APC Microbiome Ireland - Journal Articles
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Item Artificial intelligence and endo-histo-omics: new dimensions of precision endoscopy and histology in inflammatory bowel disease(Elsevier Ltd., 2024-07-03) Iacucci, Marietta; Santacroce, Giovanni; Zammarchi, Irene; Maeda, Yasuharu; Del Amor, Rocío; Meseguer, Pablo; Kolawole, Bisi Bode; Chaudhari, Ujwala; Di Sabatino, Antonio; Danese, Silvio; Mori, Yuichi; Grisan, Enrico; Naranjo, Valery; Ghosh, SubrataIntegrating artificial intelligence into inflammatory bowel disease (IBD) has the potential to revolutionise clinical practice and research. Artificial intelligence harnesses advanced algorithms to deliver accurate assessments of IBD endoscopy and histology, offering precise evaluations of disease activity, standardised scoring, and outcome prediction. Furthermore, artificial intelligence offers the potential for a holistic endo-histo-omics approach by interlacing and harmonising endoscopy, histology, and omics data towards precision medicine. The emerging applications of artificial intelligence could pave the way for personalised medicine in IBD, offering patient stratification for the most beneficial therapy with minimal risk. Although artificial intelligence holds promise, challenges remain, including data quality, standardisation, reproducibility, scarcity of randomised controlled trials, clinical implementation, ethical concerns, legal liability, and regulatory issues. The development of standardised guidelines and interdisciplinary collaboration, including policy makers and regulatory agencies, is crucial for addressing these challenges and advancing artificial intelligence in IBD clinical practice and trials.Item In vitro digestibility of bioprocessed brewer’s spent yeast: Demonstrating protein quality and gut microbiome modulation potential(Elsevier Ltd., 2025-01-23) Jaeger, Alice; Nyhan, Laura; Sahin, Aylin W.; Zannini, Emanuele; Meehan, Dara; Li, Junhui; O’Toole, Paul W.; Arendt, Elke K.; Horizon 2020; Science Foundation IrelandWith an ever-increasing global population and dwindling natural resources, a shift towards more sustainable food systems is required. Important aspects to aid in this transition are the reduction of food waste, and a movement towards non-animal protein sources. Brewers spent yeast (BSY) is an abundant by-product of the brewing industry, which is generally regarded as waste, despite its high nutritional value. Previous work has shown that fermentation of BSY with Lactobacillus amylovorus FST 2.11 resulted in changes in composition, functionality, and improved palatability of the processed raw material (PBSY). In this study, in vitro protein digestibility, amino acid bioaccessability, and protein quality of PBSY was explored using the static INFOGEST in vitro model. In vitro protein digestibility of PBSY (73.0 %) was almost two-fold higher than that of CBSY (40.0 %), while PBSY also displayed significantly higher in vitro bioaccessability values for all essential amino acids, except for tryptophan. Investigation of protein quality using the digestible indispensable amino acid score (DIAAS) values and the FAO recommended amino acid scoring pattern for individuals >3 years old showed that the protein quality for CBSY was low (DIAAS of 17.0 %), while PBSY was considered to be of “good” protein quality (DIAAS of 98.2 %). Investigation of the modulation potential of PBSY on the gut microbiome using an in vitro colon model system showed an increase in gut microbiome α-diversity indices and an abundance of beneficial Mediterranean diet-responsive taxa after 24 h. Overall, this study highlights the potential of BSY as raw material for the production of a high-quality food ingredient with potential prebiotic effects, aiding in the reduction food waste and supporting global food systems.Item More than just a number: the gut microbiota and brain function across the extremes of life(Taylor & Francis, 2024) Nuzum, Nathan D.; Deady, Clara; Kittel-Schneider, Sarah; Cryan, John F.; O'Mahony, Siobhain M.; Clarke, Gerard; Science Foundation IrelandUnderstanding the interrelationship between the gut microbiota and host physiology, although still in its relative infancy, has taken important steps forward over the past decade. In the context of brain disorders including those characterized by neurodevelopmental and neurodegenerative changes there have been important advances. However, initially research involved correlational analyses, had limited translational scope, and lacked functional assessments. Thus, largescale longitudinal clinical investigations that assess causation and underlying mechanisms via in depth analysis methods are needed. In neurodegeneration research, strong causal evidence now links the gut microbiome to Alzheimer's (AD), and Parkinson's Disease (PD), as supported by human-to-animal transplantation studies. Longitudinal interventions are being conducted in AD, PD, amyotrophic lateral sclerosis, Huntington's disease, and multiple sclerosis. Neurodevelopmental research has also seen a boon in microbiome-related clinical research including in autism, Attention-deficit/hyperactivity disorder, and schizophrenia, which is confirming prior animal model work regarding the key time-windows in the gut microbiome important for infant cognition. While recent research advances represent important progress, fundamental knowledge gaps and obstacles remain. Knowing how and why the gut microbiome changes at the extremes of life will develop our mechanistic understanding and help build the evidence base as we strive toward counteracting microbial missteps with precision therapeutic interventions.Item T lymphocyte plasticity in chronic inflammatory diseases: The emerging role of the Ikaros family as a key Th17-Treg switch(Elsevier B.V., 2024-12-30) Ramón-Vázquez, Ana; Flood, Peter; Cashman, Thuy Linh; P. Patil; Ghosh, Subrata; Science Foundation IrelandT helper (Th) 17 and regulatory T (Treg) cells are highly plastic CD4+ Th cell subsets, being able not only to actively adapt to their microenvironment, but also to interconvert, acquiring mixed identity markers. These phenotypic changes are underpinned by transcriptional control mechanisms, chromatin reorganization events and epigenetic modifications, that can be hereditable and stable over time. The Ikaros family of transcription factors have a predominant role in T cell subset specification through mechanisms of transcriptional program regulation that enable phenotypical diversification. They are crucial factors in maintaining Th17/Treg balance and therefore, homeostatic conditions in the tissues. However, they are also implicated in pathogenic processes, where their transcriptional repression contributes to the control of autoimmune processes. In this review, we discuss how T cell fate, specifically in humans, is regulated by the Ikaros family and its interplay with additional factors like the Notch signaling pathway, gut microbiota and myeloid-T cell interactions. Further, we highlight how the transcriptional activity of the Ikaros family impacts the course of T cell mediated chronic inflammatory diseases like rheumatoid and psoriatic arthritis, inflammatory bowel disease, systemic lupus erythematosus and multiple sclerosis. We conclude by discussing recently developed therapeutics designed to target Ikaros family members.Item Differential cortical aspartate uptake across the oestrous cycle is associated with changes in gut microbiota in Wistar-Kyoto rats(Elsevier B.V., 2024-12-26) Sajjad, Jahangir; Morael, Jennifer; Melo, Thieza G.; Foley, Tara; Murphy, Amy; Keane, James; Popov, Jelena; Stanton, Catherine; Dinan, Timothy G.; Clarke, Gerard; Cryan, John F.; Collins, James M.; O’Mahony, Siobhain M.; Science Foundation IrelandPain and psychological stress are intricately linked, with sex differences evident in disorders associated with both systems. Glutamatergic signalling in the central nervous system is influenced by gonadal hormones via the hypothalamic–pituitary–adrenal axis and is central in pain research. Emerging evidence supports an important role for the gut microbiota in influencing pain signalling. Here, the functional activity of excitatory amino acid transporters (EAATs) in the anterior cingulate cortex (ACC) and lumbosacral spinal cord of male and female Wistar-Kyoto rats, an animal model of comorbid visceral hypersensitivity and enhanced stress responsivity, was investigated across the oestrous cycle. Correlations between the gut microbiota and changes in the functional activity of the central glutamatergic system were also investigated. EAAT function in the lumbosacral spinal cord was similar between males and females across the oestrous cycle. EAAT function was higher in the ACC of dioestrus females compared to proestrus and oestrus females. In males, aspartate uptake in the ACC positively correlated with Bacteroides, while aspartate uptake in the spinal cord positively correlated with the relative abundance of Lachnospiraceae NK4A136. Positive associations with aspartate uptake in the spinal cord were also observed for Alistipes and Bifidobacterium during oestrus, and Eubacterium coprostanoligenes during proestrus. Clostridium sensu stricto1 was negatively associated with aspartate uptake in the ACC in males and dioestrus females. These data indicate that glutamate metabolism in the ACC is oestrous stage-dependent and that short-chain fatty acid-producing bacteria are positively correlated with aspartate uptake in males and during specific oestrous stages in females.
