are essential to maintaining appropriate responses to the environment, are known to be impacted by the gut microbiota. Although gut microbes have been shown to modulate circadian rhythms and stress response, such studies were conducted in an independent manner. Since these systems are interconnected through the hypothalamic-pituitary-adrenal (HPA) axis, there is a need to examine how the gut microbiota may play a role in regulating the integration of stress and circadian signals. In this thesis, I aimed to investigate the influence of circadian rhythmicity in the microbiota-gut-brain axis communication and the consequences of that to stress responsivity. To this end we developed a computational tool, Kronos, that allows us to determine rhythmicity of genes and metabolites in brain regions important to stress and circadian regulation under different microbial status. Moreover, we investigate the interplay of the circadian and stress systems in the absence of the microbiota to dissect its role in the modulation of these systems. Using transcriptomics, and applying Kronos, we demonstrate that microbial depletion by antibiotic administration or germ-free status disrupts the molecular clock in the superchiasmatic nucleus (SCN). Such alterations to the master clock were accompanied with disruptions in the rhythmicity of circulating corticosterone. Furthermore, multi-omics analysis in the hippocampus and amygdala, indicated that microbial status disrupted the diurnal oscillations in genes and metabolites that compose pathways important for the stress response. We then investigate the expression of genes related to circadian rhythms and HPA-axis in the paraventricular nucleus, pituitary, and adrenal glands across the day. This, together with alterations in corticosterone demonstrates a hyper-activation of the HPA-axis at the sleep/wake transition in microbial depleted animals. Such disruption to the rhythmic function of the HPA-axis resulted in a time-of-day specific impairment of the stress response and stress-sensitive behaviors. Lastly, we identify changes in the rhythmic profile of the gut microbiota following microbial depletion. This manifested as peak of bacterial load at the same time the impairments in HPA-axis function were observed. Furthermore, by conducting fecal microbiota transplantation we confirm that the diurnal oscillations in gut microbes after antibiotic treatment regulates glucocorticoids secretion and explore the microbial compositional changes underlying it. This work provides compelling evidence that the gut microbiota regulates stress responsivity via the circadian system. Moreover, we identify the gut microbiota as an important regulator of HPA-axis rhythmic function, demonstrating that the microbiota is essential to adaptively respond to psychological stressors throughout the day.
The bacteriome and virome in social and stress-related disorders
(University College Cork, 2023) Ritz, Nathaniel L.; Cryan, John; Dinan, Timothy G.; Science Foundation Ireland
The gastrointestinal microbiota has been shown to influence mammalian health and well-being in many conditions but has also been implicated in a variety of diseases and disorders. The multi-faceted interaction of the microbiota with the host that affects the brain and behaviour is termed the microbiota-gut-brain axis. While this axis plays an important role in stress and social behaviour, research has largely focused on associations with the bacterial fraction of the community. The gut also harbours viruses, fungi, archaea, and other microbial forms of life that can affect the health of the mammalian host. Gut viruses, which are dominated by bacteriophages, are also ubiquitous in the gut and have the ability to infect bacteria and alter their structure and activity. Moreover, these populations of viruses are intimately associated with the bacterial community, but little is known about their involvement within the microbiota-gut-brain axis. Whether bacteriophages are capable of exerting effects on the brain and behaviour is largely unknown. To this end, we tested whether the virome was affected by stress followed by the capability of the virome to prevent stress-related sequelae. We found that the virome is stress sensitive and that restoring the virome to mice undergoing stress reduced anxiety-like behaviour, immune activation, inflammation, and gene expression in the brain. These data provide evidence that the gut virome can be harnessed to improve stress-coping outcomes. Social diseases and disorders have been implicated in the microbiota-gut-brain axis. Social anxiety disorder is a common but understudied psychiatric condition. Whether specific microbiota communities play a role in social fear responsivity or are capable of driving social fear behaviour is also unknown. Preclinical animal models of social fear allow for testing translational hypotheses that can then be returned to the clinic. We sought to characterize associations of the microbiota with social fear resiliency and susceptibility. Then, we transferred microbiota from individuals with social anxiety disorder to mice to test whether the microbiota played a causative role in the disorder. We found a strong correlation between microbiota and social fear variability along with differential expression of amygdalar genes involved in social behaviour, immunity, and host-microbe interaction. We also found that microbiota from individuals with social anxiety disorder could drive social fear sensitivity in mice. Mice that received microbiota from social anxiety disorder donors also had impaired cytokine release in the gut, reduced immune cell populations in the mesenteric lymph nodes and circulation, altered basal HPA axis, and diminished oxytocin and oxytocin-related expression of genes in the brain. These data indicate that social fear and anxiety are linked with the microbiota and that the gut-brain axis is a target for future research for social anxiety disorder therapeutics. Herein we tested whether gut viruses could alter stress response, whether social fear behaviour is associated with differential microbial communities, and whether human microbiota from individuals with social anxiety disorder can drive social fear behaviour in the mouse. Collectively we have shown that stress-related sequelae can be restored by virome transfer and that the microbiota can play a causal role in social anxiety disorder.
The role of the gut microbiota in the function and integrity of brain barriers
(University College Cork, 2023) Knox, Emily G.; Cryan, John; O'Driscoll, Caitriona M.; Rodriguez Aburto, Maria; Clarke, Gerard
The barriers of the brain help maintain an optimal environment for central nervous system (CNS) function and homeostasis. There are many instances such as during age related disorders and neuropsychiatric disorders in which these barriers are under threat. Importantly, the gut-microbiota can interact with the brain barriers, thereby altering barrier physiology and communication with the brain. This bidirectional communication is known as the microbiota-gut-brain axis. Modulation of the gut microbiota can thereby alter functions in the brain, potentially through influence of the brain barriers. In this thesis we focus on the interface of both brain barriers; the blood-cerebrospinal fluid barrier (CSF) and blood-brain barrier (BBB) in microbiota-gut-brain axis communication. In particular, using germ-free mice which lack a gut microbiota, we investigated the contributing role of the gut microbiota in regulation of the blood-CSF barrier. Following confocal microscopy for visualization of the tight junction protein, ZO-1, germ-free mice were found to have a disruption of the tight junction protein networks in isolated choroid plexus tissue. Similar assessment of the choroid plexus capillaries revealed no difference between germ-free and conventional mice. Since microbial metabolites are some of the known contributing factors of the gut microbiota’s manipulation of the barriers, we next investigated the effects of physiological concentrations of short chain fatty acids (SCFAs), butyrate and propionate, with and without induced barrier dysfunction (LPS) on the actin cytoskeleton and tight junction protein dynamics using an in vitro BBB model. We found that the butyrate and propionate altered filamentous actin directionality, increased tight junction protein spikes, and protected from LPS induced decrease in mitochondrial footprint and barrier integrity measured by trans-endothelial electrical resistance (TEER). While we do not yet understand the dynamics of the BBB following acute stress, we know that microbial metabolites can interact with BBB function, so we next assessed the potential for acute-stress induced metabolites to regulate BBB integrity using the same in vitro model. Following TEER assessment of a broad range of concentrations, we found that microbial metabolites from different classes; SCFAs, bile acids, and tryptophan metabolites impact BBB integrity. Specifically, butyrate, propionate, acetate, 3β-hydroxy-5-cholenic acid, and tryptamine exerted protective effects while acetate and cholic acid exerted detrimental effects at various concentrations. Lastly, since diet is a major modulator of the gut microbiota and especially in infancy, we assessed the impact of infant formulations fermented with probiotic strains of Bifidobacterium uniquely isolated from infant stool samples for potential effects on BBB integrity. Cell-free supernatants from the fermentation process which would contain a pool of microbial metabolites were then collected and exposed to the same in vitro model for assessment of barrier integrity with and without LPS disruption. We found that in each of the four infant formulations, there was protection from LPS disruption following fermentation with some of the Bifidobacterium strains. Overall, these results provide valuable insight into the interphase of brain barriers in microbiota-gut-brain axis communication. We highlight the role of another brain barrier in this interface, the blood-CSF barrier and further elucidate the microbial metabolite interaction in BBB physiology. Further, using two of the major modulators of the gut microbiota, stress and diet, we reveal that there is scope for the impacted metabolites or metabolic pools to influence brain barrier interactions.
The gut microbiome in inflammatory bowel disease and its confounders
(University College Cork, 2023) Eckenberger, Julia; Claesson, Marcus; Science Foundation Ireland
Inflammatory bowel disease (IBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), is a chronic remittent-relapsing inflammatory disorder of the gastrointestinal tract that affects millions of people worldwide. Despite progress in disentangling the pathogenesis of this disease, the exact cause of IBD remains unknown. As with other chronic inflammatory disorders, the tissue damage is immune mediated and arises from an interaction of genetic susceptibility factors, environmental triggers and indigenous gut microbiota. The gut microbiota play a central role in IBD pathogenesis. However, despite consistent reports of alterations in gut microbial composition, a coherent microbial signature for IBD remains elusive. Therefore, this work investigated the influence of IBD on the gut microbiota with a particular focus on the multitude of factors, both external and internal, that can potentially confound the distinctions between healthy and diseased states. Our investigation uncovered significant compositional disparities, especially in the case of CD, when comparing individuals with diseases to the control group. Furthermore, longitudinal analyses revealed reduced temporal stability in the microbiota of IBD patients, especially those experiencing fluctuations in disease activity. Geographic location emerged as one of the strongest drivers of microbiota variance, only second to a diagnosis with CD, followed by a history of surgical resection and a diagnosis with UC. Other life style factors also exerted an influence, however, the majority of the compositional variance remained either unexplained or was stochastic in nature. In view of the increasing evidence that commonly prescribed, non-antibiotic drugs interact with the gut microbiome, we re-examined the microbiota variance in IBD to determine the degree to which medications might account for compositional differences between disease-subtypes and geographic location. Although there were variations in medication profiles among individuals from different countries, treatments accounted for a relatively small proportion of the geographic contribution to microbiome. With that said, the cumulative effects of multiple medications significantly contributed to the microbiome differences between patients with UC and CD. Cognizant of the crucial role that microbial metabolites play as molecular messengers facilitating communication between the gut microbiota and the host, we next conducted an investigation into the role of microbial metabolites in patients with CD within the context of the liver-bile acid-microbiota axis. Our findings indicate that the typical signalling from the gut to the liver is disrupted in patients with CD compared to healthy controls, which led to excessive hepatic bile acid (BA) synthesis in a subset of patients. Moreover, variations in hepatic BA synthesis and BA reabsorption within the CD patient group were associated with the resection status. As a result of this disruption, we observed specific microbial changes among CD patients marked by an increase in bile-resistant and a decrease in bile-sensitive genera. This suggests that changes in BA metabolites significantly contribute to the observed differences in microbial composition between health and disease as well as between patients with CD. Collectively, these findings underscore the dynamic nature of microbiomes, highlighting their capacity to adapt to changing environmental conditions while also being subject to host-driven regulation. This added complexity, as well as the increasing data volumes, underscores the need for innovative analytical methodologies that can effectively capture all available information, especially considering the unique characteristics of microbiome data. Hence, we assessed machine learning algorithms, including Support Vector Machines (SVM), Extreme Gradient Boosting (XGB), and Random Forest (RF), for their ability to classify IBD phenotypes using gut microbiome data. All of the tested models successfully differentiated between IBD and non-IBD controls and, to a lesser degree, between IBD subtypes across studies conducted in diverse geographic locations. Importantly, all three algorithms exhibited variations in the selection of taxonomic features considered significant for the classification task, underscoring the need for caution when applying machine learning to tasks aimed at understanding underlying biological aspects rather than solely achieving precise phenotype predictions. In conclusion, the multifaceted approaches undertaken in this body of work yielded valuable insights into the complex interplay of lifestyle, medication, and microbial metabolites in the context of IBD, emphasising the importance of personalized approaches for host heterogeneity and environmental factors in the pursuit of precision medicine.

Browse

Recent Submissions