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Cork Open Research Archive (CORA) is UCC’s Open Access institutional repository which enables UCC researchers to make their research outputs freely available and accessible.
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Outsmarting phages to generate better dairy products
(University College Cork, 2024) White, Kelsey; van Sinderen, Douwe; Mahony, Jennifer; Irish Research Council
The dairy fermentation industry relies on the activity of various lactic acid bacteria in starter cultures to acidify milk and produce a variety of fermented dairy products. Undefined mesophilic starter cultures are predominantly composed of many strains (in an unknown composition) belonging to species such as Lactococcus lactis and Lactococcus cremoris. Bacteriophage infection of the bacterial strains within these starter cultures are one of the most significant and persistent threats to successful dairy fermentations. Delayed or disrupted fermentations, as a result of phage attacks, may cause costly disruptions resulting in unnecessary waste and a loss of product. One of the most problematic and abundant lactococcal phage genera is Skunavirus. Most lactococcal phages, including skunaviruses, commence infection with the binding of a phage-encoded receptor binding protein (RBP) to a surface-exposed host receptor, which in the case of skunaviruses is a cell wall polysaccharide (CWPS). To ensure the manufacture of consistent and high-quality fermentation end products, it is essential that the composition and integrity of starter cultures is maintained. Therefore, this thesis aims to investigate phage-host interactions between skunaviruses and their lactococcal hosts pertinent to dairy fermentation facilities utilising undefined mesophilic starter cultures.
Chapter 2 of this thesis outlines a combined culture-based analysis and metagenomics investigation to evaluate the composition of two mesophilic undefined starter cultures. A novel qPCR-based genotype detection assay, capable of discerning nine distinct lactococcal genotypes, was devised and used to examine compositional changes of an undefined starter culture. These analytical approaches facilitated a multifaceted assessment of starter culture compositional stability during milk fermentation, which has become an important quality control aspect due to increasing demand for reliable and high-quality dairy products.
In Chapter 3, a phageome analysis of whey samples originating from dairy fermentation factories employing mesophilic undefined starter cultures was conducted to investigate the phage prevalence and diversity in the samples. Particular focus was placed on investigating the range of Skunavirus RBP genotypes and associated RBP-CWPS binding abilities present in these whey phageomes. These findings allowed for the refinement and expansion of the Skunavirus RBP grouping systems thereby vastly expanding our knowledge on lactococcal Skunavirus RBP diversity and CWPS specificity.
Chapter 4 of this thesis details the diversity of skunaviruses present in the same whey samples used for the phageome analysis described in Chapter 3 through culture-dependent phage screening, targeted isolation based on RBP specificity, and phage RBP-activated cell sorting (PhRACS). Through this investigation, the genomes of 26 newly isolated Skunavirus members were sequenced and analysed, with a specific focus placed on surveying genes encoding auxiliary carbohydrate binding module-containing proteins. Host range analysis of the skunaviruses revealed a clear correlation between the encoded RBP phylogroups and cwps genotypes of corresponding host strains. In addition, phageome-derived Skunavirus contigs were analysed to further determine the diversity of phages present in the dairy fermentation facilities.
Chapter 5 assesses the strain-level diversity of lactococcal strains originating from mesophilic undefined starter cultures. Culture-dependent approaches were used to assess the technological attributes, such as acidification, proteolytic activity, and phage sensitivity, of these isolates. Genomic analysis of sequenced lactococcal strains was focused on industrially relevant genomic elements such as cwps biosynthesis gene clusters, plasmids, and phage-defense systems. In addition, a genomic analysis of strains belonging to the emerging dairy-associated species Lactococcus laudensis was carried out.
In summation, both the bacterial composition of starter cultures as well as the phage diversity of corresponding whey samples were thoroughly investigated, generating comprehensive insights into the complex microbial community of these mesophilic fermentation systems. Understanding the intricate phage-host interactions occurring in the environment in which mesophilic fermentation systems are extensively applied will aid in efforts to development and maintain robust dairy starter culture systems for sustainable food production practices.
Foe, friend, or all? The position of nature in international law on disaster risk reduction
(Edward Elgar Publishing, 2024-09-27) Aronsson-Storrier, Marie
This chapter focuses on the role of and position of nature in international law on disaster risk reduction. It argues that the undertheorisation of nature international law has led to tensions and unarticulated conflicts both between and within legal instruments on disaster risk, making current international law and policy unfit for purpose in meeting the challenges of the present. The chapter invites the reader not only to reconsider how nature is perceived in international law and policy, but also to reflect upon the wider context in which our work as researchers on international law and disasters is positioned, and how we can avoid (invertedly) reinforcing and recreating existing problems and injustices.
Assessment of the American crocodile (Crocodylus acutus) population in Ambergris caye, Belize
(University College Cork, 2024) Ó Mórdha, Ciarán; Collins, Courtney; Ramsay, Ruth; Summers, Chris; Manzi, Christina; Crocodile Specialist Group; European Crocodile Network
American crocodiles (Crocodylus acutus) have the second largest global distribution of all extant crocodilians, ranging from South Florida through Hispaniola, Cuba, and Jamaica, along the Caribbean coast from southern Mexico to Venezuela, and along the Pacific coast from Mexico to Peru. The species is considered Vulnerable by the IUCN throughout its range, with habitat loss currently a major threat facing the species in parts of its range, including Belize. In Belize, C. acutus is found throughout the coastal zone. Ambergris caye, the country’s largest and most densely populated caye, is inhabited by C. acutus, but its present status there is poorly understood. The aim of this study was to address these data gaps by assessing the status and life history of C. acutus on Ambergris caye and comparing this information with that from other areas within the species’ range to inform the development of a local American crocodile management plan.
During 19 nocturnal eyeshine surveys covering 171.5 km of shoreline on Ambergris caye carried out between May and September 2023, 199 American crocodiles were observed, an encounter rate of 1.16 crocodiles/km consisting of 22% adults, 10% subadults, 16% juveniles, 22% yearlings/hatchlings and 30% whose size class could not be determined. These results were similar to those of previous surveys carried out in 2010-2011, but with a higher encounter rate in 2023, suggesting a stable, if not slowly increasing, population. Crocodile nests were located by visiting previously identified nest sites, conducting additional surveys by boat and drone, and utilising social media to investigate reports of nesting activity by residents. A total 9 nests were found during the study. More than half (56%) of these were concentrated along the sand banks adjacent to the caye’s three sewage treatment ponds. Utilizing the 13 years of crocodile capture data (n=865) collected by ACES Wildlife Rescue in Ambergris caye, this study investigated growth rates, morphometrics, and sexual size dimorphism of the local crocodile population. Analysis revealed the growth rate (total length [TL]) of 115 crocodiles averaged 0.045 ± 0.027 cm/day. The growth rates found in adults differed by sex, with females (n=20) exhibiting a slightly lower average growth rate (0.039 ± 0.028 cm/day) compared to males (n=47) (0.048 ± 0.028 cm/day); however, the difference was not statistically significant. Notably, as total length (TL) increased with age, growth rates slowed more significantly in females than in males, with no significant relationship observed between TL and growth rates in males. Morphometric analysis encompassed 332 juveniles (TL<120cm), 25 female sub-adults (120≤ TL<180 cm), 31 male sub-adults (120≤ TL<180 cm), 40 female adults (TL≥180 cm) and 62 male adults (TL≥180 cm). Allometric relationships between TL and dorscal cranial length (DCL), snout length (SL), snout vent length anterior (SVLa) and snout vent length posterior (SVLp) revealed both positive and negative associations, all of which followed linear regressions. The dorsal cranial length to cranial width ratio (DCL: CW) of 2.7 to 4.2 indicates a broad-snouted skull morphotype akin to that observed in other island populations of C. acutus in the Yucatan region. The sexual dimorphism index of 1.07 toward males suggests a relatively minor disparity between the TL of males and females on Ambergris caye, indicating less pronounced sexual dimorphism compared to other populations of C. acutus. The sex ratio 2.39(M):1.0(F) was biased towards males. While Ambergris caye, likely the most human-populated caye in Belize, faces increasing development, pollution, and human-crocodile interactions, it may harbor one of the largest and most stable American crocodile populations in the country. The encounter rate of 1.16 on Ambergris caye is notably higher than that reported for nearby Turneffe atoll (0.34 in 2009) and the Belizean cayes overall (0.43 in 2000), suggesting this population is among the most robust in Belize. However, the study’s findings indicate that insufficient nesting habitat could pose a risk to the long-term stability of the population if not addressed through targeted conservation efforts. To mitigate this risk, it is imperative to conduct annual surveys to ascertain long-term population trends. Additionally, implementing protective measures for nests and intensifying surveys within the Bacalar Chico National Park and Marine Reserve to investigate nesting activity are vital steps in formulating a robust species management plan. Addressing these research gaps will not only enhance our understanding of the ecology of C. acutus in Belize but also inform targeted conservation efforts essential for safeguarding this population's viability and ecological role in the region.
Ireland and Islam: James O’Kinealy and Wahhabism in India
(Taylor & Francis, 2025-01-23) McNamara, Brendan
The purpose of this article is to explore James O’Kinealy’s (1838–1903) contribution to scholarship around Islamic movements in India, while a functionary of the Indian Civil Service (ICS) from 1862 to 1899. It seeks to recover from obscurity a little-known personage and his involvement in significant episodes in the history of Islam and British colonialism in India. O’Kinealy’s situatedness as an Irish Catholic in the ICS, and how this influenced his approach to Islam and his study of Wahhabism, will be closely examined. Serving the same imperial system in India that prevailed in Ireland presents a complex and entangled history. O’Kinealy’s background, it will be argued, influenced his activities as a senior official in the colonial administration. His writings (and translations), directed towards preserving the status quo against the fear of Muslim revolt, evidence a nuanced perspective when set against that of his ‘Anglicist’ contemporaries. Juxtaposing his approach and attitudes against that of the influential colonialist and scholar, W.W. Hunter (d.1900), will highlight his discreet approach and serve to foreground the intricate nature of this history. Though his publications are few, O’Kinealy’s work is unique, and represents one of the earliest engagements with the Wahhabi movement in the English language.
The development of a health communication passport for stroke
(University College Cork, 2024) O'Leary, Norma; Kelly, Helen; O'Toole, Ciara
Introduction: The Irish National Stroke Strategy (2022-2027) (HSE, 2022) has recommended the introduction of a Stroke Passport. However, the perspectives of stakeholders on the purpose, design, format, and content of a stroke passport are not yet known. Moreover, given that a Stroke Passport can be categorised as a complex intervention, characterised by multiple interacting components and the need to modify established practices, it is crucial to examine current practices related to information provision across the stroke care continuum. Consequently, this study also seeks to investigate the methods currently employed by Healthcare Professionals (HCPs) to provide information to stroke patients and their families or caregivers. Additionally, it aims to identify the barriers and facilitators influencing information provision throughout the stroke care continuum from the perspective of HCPs.
Methods: The study took place over two phases. A cross-sectional online survey initially explored the perceptions of HCPs working in stroke care in Ireland and UK. Focus groups interviews were then conducted with HCPs who worked in an acute stroke ward and/or Early Stroke Discharge (ESD) team. Phase one quantitative data was analysed using descriptive and inferential statistics. Qualitative survey data was analysed using content analysis mapped onto the Theoretical Domains Framework (TDF). Phase two interview data were analysed using Braun & Clark’s (2022) six-step Thematic Analysis framework.
Results: The survey was completed by 111 HCPs (64% Ireland:36% UK). Wide variation in methods and terminology was noted. Differences across countries was observed relating to opinions about patient and family satisfaction with current information provision. There was consensus that information be provided at multiple care pathway timepoints and be available in both digital and paper formats.
Phase two consisted of 22 HCPs who took part in one of the four focus groups (acute stroke ward n=19, ESD n=3). Participants included: Allied Health Professionals (n=10), Nursing staff (n=6), Medical doctors (n=3), Pharmacy (n=1), Psychology (n=1) and Medical Social Work (n=1). Findings suggest that a Stroke Passport, as a central source of information, has the potential to empower patients and family/caregivers. Participants offered suggestions regarding the ideal content, format, and timing of the provision of information. There was a general agreement that a Stroke Passport should be digital rather than paper based.
They suggested that issues relating to data protection, longevity of the Stroke Passport, and user buy-in are more challenging with a paper version. Key factors were identified that pose potential obstacles to implementation. This includes a lack of digital infrastructure and the ability of Healthcare Information Systems (HIS) to communicate across systems (interoperability). In addition, the identification of the HCP(s) who would take responsibility for updating the Stroke Passport beyond acute care was considered a necessary component to successful implementation.
Conclusion: The provision of a resource such as a Stroke Passport was considered an important asset to patient care. Our findings emphasise the critical role of co-design in its development to better address the complex needs of stroke patients, improving outcomes, satisfaction, and engagement. However, greater attention to addressing current gaps in our stroke healthcare system, particularly digital infrastructure, and interoperability, during the transition from hospital to home is required prior to implementation of a Stroke Passport.