The core objective of the Food Biosciences Department is to engage in advanced research and technology development in support of the Irish Agri-Food industry sector. Activities fall into three research areas: Food for Health; Cheese Microbiology and Biochemistry and Milk and Product Quality.

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Food Biosciences

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  • High-Pressure Processing on Whole and Peeled Potatoes: Influence on Polyphenol Oxidase, Antioxidants, and Glycaemic Indices

    Tsikrika, Konstantina; Muldoon, Aine; O'Brien, Nora, M.; Rai, Dilip; Department of Agriculture, Food and the Marine; 17/F/299 (Multidisciplinary Digital Publishing Institute, 2021-10-13)
    Polyphenol oxidase (PPO) inactivation in five whole and peeled Irish potato cultivars was investigated using high-pressure processing (HPP) at 400 MPa and 600 MPa for 3 min. PPO activity was significantly lower in most of the HPP-treated samples, while the highest PPO inactivation was observed after HPP at 600 MPa. No significant (p > 0.05) changes were observed on the total phenolic content and antioxidant activity of all the HPP-treated potatoes. Regarding individual phenolic acids, chlorogenic acid was decreased significantly (p < 0.05) in all studied varieties with a concomitant increase (p < 0.05) in caffeic and quinic acid. Similarly, ferulic acid was also increased (p < 0.05) in all studied varieties after the HPP treatment, while there was a variation in rutin and 4-coumaric acid levels depending on the cultivar and the sample type. Anthocyanins in the coloured whole potato varieties (i.e., Kerr’s Pink and Rooster), tentatively identified as pelargonidin-O-ferulorylrutinoside-O-hexoside and pelargonidin-O-rutinoside-O-hexoside, also exhibited significantly (p < 0.05) higher levels in the HPP-treated samples as opposed to those untreated. Glycaemic indices of the potatoes treated with HPP did not differ with the corresponding untreated cultivars.
  • Migration of Cefquinome Antibiotic Residues from Milk to Dairy Products

    Di Rocco, Melissa; Scollard, Jonathan; Sayers, Riona; Furey, Ambrose; Danaher, Martin; Jordan, Kieran; Lourenco, Antonio; Department of Agriculture, Food, and the Marine; 13/F/484 (Multidisciplinary Digital Publishing Institute, 2021-11-19)
    The aim of this study was to investigate the distribution of cefquinome in different dairy products during the processing of naturally contaminated milk or spiked milk. The analysis of cefquinome residues in milk, skimmed milk, buttermilk, whey, cream, butter, curd, and cheese samples was performed using a water:acetonitrile solvent extraction and C18 dispersive solid-phase extraction (d-SPE) clean-up, followed by ultrahigh-performance liquid chromatography coupled with tandem mass spectrometry (UHPLC–MS/MS) determination. The target concentration of cefquinome was achieved in the spiked milk (100 µg kg−1). During its processing, the antibiotic migrated primarily with the skimmed milk as opposed to cream (ratios of 3.6:1 and 2.8:1 for experiments A and B, respectively), and with the buttermilk during butter manufacture (ratios of 6.9:1 and 4.6:1), but was equal in the curd and whey during the manufacture of cheese. In the milk collected from treated animals, the measured concentration of cefquinome was considerably high (approx. 5000 µg kg−1). The results obtained from the dairy products were similar to those obtained in the spiked study (ratios of 8.2:1 and 3.1:1 for experiments A and B, respectively, during the separation of skimmed milk and cream; 6.0:1 and 5.0:1 for A and B, respectively, during the separation of buttermilk and butter). However, during cheesemaking, cefquinome migrated with the whey after cutting the curd, with ratios of 0.54:1 and 0.44:1 for experiments A and B, respectively. The difference in the migration of cefquinome between curd and whey in spiked and animal studies is probably due to the different concentration levels in the two different experiments. The results of this study showed that, in dairy products manufactured from milk containing cefquinome residues, the drug migrated primarily with the high-water-containing fractions.
  • Rehydration Properties of Whey Protein Isolate Powders Containing Nanoparticulated Proteins

    Guralnick, Jacob R.; Panthi, Ram R.; Cenini, Valeria L.; Mishra, Vinay S. N.; O’Hagan, Barry M. G.; Crowley, Shane V.; O’Mahony, James A.; Irish Department of Agriculture, Food and the Marine; Department of Agriculture, Environment and Rural Affairs in Northern Ireland; DAIRYDRY 15-F-679 (Multidisciplinary Digital Publishing Institute, 2021-10-27)
    The rehydration properties of original whey protein isolate (WPIC) powder and spray-dried WPI prepared from either unheated (WPIUH) or nanoparticulated WPI solutions were investigated. Nanoparticulation of whey proteins was achieved by subjecting reconstituted WPIC solutions (10% protein, w/w, pH 7.0) to heat treatment at 90 °C for 30 s with no added calcium (WPIH) or with 2.5 mM added calcium (WPIHCa). Powder surface nanostructure and elemental composition were investigated using atomic force microscopy and X-ray photoelectron spectroscopy, followed by dynamic visualisation of wetting and dissolution characteristics using environmental scanning electron microscopy. The surface of powder particles for both WPIUH and WPIC samples generally appeared smooth, while WPIH and WPIHCa displayed micro-wrinkles with more significant deposition of nitrogen and calcium elements. WPIH and WPIHCa exhibited lower wettability and solubility performance than WPIUH and WPIC during microscopic observation. This study demonstrated that heat-induced aggregation of whey proteins, in the presence or absence of added calcium, before drying increases aggregate size, alters the powder surface properties, consequently impairing their wetting characteristics. This study also developed a fundamental understanding of WPI powder obtained from nanoparticulated whey proteins, which could be applied for the development of functional whey-based ingredients in food formulations, such as nanospacers to modulate protein–protein interactions in dairy concentrates.
  • Changes to the Oligosaccharide Profile of Bovine Milk at the Onset of Lactation

    Quinn, Erin M.; O'Callaghan, Tom F.; T. Tobin, John; Murphy, John Paul; Sugrue, Katie; Slattery, Helen; O'Donovan, Michael; Hickey, Rita M.; Teagasc (Multidisciplinary Digital Publishing Institute, 2020-12-01)
    Numerous bioactive components exist in human milk including free oligosaccharides, which represent some of the most important, and provide numerous health benefits to the neonate. Considering the demonstrated value of these compounds, much interest lies in characterising structurally similar oligosaccharides in the dairy industry. In this study, the impacts of days post-parturition and parity of the cows on the oligosaccharide and lactose profiles of their milk were evaluated. Colostrum and milk samples were obtained from 18 cows 1–5 days after parturition. Three distinct phases were identified using multivariate analysis: colostrum (day 0), transitional milk (days 1–2) and mature milk (days 3–5). LS-tetrasaccharide c, lacto-N-neotetraose, disialyllacto-N-tetraose, 3’-sial-N-acetyllactosamine, 3’-sialyllactose, lacto-N-neohexaose and disialyllactose were found to be highly affiliated with colostrum. Notably, levels of lactose were at their lowest concentration in the colostrum and substantially increased 1-day post-parturition. The cow’s parity was also shown to have a significant effect on the oligosaccharide profile, with first lactation cows containing more disialyllacto-N-tetraose, 6’-sialyllactose and LS-tetrasaccharide compared to cows in their second or third parity. Overall, this study identifies key changes in oligosaccharide and lactose content that clearly distinguish colostrum from transitional and mature milk and may facilitate the collection of specific streams with divergent biological functions.
  • Lactobacillus rhamnosus GG soluble mediators ameliorate early life stress-induced visceral hypersensitivity and changes in spinal cord gene expression

    McVey Neufeld, Karen-Anne; Strain, Conall R.; Pusceddu, Matteo M.; Waworuntu, Rosaline V.; Manurung, Sarmauli; Gross, Gabriele; M. Moloney, Gerry; Hoban, Alan E.; Murphy, Kiera; STANTON, CATHERINE; et al. (Portland Press Ltd., 2020-11-23)
    Visceral hypersensitivity is a hallmark of many functional and stress-related gastrointestinal disorders, and there is growing evidence that the gut microbiota may play a role in its pathophysiology. It has previously been shown that early life stress-induced visceral sensitivity is reduced by various probiotic strains of bacteria (including Lactobacillus rhamnosus GG (LGG)) alone or in combination with prebiotic fibres in rat models. However, the exact mechanisms underpinning such effects remain unresolved. Here, we investigated if soluble mediators derived from LGG can mimic the bacteria’s effects on visceral hypersensitivity and the microbiota–gut–brain axis. Rats were exposed to maternal separation (MS) from postnatal days 2–12. From weaning onwards both non-separated (NS) and MS offspring were provided drinking water with or without supplementation of standardized preparations of the LGG soluble mediators (LSM). Our results show that MS led to increased visceral sensitivity and exaggerated corticosterone plasma levels following restraint stress in adulthood, and both of these effects were ameliorated through LSM supplementation. Differential regulation of various genes in the spinal cord of MS versus NS rats was observed, 41 of which were reversed by LSM supplementation. At the microbiota composition level MS led to changes in beta diversity and abundance of specific bacteria including parabacteroides, which were ameliorated by LSM. These findings support probiotic soluble mediators as potential interventions in the reduction of symptoms of visceral hypersensitivity.
  • The gut microbiome influences the bioavailability of olanzapine in rats

    Cussotto, Sofia; Walsh, Jacinta; Golubeva, Anna V.; Zhdanov, Alexander V.; Strain, Conall R.; Fouhy, Fiona; STANTON, CATHERINE; Dinan, Timothy G.; Hyland, Niall P.; Clarke, Gerard; et al. (Elsevier BV, 2021-03-11)
    Background: The role of the gut microbiome in the biotransformation of drugs has recently come under scrutiny. It remains unclear whether the gut microbiome directly influences the extent of drug absorbed after oral administration and thus potentially alters clinical pharmacokinetics. Methods: In this study, we evaluated whether changes in the gut microbiota of male Sprague Dawley rats, as a result of either antibiotic or probiotic administration, influenced the oral bioavailability of two commonly prescribed antipsychotics, olanzapine and risperidone. Findings: The bioavailability of olanzapine, was significantly increased (1.8-fold) in rats that had undergone antibiotic-induced depletion of gut microbiota, whereas the bioavailability of risperidone was unchanged. There was no direct effect of microbiota depletion on the expression of major CYP450 enzymes involved in the metabolism of either drug. However, the expression of UGT1A3 in the duodenum was significantly downregulated. The reduction in faecal enzymatic activity, observed during and after antibiotic administration, did not alter the ex vivo metabolism of olanzapine or risperidone. The relative abundance of Alistipes significantly correlated with the AUC of olanzapine but not risperidone. Interpretation: Alistipes may play a role in the observed alterations in olanzapine pharmacokinetics. The gut microbiome might be an important variable determining the systemic bioavailability of orally administered olanzapine. Additional research exploring the potential implication of the gut microbiota on the clinical pharmacokinetics of olanzapine in humans is warranted.
  • Shared and non-shared sIgA-coated and uncoated bacteria in intestine of mother-infant pairs

    Ding, Mengfan; Chen, Haiqin; Yu, Renqiang; Ross, R. Paul; STANTON, CATHERINE; Zhang, Hao; Yang, Bo; Chen, Wei; National Key R&D Program of China; National Natural Science Foundation of China; et al. (Research Square Platform LLC, 2022-04-20)
    Background The infant gut microbiota is critical for promoting and maintaining early life health. Bacteria coated by secretory immunoglobulin A (sIgA) may help commensal bacteria colonize the gastrointestinal tract. The study aimed to analyze the composition of sIgA-coated and sIgA-uncoated bacterial communities at genus level, and lactobacilli and bifidobacterial communities at species level in human breast milk (HBM), infant, and maternal feces. Results Eleven pregnant women were recruited successfully. HBM, infant feces during colostrum, transition, and mature stages, and maternal feces within the mature stage were collected. sIgA-coated and sIgAuncoated bacteria were separated with magnetic-activated cell sorting. Then 16S rRNA sequencing, bifidobacterial groEL gene sequencing, and lactobacilli groEL gene sequencing were performed to analyze the bacterial community. The richness of sIgA-coated bacteria was significantly higher than that of sIgA-uncoated bacteria in HBM. PCoA revealed that the compositions of sIgA-coated and sIgAuncoated bacteria were different among HBM, infant and maternal feces. The dominant sIgA-coated bacteria in those samples were Escherichia/shigella and the dominant sIgA-uncoated bacteria was Pseudomonas. Higher relative abundance of sIgA-uncoated Bifidobacterium was found in the three lactation stages in infant feces compared to the corresponding HBM, and a higher relative abundance of sIgA-uncoated Faecalibacterium was found in maternal feces compared to HBM and infant feces. For the bifidobacterial community, PCoA analysis revealed a significantly different Bifidobacterium composition only in the sIgA-uncoated segments of infant feces and maternal feces. sIgA-coated and sIgA-uncoated B. longum subsp. infantis and B. pseudocatenulatum was dominant in infant feces and maternal feces, respectively. Additionally, the relative abundance of sIgA-uncoated B. longum subsp. infantis was significantly higher in infant feces compared to that in maternal feces. For the Lactobacillus community, the composition was significantly different in infant and maternal feces, while at species level, L. paragasseri and L. mucosae were dominant in infant and maternal feces, respectively. Conclusion HBM, infant, and maternal feces showed distinct diversity and composition of both sIgA-coated and sIgAuncoated bacteria at genus level. Infant and maternal feces showed similar diversity and similar composition of Bifidobacterium at species level. The same Bifidobacterium species could be detected both in sIgA-coated and sIgA-uncoated form
  • Bifidobacterium longum counters the effects of obesity: Partial successful translation from rodent to human

    Schellekens, Harriët; Torres-Fuentes, Cristina; van de Wouw, Marcel; Long-Smith, Caitriona M.; Mitchell, Avery; Strain, Conall; Berding, Kirsten; Bastiaanssen, Thomaz, F. S.; Rea, Kieran; Golubeva, Anna V.; et al. (Elsevier, 2021-01-31)
    BackgroundThe human gut microbiota has emerged as a key factor in the development of obesity. Certain probiotic strains have shown anti-obesity effects. The objective of this study was to investigate whether Bifidobacterium longum APC1472 has anti-obesity effects in high-fat diet (HFD)-induced obese mice and whether B. longum APC1472 supplementation reduces body-mass index (BMI) in healthy overweight/obese individuals as the primary outcome. B. longum APC1472 effects on waist-to-hip ratio (W/H ratio) and on obesity-associated plasma biomarkers were analysed as secondary outcomes. MethodsB. longum APC1472 was administered to HFD-fed C57BL/6 mice in drinking water for 16 weeks. In the human intervention trial, participants received B. longum APC1472 or placebo supplementation for 12 weeks, during which primary and secondary outcomes were measured at the beginning and end of the intervention. FindingsB. longum APC1472 supplementation was associated with decreased bodyweight, fat depots accumulation and increased glucose tolerance in HFD-fed mice. While, in healthy overweight/obese adults, the supplementation of B. longum APC1472 strain did not change primary outcomes of BMI (0.03, 95% CI [-0.4, 0.3]) or W/H ratio (0.003, 95% CI [-0.01, 0.01]), a positive effect on the secondary outcome of fasting blood glucose levels was found (-0.299, 95% CI [-0.44, -0.09]). InterpretationThis study shows a positive translational effect of B. longum APC1472 on fasting blood glucose from a preclinical mouse model of obesity to a human intervention study in otherwise healthy overweight and obese individuals. This highlights the promising potential of B. longum APC1472 to be developed as a valuable supplement in reducing specific markers of obesity. FundingThis research was funded in part by Science Foundation Ireland in the form of a Research Centre grant (SFI/12/RC/2273) to APC Microbiome Ireland and by a research grant from Cremo S.A.
  • Comparison of lactose free and traditional mozzarella cheese during shelf-life by aroma compounds and sensory analysis

    Condurso, Concetta; Tripodi, Gianluca; Merlino, Maria; Prestia, Ottavia; STANTON, CATHERINE; Verzera, Antonella; Italian Ministry for Education, University and Research; AIM 1823923-3 - CUP J44I18000190006 (Elsevier, 2021-04-30)
    Aroma compounds and sensory features of lactose free (LFM) and traditional (TM) Mozzarella cheese have been investigated during their labeled shelf-life. Acetoin and 2-heptanone characterized both types of cheese at the production time. During the shelf-life, a statistically significant increase in the amount of the volatiles coming from amino acid and fatty acid metabolism occurred in the LFM samples after 8 days of storage and, to a lesser extent, in TM cheese after 13 days of storage. As regard sensory analysis, milk odor and milk flavor descriptors characterized TM and LFM in the early stage of their shelf-life; bitter and acid taste and yoghurt odor descriptors characterized LFM after 8 days and TM after 13 days. The differences between the two cheese types can be attributed to the proteolytic activity of the lactase enzyme. As a result, the volatile aroma profile and the sensory quality should be taken into account for a proper shelf-life definition of Mozzarella cheese and a shorter shelf-life should be suggested for LFM than TM cheese.
  • Assessing the ability of nisin A and derivatives thereof to inhibit gram-negative bacteria from the genus Thermus

    Jonnala, Bhagya R. Yeluri; Feehily, Conor; O'Connor, Paula M.; Field, Des; Hill, Colin; Ross, R Paul; McSweeney, P.L.H.; Sheehan, Diarmuid (JJ); Cotter, Paul D; Teagasc Walsh Fellowship Programme; et al. (Elsevier, 2021-03-31)
    Nisin is a bacteriocin that is globally employed as a biopreservative in food systems to control gram-positive, and some gram-negative, bacteria. Here we tested the bioactivity of nisin A-producing Lactococcus lactis NZ9700 and producers of bioengineered variants thereof against representatives of the gram-negative genus Thermus, which has been associated with the pink discoloration defect in cheese. Starting with a total of 73 nisin variant-producing Lactococcus lactis, bioactivity against Thermus was assessed via agar diffusion assays, and 22 variants were found to have bioactivity greater than or equal to that of the nisin A-producing control. To determine to what extent this enhanced bioactivity was attributable to an increase in specific activity, minimum inhibitory concentrations were determined using the corresponding purified form of these 22 nisin A derivatives. From these experiments, nisin M17Q and M21F were identified as peptides with enhanced antimicrobial activity against the majority of Thermus target strains tested. In addition, several other peptide variants were found to exhibit enhanced specific activity against a subset of strains.
  • Improvements in sleep indices during exam stress due to consumption of a Bifidobacterium longum

    Moloney, Gerard M.; Long-Smith, Caitriona M.; Murphy, Amy; Dorland, Danielle; Hojabri, Sara Firuzeh; Ramirez, Loreto Olavarría; Marin, David Campos; Bastiaanssen, Thomaz, F. S.; Cusack, Anne-Marie; Berding, Kirsten; et al. (Elsevier, 2021-01-31)
    Targeting the gut microbiome as an effective therapeutic strategy for psychological disorders has shown promise in recent years. Variation in the composition of the microbiota and restoration of a stable microbiome using targeted interventions (psychobiotics) including Bifidobacteria have shown promise in pre-clinical studies, but more human data is required on the potential health benefits of these live microorganisms. Bifidobacterium including Bif. longum 1714 has been shown to dampen the effects of acute stress in humans. However, its effects over a period of prolonged stress have not been examined. A randomised, placebo-controlled, repeated measures, cross-over intervention study was conducted to examine the effects of a probiotic intervention on measures of stress, cognitive performance, and mood in healthy human volunteers. Twenty male students participated in this crossover study. Post-intervention assessments took place during the university exam period, which was used as a naturalistic chronic stressor. Self-reported measures of stress, depression, sleep quality, physical activity, gastrointestinal symptoms, cognition, and mood were assessed by questionnaire. In addition, tests from the Cambridge Neuropsychological Test Automated Battery (CANTAB) were administered to all participants. Stress and depression scores increased in both placebo and probiotic treated groups during the exam period. While overall sleep quality and duration of sleep improved significantly in the probiotic treated group during exam stress compared with the placebo treated group, B. longum 1714, similar to placebo treatment, showed no efficacy in improving measures of working memory, visual memory, sustained attention or perception. Overall, while B. longum 1714 shows promise in improving sleep quality and duration, it did not alleviate symptoms of chronic stress, depression, or any measure of cognitive assessment. Thus, further mechanistic studies into the ability of B. longum 1714 to modulate sleep during prolonged periods of stress are now warranted.
  • The Prebiotic Effect of Australian Seaweeds on Commensal Bacteria and Short Chain Fatty Acid Production in a Simulated Gut Model

    Shannon, Emer; Conlon, Michael; Hayes, Maria (MDPI AG, 2022-05-23)
    Diet is known to affect the composition and metabolite production of the human gut microbial community, which in turn is linked with the health and immune status of the host. Whole seaweeds (WH) and their extracts contain prebiotic components such as polysaccharides (PS) and polyphenols (PP). In this study, the Australian seaweeds, Phyllospora comosa, Ecklonia radiata, Ulva ohnoi, and their PS and PP extracts were assessed for potential prebiotic activities using an in vitro gut model that included fresh human faecal inoculum. 16S rRNA sequencing post gut simulation treatment revealed that the abundance of several taxa of commensal bacteria within the phylum Firmicutes linked with short chain fatty acid (SCFA) production, and gut and immune function, including the lactic acid producing order Lactobacillales and the chief butyrate-producing genera Faecalibacteria, Roseburia, Blautia, and Butyricicoccus were significantly enhanced by the inclusion of WH, PS and PP extracts. After 24 h fermentation, the abundance of total Firmicutes ranged from 57.35–81.55% in the WH, PS and PP samples, which was significantly greater (p ≤ 0.01) than the inulin (INU) polysaccharide control (32.50%) and the epigallocatechingallate (EGCG) polyphenol control (67.13%); with the exception of P. comosa PP (57.35%), which was significantly greater than INU only. However, all WH, PS and PP samples also increased the abundance of the phylum Proteobacteria; while the abundance of the phylum Actinobacteria was decreased by WH and PS samples. After 24 h incubation, the total and individual SCFAs present, including butyric, acetic and propionic acids produced by bacteria fermented with E. radiata and U. ohnoi, were significantly greater than the SCFAs identified in the INU and EGCG controls. Most notably, total SCFAs in the E. radiata PS and U. ohnoi WH samples were 227.53 and 208.68 µmol/mL, respectively, compared to only 71.05 µmol/mL in INU and 7.76 µmol/mL in the EGCG samples. This study demonstrates that whole seaweeds and their extracts have potential as functional food ingredients to support normal gut and immune function.
  • Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021

    Funk, Tjede; Pharris, Anastasia; Spiteri, Gianfranco; Bundle, Nick; Melidou, Angeliki; Carr, Michael; Gonzalez, Gabriel; Garcia-Leon, Alejandro; Crispie, Fiona; O’Connor, Lois; et al. (European Centre for Disease Control and Prevention (ECDC), 2021-04-22)
    We compared 19,207 cases of SARS-CoV-2 variant B.1.1.7/S gene target failure (SGTF), 436 B.1.351 and 352 P.1 to non-variant cases reported by seven European countries. COVID-19 cases with these variants had significantly higher adjusted odds ratios for hospitalisation (B.1.1.7/SGTF: 1.7, 95% confidence interval (CI): 1.0–2.9; B.1.351: 3.6, 95% CI: 2.1–6.2; P.1: 2.6, 95% CI: 1.4–4.8) and B.1.1.7/SGTF and P.1 cases also for intensive care admission (B.1.1.7/SGTF: 2.3, 95% CI: 1.4–3.5; P.1: 2.2, 95% CI: 1.7–2.8).
  • Next-Generation Food Research: Use of Meta-Omic Approaches for Characterizing Microbial Communities Along the Food Chain

    Yap, Min; Ercolini, Danilo; Álvarez-Ordóñez, Avelino; O'Toole, Paul W.; O'Sullivan, Orla; Cotter, Paul D.; Irish Dairy Levy; Science Foundation Ireland; European Commission; SFI/12/RC/2273; et al. (Annual Reviews, 2021-10-22)
    Microorganisms exist along the food chain and impact the quality and safety of foods in both positive and negative ways. Identifying and understanding the behavior of these microbial communities enable the implementation of preventative or corrective measures in public health and food industry settings. Current culture-dependent microbial analyses are time-consuming and target only specific subsets of microbes. However, the greater use of culture-independent meta-omic approaches has the potential to facilitate a thorough characterization of the microbial communities along the food chain. Indeed, these methods have shown potential in contributing to outbreak investigation, ensuring food authenticity, assessing the spread ofantimicrobial resistance, tracking microbial dynamics during fermentation and processing, and uncovering the factors along the food chain that impact food quality and safety. This review examines the community-based approaches, and particularly the application of sequencing-based meta-omics strategies, for characterizing microbial communities along the food chain.
  • Influence of pasture feeding on milk and meat products in terms of human health and product quality

    STANTON, CATHERINE; Mills, S.; Ryan, A.; Di Gioia, D.; Ross, R. Paul (Teagasc, 2021-02-02)
    Cows are fed either indoors on a diet of mixed ration or in areas with temperate climates, such as Ireland and New Zealand, the feeding regime of dairy and beef herds is almost entirely pasture-based. Animal feeding regimes and herd management practices are linked to differences in organoleptic and nutritional quality attributes of milk, dairy and meat/beef products, with pasture-based feeding systems being associated with superior quality produce. Consumers generally perceive that milk and meat products produced from outdoor grazing pastures are “healthier” than produce derived from indoor feeding systems, based on animals fed typical indoor rations and concentrates. However, while research has demonstrated differences in milk and meat quality, especially in terms of fatty acids, based on different feeding systems, data are limited on the impact of dairy and meat products produced from different feeding systems on human health.
  • Irish research response to dairy quality in an era of change

    O'Brien, Bernadette J.; Beresford, Tom; Cotter, Paul D.; Gleeson, D.; Kelly, A.; Kilcawley, Kieran; Magan, J.; McParland, Sinead; Murphy, E.; O’Callaghan, Tom; et al. (Teagasc, 2022-02-26)
    The Irish dairy sector is recognised for its very significant contribution to the national economic status; it is now worth ∼€5 billion annually and represents the largest food and drink export category, which, in turn, represents one of the four largest manufacturing industries in the country. Given anticipated further growth in global demand for dairy products and the positive attributes and capabilities that Ireland has to meet that demand, in terms of pasture-based production and cost competitiveness, it is incumbent for the sector to attain the highest quality milk and dairy products. The combined collaborative approach between research and industry has ensured significant progress and enabled Ireland to remain at the forefront globally in terms of production of quality milk and dairy products. This paper highlights some specific scientific platforms and technologies currently shaping the industry in this regard and discusses current research activity as well as anticipating key requirements for future progress. While research, and farm and processing plant management have accomplished very significant advances in milk and dairy product quality, some overarching emerging challenges include product substitution and sustainability. Some key pillars for the future have been identified on which a strong, efficient dairy sector can be maintained and progressed. Specifically, the use of evidence-based information and real-time measures in prediction and decision-making will be a crucial pillar for the dairy sector of the future. This can promote an approach of proactive maintenance and optimisation of production through improved predictability and control of manufacturing processes.
  • Meta-analysis of cheese microbiomes highlights contributions to multiple aspects of quality

    Walsh, Aaron M.; Macori, Guerrino; Kilcawley, Kieran N.; Cotter, Paul D.; Science Foundation Ireland; European Commission; Department of Agriculture, Food and Marine; SFI/12/RC/2273P1; SFI/12/RC/2273P2; 818368; et al. (Springer Science and Business Media LLC, 2020-08-13)
    A detailed understanding of the cheese microbiome is key to the optimization of flavour, appearance, quality and safety. Accordingly, we conducted a high-resolution meta-analysis of cheese microbiomes and corresponding volatilomes. Using 77 new samples from 55 artisanal cheeses from 27 Irish producers combined with 107 publicly available cheese metagenomes, we recovered 328 metagenome-assembled genomes, including 47 putative new species that could influence taste or colour through the secretion of volatiles or biosynthesis of pigments. Additionally, from a subset of samples, we found that differences in the abundances of strains corresponded with levels of volatiles. Genes encoding bacteriocins and other antimicrobials, such as pseudoalterin, were common, potentially contributing to the control of undesirable microorganisms. Although antibiotic-resistance genes were detected, evidence suggested they are not of major concern with respect to dissemination to other microbiomes. Phages, a potential cause of fermentation failure, were abundant and evidence for phage-mediated gene transfer was detected. The anti-phage defence mechanism CRISPR was widespread and analysis thereof, and of anti-CRISPR proteins, revealed a complex interaction between phages and bacteria. Overall, our results provide new and substantial technological and ecological insights into the cheese microbiome that can be applied to further improve cheese production.
  • Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples

    McHugh, Aoife J.; Yap, Min; Crispie, Fiona; Feehily, Conor; Hill, Colin; Cotter, Paul D.; Department of Agriculture, Food and the Marine; Science Foundation Ireland; European Commission; 14/F/883; et al. (Springer Science and Business Media LLC, 2021-02-15)
    Efficient and accurate identification of microorganisms throughout the food chain can potentially allow the identification of sources of contamination and the timely implementation of control measures. High throughput DNA sequencing represents a potential means through which microbial monitoring can be enhanced. While Illumina sequencing platforms are most typically used, newer portable platforms, such as the Oxford Nanopore Technologies (ONT) MinION, offer the potential for rapid analysis of food chain microbiomes. Initial assessment of the ability of rapid MinION-based sequencing to identify microbes within a simple mock metagenomic mixture is performed. Subsequently, we compare the performance of both ONT and Illumina sequencing for environmental monitoring of an active food processing facility. Overall, ONT MinION sequencing provides accurate classification to species level, comparable to Illumina-derived outputs. However, while the MinION-based approach provides a means of easy library preparations and portability, the high concentrations of DNA needed is a limiting factor.
  • Seasonality and Geography Have a Greater Influence than the Use of Chlorine-Based Cleaning Agents on the Microbiota of Bulk Tank Raw Milk

    Yap, Min; Gleeson, David; O’Toole, Paul W.; O'Sullivan, Orla; Cotter, Paul D.; Irish Dairy Levy (American Society for Microbiology, 2021-10-28)
    Cleaning of the production environment is vital to ensure the safety and quality of dairy products. Although cleaning with chlorine-based agents is widely adopted, it has been associated with detrimental effects on milk quality and safety, which has garnered increasing interest in chlorine-free cleaning. However, the influence of these methods on the milk microbiota is not well documented. This study investigated the factors that influence the raw milk microbiota, with a focus on the differences when chlorine-based and chlorine-free cleaning of milking equipment are used. Bulk tank raw milk was sampled during three sampling months (April, August, and November), from farms across Ireland selected to capture the use of different cleaning methods, i.e., exclusively chlorine-based (n = 51) and chlorine-free cleaning (n = 92) and farms that used chlorine-free agents for the bulk tank and chlorine-based cleaning agents for the rest of the equipment (n = 28). Shotgun metagenomic analysis revealed the significant influence of seasonal and geographic factors on the bulk tank milk microbiota, indicated by differences in diversity, taxonomic composition, and functional characteristics. Taxonomic and functional profiles of samples collected in November clustered separately from those of samples collected in other months. In contrast, cleaning methods only accounted for 1% of the variation in the bulk tank milk bacterial community, and samples collected from farms using chlorine-based versus chlorine-free cleaning did not differ significantly, suggesting that the chlorine-free approaches used did not negatively impact microbiological quality. This study shows the value of shotgun metagenomics in advancing our knowledge of the raw milk microbiota.
  • Transcriptional control of central carbon metabolic flux in Bifidobacteria by two functionally similar, yet distinct LacI-type regulators

    Lanigan, Noreen; Kelly, Emer; Arzamasov, Aleksandr A.; Stanton, Catherine; Rodionov, Dmitry A.; van Sinderen, Douwe; Science Foundation Ireland; Department of Agriculture, Food and the Marine; Russian Science Foundation; SFI/12/RC/2273-P1; et al. (Springer Science and Business Media LLC, 2019-11-28)
    Bifdobacteria resident in the gastrointestinal tract (GIT) are subject to constantly changing environmental conditions, which require rapid adjustments in gene expression. Here, we show that two predicted LacI-type transcription factors (TFs), designated AraQ and MalR1, are involved in regulating the central, carbohydrate-associated metabolic pathway (the so-called phosphoketolase pathway or bifd shunt) of the gut commensal Bifdobacterium breve UCC2003. These TFs appear to not only control transcription of genes involved in the bifd shunt and each other, but also seem to commonly and directly afect transcription of other TF-encoding genes, as well as genes related to uptake and metabolism of various carbohydrates. This complex and interactive network of AraQ/MalR1-mediated gene regulation provides previously unknown insights into the governance of carbon metabolism in bifdobacteria.

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