CORA
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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Translating environmentally optimized agri-food systems into diets: A case study
(Elsevier B.V., 2026-06-13) Cardinaals, Renee; Maindl, Thomas; Huppertz, Thom; Van Zanten, Hannah
Food system optimization models that allow for assessing food system redesigns in line with sustainability objectives often lack a translation from crop and livestock production into food products that make up diets. Not making the translation from commodities into food products could limit the assessment of whether redesigned agri-food systems can cater to culturally adapted diets, as well as an accurate health assessment thereof. To explore the methodological aspects that should be considered when bridging the gap between food system optimization and healthy diets, we used results from the Circular Food Systems (CiFoS) model in a case study. CiFoS results consisted of commodities (n=154) produced in a redesigned European agri-food system which were mapped to food products (n=602) that are currently included in European diets. Two different diet scenarios were explored that translated CiFoS commodities into diets that: (1) matched the current consumption, (2) could be considered to be healthier and maximized the use of available commodities. Results demonstrated that applying the objective to match current diets, the available commodities could only partially be translated into product-level diets, and more than half of the total available commodities was left unused. However, maximizing the use of commodities resulted in diets that could be considered healthier than, but also deviating considerably from, current diets. This study highlights relevant methodological aspects and emphasizes the need to look beyond commodity-level diets when optimizing agri-food systems for sustainable healthy diets as a translation into food products allows for better evaluation of these diets.
A systematic review to reassess the formula for early life growth
(Elsevier B.V., 2026-06-11) Nilaweera, Kanishka N.; van Sinderen, Douwe; Cotter, Paul D.
Mammals have species-specific adaptations to sustain growth during the suckling stage of life. These include species-specific milk composition and associated whey protein (WP)-to-casein (CN) ratio. Consuming milk (proteins) from other species may therefore cause different growth outcomes during early life. This systematic review examined the effect of intake of feeds with a high bovine WP-to-CN ratio on growth outcomes in infants, piglets, and rodent pups, focusing on milk and/or protein intake, body weight, and gut morphology and its cellular activity. The relevant studies were identified from PUBMedR using the keywords, “whey,” “infant formula,” and “growth” for infant studies and “whey” and “suckling stage” for animal studies. Of the original research articles reviewed (280 in total), 16 infant (with 3207 participants) and 13 animal studies met the imposed inclusion criteria and were independently reviewed by the authors. Data show that consumption of infant formula with bovine whey-to-casein ratio equal to or exceeding that of human milk (60:40), and with proteins supplying ≥8% of total energy, is associated with a discordance between energy intake and weight gain, consistent with net nutrient loss. Data from porcine and rodent models further indicate that the nutrient loss occurs because of reduced nutrient absorption through the gut, and that the effect appears to be driven primarily by bovine WP. We present further evidence supporting a role for gut microbiota in mediating the reduced nutrient absorption and that hydrolysis of bovine WP mitigates, at least some of, this effect and increases growth compared with formulas with intact proteins. We envisage that these findings, based on proteins sourced from cow’s milk, will inform improvements in infant formula that increases nutrient absorption and support healthier growth using a protein content much lower than the current regulatory threshold of 1.8 g/100 kcal.
Impact of management intensity of agricultural systems and soil intrinsic characteristics on soil organic carbon stocks
(Elsevier B.V., 2026-10-15) Castellón Meyrat, Alex; O’Sullivan, Lilian; Holloway, Paul; Wall, David; Bondi, Giulia
Enhancing carbon in soils is crucial for improving soil health and building sustainable agroecosystems. Inherent SOC stocks are site-specific and vary due to complex interactions between climate, soils, land use, and management practices. However, the coupled effects of these factors on SOC dynamics are not fully understood. This research aimed to evaluate the impact of different management regimes and intrinsic soil characteristics on SOC stocks and identify pathways that can boost carbon sequestration in agricultural soils. This study relied on data of 143 soil profiles distributed across the south of Ireland. Each site was sampled at four depths (0–15, 15–30, 30–45, and 45–60 cm) and characterized according to the land use and management practices implemented over the past five years. A Regression Tree (RT) model was employed to estimate the single and combined contribution of key soil properties and management practices on SOC stocks. Overall, intrinsic soil characteristics, especially the presence of humic layers and clay, are decisive to determine the SOC storage potential in soils. Land use and management practices primarily impact the top 15 cm, and their accumulated effect (e.g. stocking rates in grassland systems) can shift SOC stocks trends over time. Finally, the heterogeneity in subsoils controls the variability of SOC stocks in depth. The outcomes of this study can help tailor carbon farming strategies to boost carbon sequestration accounting for specific soil conditions.
Establishing experimental parameters for biphasic transfer in vitro lipolysis model
(Elsevier B.V., 2026-07-10) Kirschbaum, Hannah S.; Jede, Christian; Koehl, Laura J.; Kuentz, Martin; Holm, René; Griffin, Brendan T.; Blechar, Johannes A.; ÓDwyer, Patrick J.
Lipid-based–formulations (LBFs) are widely used to improve oral bioavailability of poorly water–soluble drugs. Despite their widespread use in predicting formulation performance, standard in vitro lipolysis assays often lack an absorptive sink and fail to capture the transition from gastric to intestinal environments, thereby reducing their predictive relevance for in vivo outcomes. The aim of this study was to develop a biphasic in vitro lipolysis model incorporating an absorptive sink. This might offer the potential to increase the predictive power of in vitro digestion models in the future. In this model, the absorptive sink was provided by a decanol layer, and to simulate gastrointestinal transit, two dynamic pH–transition approaches were employed: a biphasic GI–transfer model and a biphasic pH–shift model. Using nilotinib–loaded LBFs, the study established conditions for this biphasic system and examined how media composition and lipase source influence drug concentrations during formulation dispersion, digestion, and partitioning into the organic sink. The results showed that digestion experiments conducted with either porcine pancreatin or Palatase® 20000 L increased the concentration of nilotinib in the aqueous digestion medium, which correspondingly reduced partitioning of the drug into the decanol layer. For the readily dispersible Type III LBF in the biphasic GI–transfer setup, nilotinib permeation into the decanol layer decreased compared with a lipid–free control, likely due to improved drug solubilization in the aqueous digestion phase. In contrast, the poorly dispersible Type I LBF was better suited to the biphasic pH–shift setup, but it showed higher drug levels in the decanol layer, reflecting rapid partitioning of lipids—and associated crystalline drug—into the organic phase. Overall, this study establishes suitable conditions for evaluating the lipolysis of LBFs during a dynamic pH transition in the presence of an absorptive sink. This advanced approach provides additional insight to explore digestion–mediated and/or pH–mediated supersaturation during digestion of LBFs.
Probiotic human study design and reporting (PRODARE): Recommendations to improve research practice
(Elsevier B.V., 2026-01-01) Szajewska, Hania; Benninga, Marc; Chatonidi, Georgia; Costabile, Adele; Lane, Jonathan; van Loo-Bouwman, Carolien A.; Mersh, Cath; Morales, Patricia Sanz; Walton, Gemma; Collado, Maria Carmen; Francavilla, Ruggiero; Fulling, Christine; Holbech Jensen, Benjamin Anderschou; Pascual, David Perez; Ross, Paul R.; van den Akker, Chris H.P.; Vandenplas, Yvan; Vidra, Nikoletta; Ouwehand, Arthur C.
The PRObiotic human study Design And REporting recommendations provide a structured framework for designing and reporting human studies with probiotics, addressing challenges related to product viability. Five main study types are identified. Exploratory studies are early-phase, first-in-human investigations designed to evaluate effects or generate hypotheses and require specification of strain, dose, stability, and assessment of acceptance and adverse events. Pilot studies assess the feasibility of protocols and logistics before larger trials, with clearly defined objectives, compliance measures, and data management plans. Randomized controlled trials represent the reference standard for evaluating efficacy and safety and include the use of core outcome sets, blinding procedures, and adherence monitoring. Real-world studies evaluate effectiveness outside controlled research settings and require detailed protocols, comprehensive data capture, and predefined approaches for handling inconsistencies. Observational cohort studies examine associations between probiotic exposure and outcomes over time, with clearly defined endpoints, cohort selection criteria, and analysis plans. Across all study types, probiotic-specific considerations include strain characterization and sequencing, verification of identity, purity, viability, antimicrobial resistance, minimization of confounding factors, management of cross-contamination, and consistency of dosage. These recommendations aim to enhance study quality and reporting and to guide researchers in selecting study designs appropriate to their objectives.