TEAGASC - The Agriculture and Food Development Authority

The rapid change in lifestyle and socio-economic improvement has allowed cereals and cereal-based products, including bakery items, to occupy a significant ratio of the daily diet of consumers worldwide. But microbial (yeast, mold, and bacteria) spoilage, oxidation of fats, and degradation of other components like proteins may result in significant economic loss and even pose a threat to public health. Apart from product’s inherent properties, their shelf life, quality, and safety also depends on packaging materials and technologies. Hence, designing technologically effective, economically viable, and consumer-friendly packaging for these essential food commodities is imperative. Appropriate packaging can prevent undesirable food wastage, ensure food safety, and avoid financial losses affecting consumers, manufacturers, retailers, and the entire food supply chain from farm to fork. This chapter studied the functions and properties of the packaging materials commonly used for bakery products. It also highlights the factors affecting products’ shelf-life and intends to present a comprehensive review of the product-specific packaging materials. Furthermore, the advanced packaging system used to extend the shelf life of cereal and cereal-based products and the challenges and future trends in the expansion of advanced packaging in the bakery industry were also discussed. Appropriate packaging materials can effectively delay or prevent microbial contamination, reduce lipid oxidation, and enhance the safety and quality of cereals and cereal-based products.

Whey is produced in huge quantities by the dairy industry as a byproduct, and as non-food leads to serious environmental issues due to its high organic matter content. There has been a lot of research done over the last several decades how to use whey in a more sustainable and cost-effective way. The creation of value-adding goods including whey powders, functional meals, edible films and coatings, lactic acid, alcoholic beverages, sports drinks, and other biochemical, bioplastics, and biofuels is the core objective of sustainable whey management. In recent years, researchers have looked at different ways to use whey in a more affordable and ecologically friendly way, with the main goal of turning undesirable end products into useful materials. It is a source of several bioactive ingredients with various physiological and functional characteristics. It also provides an opportunity to food industries to develop functional foods with potential health benefits. Whey’s active components are advantageous because they offer antibacterial and antiviral activities, boost antioxidant activity, support bone and immune system health, improve athletic performance, and prevent cancer and cardiovascular disease. This chapter describes how to use whey and its components sustainably while using integrated processes and refining techniques to create high-value whey-based products. This is done in accordance with many international initiatives for improved planetary health, such as the EU Green Deal and the Sustainable Development Goals (UN, General Assembly. Transforming our world: The 2030 agenda for sustainable development. 2015).

Microalgae are a rich resource of lipids, proteins, carbohydrates and pigments with nutritional and health benefits. They increasingly find use as ingredients in functional foods and feeds as well as in cosmetics and agricultural products including biostimulants. One of their distinct advantages is their ability to grow on wastewaters and other waste streams, and they are considered an environmentally friendly and cheap method to recover nutrients and remove pollutants from the environment. However, there are limits concerning their applications if grown on certain waste streams. Within, we collate an overview of existing algal applications and current market scenarios for microalgal products as foods and feeds along with relevant legislative requirements concerning their use in Europe and the United States. Microalgal compounds of interest and their extraction and processing methodologies are summarized, and the benefits and caveats of microalgae cultivated in various waste streams and their applications are discussed.

The market has observed a rapid increase in the demand for plant-based foods as an alternative to animal meat products. Technologies such as high-moisture extrusion (HME) have the potential to develop anisotropic structures using alternative protein ingredients. This article discusses the different possible mechanisms responsible for structure formation and the effect of extrusion process parameters and outlines the recent advances in the long cooling dies (LCDs) used for meat alternative development. The role of different protein ingredients and the impact of combining them with other biopolymers were also evaluated. The underlying mechanism behind anisotropic structure formation during HME is a synergistic effect, with substantial dependence on the source of ingredients and their processing background. Formulation including proteins derived from plants, insects, animals, and microalgae with other biopolymers could pave the way to develop structured meat alternatives and fill nutritional interstices. Dynamic or rotating annular gap cooling dies operating at freely controllable shear and static annular gap dies are recent developments and assist to produce layered or fibrous structures. The complex chemical sites created during the HME of plant protein favour flavour and colour retention. This paper summarises the recent information published in the scientific literature and patents, which could further help researchers to fill the present knowledge gaps.

The composition and physicochemical characteristics of short-aged Pecorino Sardo PDO (Protected Designation of Origin) cheese makes it permissive to Listeria monocytogenes growth. The PDO product specification stipulates that this cheese is produced with whole sheep’s milk inoculated with cultures from the area of origin. Therefore, the use of bioprotective cultures for the inhibition of pathogens in PDO cheeses is allowed only if autochthonous microorganisms are used. Furthermore, bioprotective cultures are generally used on the cheese surface to prevent the outgrowth of L. monocytogenes, the application of which can be time-consuming and require specialist technical knowledge. In this study, we examine the direct addition of bioprotective cultures to the cheese vat and compare the activity of a commercial bioprotective culture (Lactiplantibacillus plantarum) and an autochthonous lactic acid bacterium with bioprotective properties (Lactobacillus delbruekii sups. sunkii), for the inhibition of L. monocytogenes in Pecorino Sardo PDO cheese. Three types of Pecorino Sardo PDO cheese were made with bioprotective cultures added directly to the cheese milk along with the starter inoculum: PSA, with the commercial bioprotective culture; PSB, with the autochthonous bioprotective culture; and a CTRL cheese with no bioprotective culture. A challenge test was performed on each of these cheeses by artificially contaminating the cheese surface with L. monocytogenes (2 Log10 CFU/g). Three batches of each cheese type were analyzed to enumerate mesophilic and thermophilic lactic acid bacteria and to investigate the growth potential of L. monocytogenes during manufacturing, at the end of ripening, at the end of shelf-life, and after 180 days from cheese production. Both bioprotective cultures tested in this study showed inhibitory action against the pathogen with 0.3–1.8 Log10 CFU/g (colony-forming unit per gram) reduction levels. The autochthonous organism, L. sunkii, was as effective as the commercially supplied culture, and the addition of the bioprotective cultures to the cheese-making procedure offered protection against L. monocytogenes. The direct addition of bioprotective cultures to the making procedure of Pecorino Sardo PDO cheese is a potentially innovative strategy to improve the safety of this product.

Winter oilseed rape (OSR) is becoming an increasingly popular crop in rotations as it provides a cash crop and reduces the incidence of take-all fungal disease (caused by Gaeumannomyces graminis) in subsequent wheat production. The exact mechanism of this inhibition of fungal pathogens is not fully understood; however, the selective recruitment of bacterial groups with the ability to suppress pathogen growth and reproduction is thought to play a role. Here we examine the effect of tillage practice on the proliferation of microbes that possess the phlD gene involved in the production of the antifungal compound 2,4-diacetylphloroglucinol (2,4-DAPG), in the rhizospheres of both winter oilseed rape and winter wheat grown in rotation over a two-year period. The results showed that conservation strip tillage led to a significantly greater phlD gene copy number, both in the soil and in the roots, of oilseed rape and wheat crops, whereas crop rotation of oilseed rape and wheat did not increase the phlD gene copy number in winter wheat.

Background Septoria tritici blotch caused by Zymoseptoria tritici continues to be one of the most economically destructive diseases of winter wheat in north‐western Europe. Control is heavily reliant on the application of fungicides, in particular those belonging to the azole group. Here we describe the sensitivity of European Z. tritici populations to the novel azole mefentrifluconazole and the analysis of associated mechanisms of resistance. Results A wide range of sensitivity to mefentrifluconazole was observed amongst the Z. tritici collections examined, with strong cross‐resistances also observed between mefentrifluconazole, difenoconazole and tebuconazole. Overall the Irish population displayed the lowest sensitivity to all azoles tested. Further detailed analysis of the Irish population in 2021 demonstrated differences in sensitivity occurred between sampling sites, with these differences associated with the frequencies of key resistance mechanisms (CYP51 alterations and MFS1 promoter inserts linked to overexpression). Under glasshouse conditions reductions in the efficacy of mefentrifluconazole were observed towards those strains exhibiting the lowest in vitro sensitivities. Conclusions This study demonstrates that a large range of sensitivity to mefentrifluconazole exists in European Z. tritici populations. Those strains exhibiting the lowest sensitivity to the azoles tested had the most complex CYP51 haplotypes in combination with the 519 bp insert, associated with enhanced activity of MFS1. The future use of mefentrifluconazole should take these findings into consideration to minimise the selection of these strains. This article is protected by copyright. All rights reserved.

High-throughput DNA sequencing (HTS) was used to study the microbial diversity of commercial traditional Izmir Tulum (IT) and Izmir Brined Tulum (IBT) cheeses from Izmir, Türkiye. Simultaneously, cultivation-dependent methods were used to isolate, identify and characterize bacterial strains displaying probiotic potential. At the phylum level, Firmicutes dominated the microbiota of both cheese types comprising >98% of the population. Thirty genera were observed, with Streptococcus being the most abundant genus and with Streptococcus thermophilus and S. infantarius subsp. infantarius being the most abundant species. Genera, including Bifidobacterium and Chryseobacterium, not previously associated with IT and IBT, were detected. IT cheeses displayed higher operational taxonomic units (OTUs; Richness) and diversity index (Simpson) than IBT cheeses; however, the difference between the diversity of the microbiota of IT and IBT cheese samples was not significant. Three Lacticaseibacillus paracasei strains isolated from IBT cheeses exhibited probiotic characteristics, which included capacity to survive under in vitro simulated gastrointestinal conditions, resistance to bile salts and potential to adhere to HT-29 human intestinal cells. These findings demonstrate that Tulum cheeses harbor bacterial genera not previously reported in this cheese and that some strains display probiotic characteristics.

Simple Summary Methane is a gas that ruminants naturally release during digestion, and it is a significant contributor to global warming. In efforts to reduce the environmental impact of livestock farming, we explored a red macroalga called Bonnemaisonia hamifera. This macroalga was collected from the shores of Sweden and used in an in vitro digestion experiment to evaluate its effects on ruminal fermentation and methane production from dairy cows. The study examined different inclusion levels of the macroalga in grass silage. We noticed an increase in the proportion of propionate in rumen fluid and a reduction in methane production with inclusion of the macroalga. This is important because reducing methane emissions from ruminants would be beneficial for the environment. B. hamifera exhibited antioxidant properties, which could be beneficial for the animals. In conclusion, this study shows that B. hamifera from Sweden has the potential to make livestock farming more eco-friendly by decreasing methane gas emissions. Abstract Researchers have been exploring seaweeds to reduce methane (CH4) emissions from livestock. This study aimed to investigate the potential of a red macroalga, B. hamifera, as an alternative to mitigate CH4 emissions. B. hamifera, harvested from the west coast of Sweden, was used in an in vitro experiment using a fully automated gas production system. The experiment was a randomized complete block design consisting of a 48 h incubation that included a control (grass silage) and B. hamifera inclusions at 2.5%, 5.0%, and 7.5% of grass silage OM mixed with buffered rumen fluid. Predicted in vivo CH4 production and total gas production were estimated by applying a set of models to the gas production data and in vitro fermentation characteristics were evaluated. The results demonstrated that the inclusion of B. hamifera reduced (p = 0.01) predicted in vivo CH4 and total gas productions, and total gas production linearly decreased (p = 0.03) with inclusion of B. hamifera. The molar proportion of propionate increased (p = 0.03) while isovalerate decreased (p = 0.04) with inclusion of B. hamifera. Chemical analyses revealed that B. hamifera had moderate concentrations of polyphenols. The iodine content was low, and there was no detectable bromoform, suggesting quality advantages over Asparagopsis taxiformis. Additionally, B. hamifera exhibited antioxidant activity similar to Resveratrol. The findings of this study indicated that B. hamifera harvested from temperate waters of Sweden possesses capacity to mitigate CH4 in vitro.

Marine algae are sources of bioactive components with defensive properties of great value against microbial infections. This study investigated the bioactivity of extracts from brown algae Fucus vesiculosus against rotavirus, the worldwide leading cause of acute gastroenteritis in infants and young children. Moreover, one of the extracts was tested against four foodborne bacteria: Campylobacter jejuni, Escherichia coli, Salmonella Typhimurium, and Listeria monocytogenes, and the non-pathogenic: E. coli K12. In vitro tests using MA104 cells revealed that both whole algae extracts and crude fucoidan precipitates neutralized rotavirus in a dose-responsive manner. The maximum neutralization activity was observed when the rotavirus was incubated with 100 μg mL−1 of the hydrochloric acid-obtained crude fucoidan (91.8%), although crude fucoidan extracted using citric acid also demonstrated high values (89.5%) at the same concentration. Furthermore, molecular weight fractionation of extracts decreased their antirotaviral activity and high molecular weight fractions overall exhibited higher activity compared to those of lower molecular weight. A seaweed extract with high antirotaviral activity was also found to inhibit the growth of C. jejuni, S. Typhimurium, and L. monocytogenes at a concentration of 0.2 mg mL−1. Overall, this study expands the current knowledge regarding the antimicrobial mechanisms of action of extracts from F. vesiculosus.

Common Alder (Alnus glutinosa (L.) Gaertn.) is a tree species native to Ireland and Europe with high economic and ecological importance. The presence of Alder has many benefits including the ability to adapt to multiple climate types, as well as aiding in ecosystem restoration due to its colonization capabilities within disturbed soils. However, Alder is susceptible to infection of the root rot pathogen Phytophthora alni, amongst other pathogens associated with this tree species. P. alni has become an issue within the forestry sector as it continues to spread across Europe, infecting Alder plantations, thus affecting their growth and survival and altering ecosystem dynamics. Beneficial microbiota and biocontrol agents play a crucial role in maintaining the health and resilience of plants. Studies have shown that beneficial microbes promote plant growth as well as aid in the protection against pathogens and abiotic stress. Understanding the interactions between A. glutinosa and its microbiota, both beneficial and pathogenic, is essential for developing integrated management strategies to mitigate the impact of P. alni and maintain the health of Alder trees. This review is focused on collating the relevant literature associated with Alder, current threats to the species, what is known about its microbial composition, and Common Alder–microbe interactions that have been observed worldwide to date. It also summarizes the beneficial fungi, bacteria, and biocontrol agents, underpinning genetic mechanisms and secondary metabolites identified within the forestry sector in relation to the Alder tree species. In addition, biocontrol mechanisms and microbiome-assisted breeding as well as gaps within research that require further attention are discussed.

To achieve national and global air quality and climate change objectives, the agricultural sector increasingly requires dependable decision support tools for gaseous emissions at the farm level. We evaluated thirteen greenhouse gas (GHG)-based decision support systems (DSS), considering criteria such as not only the accessibility, user-friendliness, stakeholder involvement, sustainability methodology, and modeling aspects, but also the input parameters and outputs provided, all crucial for decision making. While most DSSs provide information for facilitating their use, only four are suitable for inexperienced users, and stakeholder participation in DSS development is infrequent. The dominant methodology for farm-level GHG estimation is IPCC 2006, with quantitative models primarily used for indicators’ assessment. Scenario and contribution analyses are the prevailing decision support approaches. Soil, crop, and fertilizer types are the most implemented non-livestock-related inputs, while climate- and feed-related costs are the least required. All DSSs assess farm-level mitigation measures, but less than half offer sustainability consultation. These tools promote environmental sustainability by evaluating mitigation strategies, disseminating farm sustainability information, and guiding sustainable farm management. Yet, challenges such as disparate estimation methods, result variations, comparison difficulties, usability concerns, steep learning curves, the lack of automation, the necessity for multiple tools, the limited integration of the results, and changing regulations hinder their wider adoption.

Background Reproduction is a key feature of the sustainability of a species and thus represents an important component in livestock genetic improvement programs. Most reproductive traits are lowly heritable. In order to gain a better understanding of the underlying genetic basis of these traits, a genome-wide association was conducted for age at first calving (AFC), first inter-calving period (ICP) and scrotal circumference (SC) within the South African Bonsmara breed. Phenotypes and genotypes (120,692 single nucleotide polymorphisms (SNPs) post editing) were available on 7,128 South African Bonsmara cattle; the association analyses were undertaken using linear mixed models. Results Genomic restricted maximum likelihood analysis of the 7,128 SA Bonsmara cattle yielded genomic heritability’s of 0.183 (SE = 0.021) for AFC, 0.207 (SE = 0.022) for ICP and 0.209 (SE = 0.019) for SC. A total of 16, 23 and 51 suggestive ( P ≤ 4 × 10 ⁻⁶ ) SNPs were associated with AFC, ICP and SC, while 11, 11 and 44 significant ( P ≤ 4 × 10 ⁻⁷ ) SNPs were associated with AFC, ICP and SC respectively. A total of 11 quantitative trait loci (QTL) and 11 candidate genes were co-located with these associated SNPs for AFC, with 10 QTL harbouring 11 candidate genes for ICP and 41 QTL containing 40 candidate genes for SC. The QTL identified were close to genes previously associated with carcass, fertility, growth and milk-related traits. The biological pathways influenced by these genes include carbohydrate catabolic processes, cellular development, iron homeostasis, lipid metabolism and storage, immune response, ovarian follicle development and the regulation of DNA transcription and RNA translation. Conclusions This was the first attempt to study the underlying polymorphisms associated with reproduction in South African beef cattle. Genes previously reported in cattle breeds for numerous traits bar AFC, ICP or SC were detected in this study. Over 20 different genes have not been previously reported in beef cattle populations and may have been associated due to the unique genetic composite background of the SA Bonsmara breed.

The family of calgranulins includes S100A8 (calgranulin A), S100A9 (calgranulin B), which can appear as a heterodimer known as S100A8/A9 or calprotectin, and S100A12 (calgranulin C). These proteins are related to different inflammatory conditions, immune-mediated diseases, and sepsis and are considered biomarkers of potential interest. This study aims to evaluate if S100A8/A9 and A12 could change in pigs with diarrhea due to E. coli and to compare the changes of S100A8/A9 and A12 with other analytes in order to explore the possible causes or mechanisms involved. For this purpose, a panel integrated by analytes related to inflammation (haptoglobin, inter-alpha trypsin inhibitor 4 (ITIH4), and total protein); immune system (adenosine deaminase, ADA); stress (alpha-amylase); tissue damage (lactate and lactate dehydrogenase (LDH)); sepsis (aldolase) and redox status (ferric-reducing ability of saliva (FRAS) and advanced oxidation protein products (AOPP)) was evaluated. S100A8/A9 and A12 and the other analytes measured in this study showed increases in the saliva of pigs with diarrhea due to E. coli. S100A8/A9 and/or A12 showed a significant correlation of different magnitude with some of the other analytes evaluated. Further studies should be conducted to gain knowledge about the possible practical applications as biomarkers of the measurements of S100A8/A9 and A12 in the saliva of pigs.

Background Streptococcus suis (S. suis) is a Gram-positive bacteria that infects pigs causing meningitis, arthritis, pneumonia, or endocarditis. This increases the mortality in pig farms deriving in severe economic losses. The use of saliva as a diagnostic fluid has various advantages compared to blood, especially in pigs. In this study, it was hypothesized that saliva could reflect changes in different biomarkers related to stress, inflammation, redox status, and muscle damage in pigs with S. suis infection and that changes in these biomarkers could be related to the severity of the disease. Results A total of 56 growing pigs from a farm were selected as infected pigs (n = 28) and healthy pigs (n = 28). Results showed increases in biomarkers related to stress (alpha-amylase and oxytocin), inflammation (haptoglobin, inter-alpha-trypsin inhibitor heavy chain 4 (ITIH4), total protein, S100A8-A9 and S100A12), redox status (advanced oxidation protein producs (AOPP)) and muscle damage (creatine kinase (CK), CK-MB, troponin I, lactate, aspartate aminotransferase, and lactate dehydrogenase). An increase in adenosine deaminase (ADA), procalcitonin, and aldolase in infected animals were also observed, as previously described. The grade of severity of the disease indicated a significant positive correlation with total protein concentrations, aspartate aminotransferase, aldolase, and AOPP. Conclusions This report revealed that S. suis infection caused variations in analytes related to stress, inflammation, redox status, and muscle damage in the saliva of pigs and these can be considered potential biomarkers for this disease.

Inflammation, hypertension, and negative heart health outcomes including cardiovascular disease are closely linked but the mechanisms by which inflammation can cause high blood pressure are not yet fully elucidated. Cyclooxygenase (COX) enzymes play a role in pain, inflammation, and hypertension development, and inhibition of these enzymes is currently of great interest to researchers and pharmaceutical companies. Non-steroidal anti-inflammatory drugs are the drug of choice in terms of COX inhibition but can have negative side effects for consumers. Functional food ingredients containing cyclooxygenase inhibitors offer a strategy to inhibit cyclooxygenases without negative side effects. Several COX inhibitors have been discovered, to date, from marine and other resources. We describe here, for the first time, the generation and characterization of a bioactive hydrolysate generated using Viscozyme® and Alcalase from the red microalga Porphyridium sp. The hydrolysate demonstrates in vitro COX-1 inhibitory activity and antihypertensive activity in vivo, assessed using spontaneously hypertensive rats (SHRs). Peptides were identified and sequenced using MS and assessed using an in silico computational approach for potential bioactivities. The peptides predicted to be bioactive, including GVDYVRFF, AIPAAPAAPAGPKLY, and LIHADPPGVGL were chemically synthesized and cyclooxygenase inhibition was confirmed. Peptides AIPAAPAAPAGPKLY and LIHADPPGVGL had COX-1 IC50 values of 0.2349 mg/mL (0.16 µM) and 0.2193 mg/mL (0.2 µM), respectively. The hydrolysate was included in a food carrier (jelly candies) and an antihypertensive effect was observed in SHRs.

Purpose: Farming is a high-pressure occupation. Populations of farmers face significant health risks, including injury, mental illness, and in some cases, heavy alcohol use. However, there is little research on farmers' use of substances beyond alcohol. This study examines factors relating to Irish farmers' disordered alcohol and substance use. Methods: In accordance with STROBE guidelines for cross-sectional research and reporting, we examined disordered alcohol and substance use in 351 Irish farmers using the Alcohol Use Disorders Identification Tool (AUDIT) and Drug Use Disorders Identification Tool (DUDIT). Findings: While 28% of farmers did not drink, 40% of those who did drink exceeded the AUDIT threshold for disordered use. Similarly, while 95% of farmers did not use substances, 78% of farmers who did use substances exceeded the DUDIT threshold for disordered use. Age was the most important risk factor for disordered alcohol and substance use and correlated with other main risk factors: lower income, no children, part-time farmer, and full-time off-farm roles. Disordered drinking was highest in farmers engaged in full-time education. Conclusions: This population of Irish farmers report broadly healthy alcohol and substance use behaviors. Irish farmers may serve as a model group whose strengths can be utilized in interventions within and beyond the Irish farming community. Our results confirm the importance of analyzing demographic factors in farmers' drinking and identify younger farmers as especially at-risk for harmful alcohol and substance use.

Grass uptake and phytoaccumulation factors of N-(n-butyl) thiophosphoric triamide (NBPT) and dicyandiamide (DCD) were quantified. Following the application of urea fertilizer treated with the inhibitors in Irish grassland, grass samples were collected at 5, 10, 15, 20, and 30 day time intervals following five application cycles. Uptake of NBPT by grass was below the limit of quantitation of the analytical method (0.010 mg NBPT kg⁻¹). Dicyandiamide concentrations in grass ranged from 0.004 to 28 mg kg⁻¹ with the highest concentrations measured on days 5 and 10. A reducing trend in concentration was found after day 15. The DCD phytoaccumulation factor was ranged from 0.004% to 1.1% showing that DCD can be taken up by grass at low levels when co-applied with granular urea. In contrast, NBPT was not detected indicating that grass uptake is unlikely when co-applied with granular urea fertilizer. The contrasting results are likely due to very different longevity of DCD and NBPT along with the much lower rate of NBPT, which is used compared with DCD.