The Teagasc Food Programme focuses on quality, safety and food product innovation. It is undertaken in collaboration with universities and research institutes in Ireland, the European Union and the USA. The Food Programme is internationally competitive from a scientific point of view while being targeted and applied to generate new opportunities for the Irish food industry The Teagasc Food Programme encompasses many aspects of food science and technology: Food Processing and Functionality, Food Safety, Foods for Health, Food Cultures, Food Quality and Structure, Meat and Meat Products, Prepared Consumer Foods. The Food Programme is run from the Teagasc Food Research Centres at Ashtown, Dublin 14 and Moorepark, Fermoy, Co. Cork

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  • Dietary Conjugated Linoleic Acid-Enriched Cheeses Influence the Levels of Circulating n-3 Highly Unsaturated Fatty Acids in Humans

    Murru, Elisabetta; Carta, Gianfranca; Cordeddu, Lina; Melis, Maria; Desogus, Erika; Ansar, Hastimansooreh; Chilliard, Yves; Ferlay, Anne; Stanton, Catherine; Coakley, Mairéad; et al. (MDPI AG, 2018-06-11)
    n-3 highly unsaturated fatty acids (n-3 HUFA) directly and indirectly regulate lipid metabolism, energy balance and the inflammatory response. We investigated changes to the n-3 HUFA score of healthy adults, induced by different types and amounts of conjugated linoleic acid (CLA)-enriched (ENCH) cheeses consumed for different periods of time, compared to dietary fish oil (FO) pills (500 mg, each containing 100 mg of eicosapentaenoic and docosahexaenoic acids—EPA+DHA) or α-linolenic acid (ALA)-rich linseed oil (4 g, containing 2 g of ALA). A significant increase in the n-3 HUFA score was observed, in a dose-dependent manner, after administration of the FO supplement. In terms of the impact on the n-3 HUFA score, the intake of ENCH cheese (90 g/day) for two or four weeks was equivalent to the administration of one or two FO pills, respectively. Conversely, the linseed oil intake did not significantly impact the n-3 HUFA score. Feeding ENCH cheeses from different sources (bovine, ovine and caprine) for two months improved the n-3 HUFA score by increasing plasma DHA, and the effect was proportional to the CLA content in the cheese. We suggest that the improved n-3 HUFA score resulting from ENCH cheese intake may be attributed to increased peroxisome proliferator-activated receptor alpha (PPAR-α) activity. This study demonstrates that natural ENCH cheese is an alternative nutritional source of n-3 HUFA in humans.
  • Hydrogel-based Bio-nanomachine Transmitters for Bacterial Molecular Communications

    Martins, Daniel P.; O'Reilly, Huong Q.; Coffey, Lee; Cotter, Paul D.; Balasubramaniam, Sasitharan; Science Foundation Ireland; Department of Agriculture, Food and Marine; 16/RC/3835 (ACM, 2020-11-16)
    Bacterial quorum sensing can be engineered with a view to the design of biotechnological applications based on their intrinsic role as a means of communication. We propose the creation of a positive feedback loop that will promote the emission of a superfolded green fluorescence protein from a bacterial population that will flow through hydrogel, which is used to encapsulate the cells. These engineered cells are heretofore referred to as bio-nanomachine transmitters and we show that for lower values of diffusion coefficient, a higher molecular output signal power can be produced, which supports the use of engineered bacteria contained within hydrogels for molecular communications systems. In addition, our wet lab results show the propagation of the molecular output signal, proving the feasibility of engineering a positive feedback loop to create a bio-nanomachine transmitter that can be used for biosensing applications.
  • Conserved redox-dependent DNA binding of ROXY glutaredoxins with TGA transcription factors

    Gutsche, Nora; Holtmannspötter, Michael; Maß, Lucia; O'Donoghue, Martin; Busch, Andrea; Lauri, Andrea; Schubert, Veit; Zachgo, Sabine; Deutsche Forschungsgemeinschaft; SPP 1710 ZA 259/7‐1; et al. (Wiley, 2017-12-14)
    The Arabidopsis thaliana CC‐type glutaredoxin (GRX) ROXY1 and the bZIP TGA transcription factor (TF) PERIANTHIA (PAN) interact in the nucleus and together regulate petal development. The CC‐type GRXs exist exclusively in land plants, and in contrast to the ubiquitously occurring CPYC and CGFS GRX classes, only the CC‐type GRXs expanded strongly during land plant evolution. Phylogenetic analyses show that TGA TFs evolved before the CC‐type GRXs in charophycean algae. MpROXY1/2 and MpTGA were isolated from the liverwort Marchantia polymorpha to analyze regulatory ROXY/TGA interactions in a basal land plant. Homologous and heterologous protein interaction studies demonstrate that nuclear ROXY/TGA interactions are conserved since the occurrence of CC‐type GRXs in bryophytes and mediated by a conserved ROXY C‐terminus. Redox EMSA analyses show a redox‐sensitive binding of MpTGA to the cis‐regulatory as‐1‐like element. Furthermore, we demonstrate that MpTGA binds together with MpROXY1/2 to this motif under reducing conditions, whereas this interaction is not observed under oxidizing conditions. Remarkably, heterologous complementation studies reveal a strongly conserved land plant ROXY activity, suggesting an ancestral role for CC‐type GRXs in modulating the activities of TGA TFs. Super‐resolution microscopy experiments detected a strong colocalization of ROXY1 with the active form of the RNA polymerase II in the nucleus. Together, these data shed new light on the function of ROXYs and TGA TFs and the evolution of redox‐sensitive transcription regulation processes, which likely contributed to adapt land plants to novel terrestrial habitats.
  • Antimicrobial effects of airborne acoustic ultrasound and plasma activated water from cold and thermal plasma systems on biofilms

    Charoux, Clémentine M. G.; Patange, Apurva D.; Hinds, Laura M.; Simpson, Jeremy C.; O’Donnell, Colm P.; Tiwari, Brijesh K; Department of Agriculture, Food and the Marine; Science Foundation Ireland; 14F845; 17/CDA/4653 (Springer Science and Business Media LLC, 2020-10-14)
    Bacterial bioflms are difcult to inactivate due to their high antimicrobial resistance. Therefore, new approaches are required for more efective bacterial bioflm inactivation. Airborne acoustic ultrasound improves bactericidal or bacteriostatic activity which is safe and environmentally friendly. While, plasma activated water (PAW) is attracting increasing attention due to its strong antimicrobial properties. This study determined efcacy of combined airborne acoustic ultrasound and plasma activated water from both cold and thermal plasma systems in inactivating Escherichia coli K12 bioflms. The application of airborne acoustic ultrasound (15 min) alone was signifcantly more efective in reducing E. coli counts in 48 and 72 h bioflms compared to 30 min treatment with PAW. The efect of airborne acoustic ultrasound was more pronounced when used in combination with PAW. Airborne acoustic ultrasound treatment for 15 min of the E. coli bioflm followed by treatment with PAW signifcantly reduced the bacterial count by 2.2—2.62 Log10 CFU/mL when compared to control bioflm treated with distilled water. This study demonstrates that the synergistic efects of airborne acoustic ultrasound and PAW for enhanced antimicrobial efects. These technologies have the potential to prevent and control bioflm formation in food and bio-medical applications.
  • Seaweed Components as Potential Modulators of the Gut Microbiota

    Shannon, Emer; Conlon, Michael; Hayes, Maria; Marie Skłodowska-Curie; 754380. (MDPI AG, 2021-06-23)
    Macroalgae, or seaweeds, are a rich source of components which may exert beneficial effects on the mammalian gut microbiota through the enhancement of bacterial diversity and abundance. An imbalance of gut bacteria has been linked to the development of disorders such as inflammatory bowel disease, immunodeficiency, hypertension, type-2-diabetes, obesity, and cancer. This review outlines current knowledge from in vitro and in vivo studies concerning the potential therapeutic application of seaweed-derived polysaccharides, polyphenols and peptides to modulate the gut microbiota through diet. Polysaccharides such as fucoidan, laminarin, alginate, ulvan and porphyran are unique to seaweeds. Several studies have shown their potential to act as prebiotics and to positively modulate the gut microbiota. Prebiotics enhance bacterial populations and often their production of short chain fatty acids, which are the energy source for gastrointestinal epithelial cells, provide protection against pathogens, influence immunomodulation, and induce apoptosis of colon cancer cells. The oral bioaccessibility and bioavailability of seaweed components is also discussed, including the advantages and limitations of static and dynamic in vitro gastrointestinal models versus ex vivo and in vivo methods. Seaweed bioactives show potential for use in prevention and, in some instances, treatment of human disease. However, it is also necessary to confirm these potential, therapeutic effects in large-scale clinical trials. Where possible, we have cited information concerning these trials
  • The potential of non-starter lactic acid bacteria from Cheddar cheese to colonise the gut

    Leeuwendaal, N.; STANTON, CATHERINE; O'Toole, P.W.; Beresford, Tom; Teagasc Walsh Fellowship Programme; Science Foundation Ireland; JPI Food Processing for Health; 2014073 (Elsevier BV, 2021-05-27)
    This study was undertaken to assess the potential of Non-Starter Lactic Acid Bacteria (NSLAB) from Cheddar cheese to survive gastric transit and display probiotic-related traits including bile salt hydrolase activity, the ability to adhere to the gut epithelium and inhibition of enteropathogen binding. Populations of NSLAB, up to 107 CFU/g per cheese were recovered following exposure of cheese to Simulated Stomach Duodenum Passage (SSDP) conditions. A total of 240 isolates were randomly selected from twelve Cheddar cheeses and assessed for probiotic traits. Two strains Lactobacillus paracasei DPC 7150 and Lactobacillus rhamnosus DPC 7102 showed the most probiotic potential. The Lb. paracasei and Lb. rhamnosus strains displayed adhesion rates of 64% and 79%, respectively and inhibited binding of pathogenic Escherichia coli by >20%. This research demonstrates that Cheddar cheese harbours potentially beneficial bacteria, a large portion of which can survive simulated digestion and potentially exhibit health beneficial effects once ingested.
  • Influence of chaperone-like activity of caseinomacropeptide on the gelation behaviour of whey proteins at pH 6.4 and 7.2.

    Gaspard, Sophie J.; Sharma, Prateek; Fitzgerald, Ciarán; Tobin, John T.; O’Mahony, James A.; Kelly, Alan L.; Brodkorb, Andre; Dairy Research Ireland; Teagasc Walsh Fellowship Programme; European Union; et al. (Elsevier, 2020-08-15)
    The effect of caseinomacropeptide (CMP) on the heat-induced denaturation and gelation of whey proteins (2.5–10%, w/v) at pH 6.4 and 7.2, at a whey protein:CMP ratio of 1:0.9 (w/w), was investigated using differential scanning calorimetry (DSC), oscillatory rheology (90 °C for 20 min) and confocal microscopy. Greater frequency-dependence in the presence of CMP suggested that the repulsive interactions between CMP and the whey proteins affected the network generated by the non-heated whey protein samples. At pH 6.4 or 7.2, CMP increased the temperature of denaturation of β-lactoglobulin by up to 3 °C and increased the gelation temperature by up to 7 °C. The inclusion of CMP strongly affected the structure of the heat-induced whey protein gels, resulting in a finer stranded structure at pH 6.4 and 7.2. The presence of CMP combined with a lower heating rate (2 °C/min) prevented the formation of a solid gel of whey proteins after heating for 20 min at 90 °C and at pH 7.2. These results show the potential of CMP for control of whey protein denaturation and gelation.
  • Development and validation of a quantitative confirmatory method for 30 β-lactam antibiotics in bovine muscle using liquid chromatography coupled to tandem mass spectrometry

    Di Rocco, Melissa; Moloney, Mary; O’Beirne, T.; Earley, S.; Berendsen, B.; Furey, A.; Danaher, Martin; Department of Agriculture, Food and the Marine; 13/F484 (Elsevier BV, 2017-06)
    A method was developed for the confirmatory and quantitative analysis of 30 β-lactam antibiotic residues in bovine muscle. The method includes 12 penicillins (amoxicillin, ampicillin, cloxacillin, dicloxacillin, mecillinam, methicillin, nafcillin, oxacillin, penicillin G, penicillin V, piperacillin, ticarcillin), 12 cephalosporins (cefacetrile, cefadroxil, cephalexin, cefalonium, cefazolin, cefoperazone, cefotaxime, cefquinome, cefuroxime, desacetyl cephapirin, desfuroylceftiofur cysteine disulfide, desfuroylceftiofur dimer), five carbapenems (biapenem, doripenem, ertapenem, imipenem, meropenem) and faropenem. Samples were extracted using a simple solvent extraction with acetonitrile:water (80:20, v/v) and C18 dispersive solid-phase extraction (d-SPE) clean-up, followed by ultra-high performance liquid chromatography coupled to tandem mass spectrometry (UHPLC–MS/MS) detection. Chromatography was performed on a reversed phase CSH C18 column, using a binary gradient separation comprising of 0.01% formic acid and 0.2 mM ammonium acetate in water (mobile phase A) and 0.01% formic acid in acetonitrile (mobile phase B). The mass spectrometer was operated in the positive electrospray ionisation mode (ESI(+)). Validation was performed following the 2002/657/EC guidelines. Trueness ranged between 69% and 143% and precision ranged between 2.0% and 29.9% under within-laboratory reproducibility conditions. The developed method uses minimal sample preparation and 30 test samples can be analysed by a single analyst in a single day. To the best of our knowledge, this is the first method for carbapenems in foodstuff that does not require derivatisation.
  • Improving the chromatographic selectivity of β-lactam residue analysis in milk using phenyl-column chemistry prior to detection by tandem mass spectrometry

    Di Rocco, Melissa; Moloney, Mary; Haren, Deirdre; Gutierrez, Montserrat; Earley, Seán; Berendsen, Bjorn; Furey, Ambrose; Danaher, Martin; Department of Agriculture, Food and the Marine; 13/F484 (Springer Science and Business Media LLC, 2020-05-23)
    Analyte isobaric interferences can limit the development of a comprehensive analytical method for the quantitative liquid chromatography-tandem mass spectrometry profiling of an important cohort of veterinary drugs. In this work, a selective chromatographic separation was developed for the analysis of 32 β-lactam antibiotic residues (12 penicillins, 14 cephalosporins, five carbapenems and faropenem) in milk samples. A range of analytical columns with different stationary phases and mobile phases were evaluated for retention and separation of the β-lactam compounds. Results showed that, among the columns tested, only phenyl-hexyl could adequately separate ampicillin from cephalexin and amoxicillin from cefadroxil, which had shown isobaric interferences on a number of stationary phases. Chromatography was performed using a water/acetonitrile binary gradient with formic acid and ammonium acetate. The β-lactam residues were extracted from the milk samples using a water:acetonitrile solution and purified by C18 dispersive solid-phase extraction (d-SPE) clean-up, followed by concentration under nitrogen and ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) determination. Analytes were monitored in positive electrospray ionisation mode (ESI(+)). Possible interfering matrix effects were overcome by using 13 internal standards. The method was fully validated according to 2002/657/EC guidelines, showing satisfactory performance characteristics. Under within-laboratory reproducibility conditions, trueness and precision ranged from 91 to 130% and from 1.4 to 38.6%, respectively. Decision limits (CCα) were in the range 2.1–133 μg kg−1. Limits of detection (LODs) and quantitation (LOQs) ranged between 0.0090 and 1.5 μg kg−1 and from 0.030 to 5.0 μg kg−1, respectively.
  • Protein quality and quantity influence the effect of dietary fat on weight gain and tissue partitioning via host-microbiota changes

    Nychyk, Oleksandr; Barton, Wiley; Rudolf, Agata M.; Boscaini, Serena; Walsh, Aaron; Bastiaanssen, Thomaz F.S.; Giblin, Linda; Cormican, Paul; Chen, Liang; Piotrowicz, Yolanda; et al. (Elsevier BV, 2021-05-11)
    We investigated how protein quantity (10%–30%) and quality (casein and whey) interact with dietary fat (20%–55%) to affect metabolic health in adult mice. Although dietary fat was the main driver of body weight gain and individual tissue weight, high (30%) casein intake accentuated and high whey intake reduced the negative metabolic aspects of high fat. Jejunum and liver transcriptomics revealed increased intestinal permeability, low-grade inflammation, altered lipid metabolism, and liver dysfunction in casein-fed but not whey-fed animals. These differential effects were accompanied by altered gut size and microbial functions related to amino acid degradation and lipid metabolism. Fecal microbiota transfer confirmed that the casein microbiota increases and the whey microbiota impedes weight gain. These data show that the effects of dietary fat on weight gain and tissue partitioning are further influenced by the quantity and quality of the associated protein, primarily via effects on the microbiota.
  • Inclusion of Healthy Oils for Improving the Nutritional Characteristics of Dry-Fermented Deer Sausage

    Vargas-Ramella, Márcio; Munekata, Paulo E. S.; Gagaoua, Mohammed; Franco, Daniel; Campagnol, Paulo C. B.; Pateiro, Mirian; Barretto, Andrea Carla da Silva; Domínguez, Rubén; Lorenzo, José M.; CYTED; et al. (MDPI AG, 2020-10-18)
    The influence of partial replacement of animal fat by healthy oils on composition, physicochemical, volatile, and sensory properties of dry-fermented deer sausage was evaluated. Four different batches were manufactured: the control was formulated with animal fat (18.2%), while in the reformulated batches the 50% of animal fat was substituted by olive, canola, and soy oil emulsions immobilized in Prosella gel. The reformulation resulted in a decrease of moisture and fat contents and an increase of protein and ash amount. Moreover, reformulated sausages were harder, darker, and had higher pH values. This fact is related to the lower moisture content in these samples. As expected, the fatty acid composition was changed by the reformulation. The use of soy and canola oils increased polyunsaturated fatty acids and omega-3 content and decreased n-6/n-3 ratio and saturated fatty acids. Thus, the use of these two oils presented the best nutritional benefits. The changes observed in the fatty acids reflected the fatty acid composition of the oils employed in the emulsions. Regarding volatile compounds (VOC), the replacement of animal fat by healthy emulsion gels increased the content of both total VOC and most of individual VOC. However, the lipid-derived VOC did not show this trend. Generally speaking, the control samples presented similar or higher VOC derived from lipid oxidation processes, which could be related to the natural antioxidant compounds present in the vegetable oils. Finally, all reformulated sausages presented higher consumer acceptability than control samples. In fact, the sausage reformulated with soy oil emulsion gel was the most preferred. Thus, as a general conclusion, the reformulation of deer sausages with soy emulsion gel improves both composition and sensory quality of the final product, which could be an excellent strategy to the elaboration of healthy fermented sausages.
  • Genome-Wide Profiling of Enterotoxigenic Staphylococcus aureus Strains Used for the Production of Naturally Contaminated Cheeses

    Macori, Guerrino; Bellio, Alberto; Bianchi, Daniela Manila; Chiesa, Francesco; Gallina, Silvia; Romano, Angelo; Zuccon, Fabio; Cabrera-Rubio, Raúl; Cauquil, Alexandra; Merda, Déborah; et al. (MDPI AG, 2019-12-27)
    Staphylococcus aureus is a major human pathogen and an important cause of livestock infections. More than 20 staphylococcal enterotoxins with emetic activity can be produced by specific strains responsible for staphylococcal food poisoning, one of the most common food-borne diseases. Whole genome sequencing provides a comprehensive view of the genome structure and gene content that have largely been applied in outbreak investigations and genomic comparisons. In this study, six enterotoxigenic S. aureus strains were characterised using a combination of molecular, phenotypical and computational methods. The genomes were analysed for the presence of virulence factors (VFs), where we identified 110 genes and classified them into five categories: adherence (n = 31), exoenzymes (n = 28), genes involved in host immune system evasion (n = 7); iron uptake regulatory system (n = 8); secretion machinery factors and toxins’ genes (n = 36), and 39 genes coding for transcriptional regulators related to staphylococcal VFs. Each group of VFs revealed correlations among the six enterotoxigenic strains, and further analysis revealed their accessory genomic content, including mobile genetic elements. The plasmids pLUH02 and pSK67 were detected in the strain ProNaCC1 and ProNaCC7, respectively, carrying out the genes sed, ser, and selj. The genes carried out by prophages were detected in the strain ProNaCC2 (see), ProNaCC4, and ProNaCC7 (both positive for sea). The strain ProNaCC5 resulted positive for the genes seg, sei, sem, sen, seo grouped in an exotoxin gene cluster, and the strain ProNaCC6 resulted positive for seh, a transposon-associated gene. The six strains were used for the production of naturally contaminated cheeses which were tested with the European Screening Method for staphylococcal enterotoxins. The results obtained from the analysis of toxins produced in cheese, combined with the genomic features represent a portrait of the strains that can be used for the production of staphylococcal enterotoxin-positive cheese as reference material.
  • Therapeutic effects of antibiotics loaded cellulose nanofiber and κ-carrageenan oligosaccharide composite hydrogels for periodontitis treatment

    Johnson, Athira; Kong, Fanbin; Miao, Song; Lin, Hong‑Ting Victor; Thomas, Sabu; Huang, Yi‑Cheng; Kong, Zwe‑Ling (Springer Science and Business Media LLC, 2020-10-22)
    Periodontitis is an infammatory disease that can lead to the periodontal pocket formation and tooth loss. This study was aimed to develop antimicrobials loaded hydrogels composed of cellulose nanofbers (CNF) and κ-carrageenan oligosaccharides (CO) nanoparticles for the treatment of periodontitis. Two antimicrobial agents such as surfactin and Herbmedotcin were selected as the therapeutic agents and the hydrogels were formulated based on the increasing concentration of surfactin. The proposed material has high thermal stability, controlled release, and water absorption capacity. This study was proceeded by investigating the in vitro antibacterial and anti-infammatory properties of the hydrogels. This material has strong antibacterial activity against periodontal pathogens such as Streptococcus mutans, Porphyromonas gingivalis, Fusobacterium nucleatum, and Pseudomonas aeruginosa. Moreover, a signifcant increase in malondialdehyde (MDA) production and a decrease in bioflm formation and metabolic activity of the bacteria was observed in the presence of hydrogel. Besides, it reduced the reactive oxygen species (ROS) generation, transcription factor, and cytokines production in human gingival fbroblast cells (HGF) under infammatory conditions. In conclusion, the hydrogels were successfully developed and proven to have antibacterial and anti-infammatory properties for the treatment of periodontitis. Thus, it can be used as an excellent candidate for periodontitis treatment.
  • Current Trends in Proteomic Advances for Food Allergen Analysis

    López-Pedrouso, María; Lorenzo, José M.; Gagaoua, Mohammed; Franco, Daniel; Programa Iberoamericano de Ciencia y Tecnología para el Desarrollo; Axencia Galega de Innovación, Xunta de Galicia, Spain; 119RT0568; IN607A2019/01 (MDPI AG, 2020-08-25)
    Food allergies are a global food challenge. For correct food labelling, the detection and quantification of allergens are necessary. However, novel product formulations and industrial processes produce new scenarios, which require much more technological developments. For this purpose, OMICS technologies, especially proteomics, seemed to be relevant in this context. This review summarises the current knowledge and studies that used proteomics to study food allergens. In the case of the allergenic proteins, a wide variety of isoforms, post-translational modifications and other structural changes during food processing can increase or decrease the allergenicity. Most of the plant-based food allergens are proteins with biological functions involved in storage, structure, and plant defence. The allergenicity of these proteins could be increased by the presence of heavy metals, air pollution, and pesticides. Targeted proteomics like selected/multiple reaction monitoring (SRM/MRM) have been very useful, especially in the case of gluten from wheat, rye and barley, and allergens from lentil, soy, and fruit. Conventional 1D and 2-DE immunoblotting have been further widely used. For animal-based food allergens, the widely used technologies are 1D and 2-DE immunoblotting followed by MALDI-TOF/TOF, and more recently LC-MS/MS, which is becoming useful to assess egg, fish, or milk allergens. The detection and quantification of allergenic proteins using mass spectrometry-based proteomics are promising and would contribute to greater accuracy, therefore improving consumer information.
  • Is there evidence for bacterial transfer via the placenta and any role in the colonization of the infant gut? – a systematic review

    Gil, Angel; Rueda, Ricardo; Ozanne, Susan E.; van der Beek, Eline M.; van Loo-Bouwman, Carolien; Schoemaker, Marieke; Marinello, Vittoria; Venema, Koen; Stanton, Catherine; Schelkle, Bettina; et al. (Taylor and Francis, 2020-08-05)
    With the important role of the gut microbiome in health and disease, it is crucial to understand key factors that establish the microbial community, including gut colonization during infancy. It has been suggested that the first bacterial exposure is via a placental microbiome. However, despite many publications, the robustness of the evidence for the placental microbiome and transfer of bacteria from the placenta to the infant gut is unclear and hence the concept disputed. Therefore, we conducted a systematic review of the evidence for the role of the placental, amniotic fluid and cord blood microbiome in healthy mothers in the colonization of the infant gut. Most of the papers which were fully assessed considered placental tissue, but some studied amniotic fluid or cord blood. Great variability in methodology was observed especially regarding sample storage conditions, DNA/RNA extraction, and microbiome characterization. No study clearly considered transfer of the normal placental microbiome to the infant gut. Moreover, some studies in the review and others published subsequently reported little evidence for a placental microbiome in comparison to negative controls. In conclusion, current data are limited and provide no conclusive evidence that there is a normal placental microbiome which has any role in colonization of infant gut.
  • Gut microbes from the phylogenetically diverse genus Eubacterium and their various contributions to gut health

    Mukherjee, Arghya; Lordan, Cathy; Ross, R. Paul; Cotter, Paul D.; Department of Agriculture, Food and the Marine; Teagasc Walsh Fellowship; Science Foundation Ireland; EU; 15/F/635; 2017047; et al. (Taylor & Francis, 2020-08-23)
    Over the last two decades our understanding of the gut microbiota and its contribution to health and disease has been transformed. Among a new ‘generation’ of potentially beneficial microbes to have been recognized are members of the genus Eubacterium, who form a part of the core human gut microbiome. The genus consists of phylogenetically, and quite frequently phenotypically, diverse species, making Eubacterium a taxonomically unique and challenging genus. Several members of the genus produce butyrate, which plays a critical role in energy homeostasis, colonic motility, immunomodulation and suppression of inflammation in the gut. Eubacterium spp. also carry out bile acid and cholesterol transformations in the gut, thereby contributing to their homeostasis. Gut dysbiosis and a consequently modified representation of Eubacterium spp. in the gut, have been linked with various human disease states. This review provides an overview of Eubacterium species from a phylogenetic perspective, describes how they alter with diet and age and summarizes its association with the human gut and various health conditions.
  • Association of Habitual Dietary Fiber Intake and Fecal Microbiome Gene Abundance with Gastrointestinal Symptoms in an Irritable Bowel Syndrome Cohort

    Roy, Nicole; Heenan, Phoebe; Wall, Catherine; Young, Wayne; Carco, Caterina; Keenan, Jacqueline; Cotter, Paul; Maclean, Paul; Mullaney, Jane; Fraser, Karl; et al. (Oxford University Press (OUP), 2020-05-29)
    Objectives: Dietary fibre supplementation is recognised as important for functional gastrointestinal disorders (FGID). The exact role of the microbiome in this relationship remains unclear. We explored differences in dietary fibre intake, GI symptoms and the fecal microbiome in those with FGID.
  • Proteomic biomarkers of beef colour

    Gagaoua, Mohammed; Hughes, Joanne; Terlouw, E.M. Claudia; Warner, Robyn D.; Purslow, Peter P.; Lorenzo, José M.; Picard, Brigitte; European Union; Enterprise Ireland; 713654; et al. (Elsevier BV, 2020-07)
    Background Implementation of proteomics over the last decade has been an important step toward a better understanding of the complex biological systems underlying the conversion of muscle to meat. These sophisticated analytical tools have helped to reveal the biochemical pathways involved in fresh meat colour and have identified key protein biomarkers. Scope and approach Until recently, there have been no detailed or critical studies on the role of protein biomarkers in determining meat colour. This review presents an integromics of recent muscle proteomic studies to investigate pathways and mechanisms of beef colour. A database was created from 13 independent proteomic-based studies including data on five muscles and a list of 79 proteins which were significantly correlated with colour traits. The database was subjected to a multistep analysis including Gene Ontology annotations, pathway analysis and literature mining. This report discusses the key protein biomarkers and the biological pathways associated with fresh beef colour. Biomarkers were prioritised by the frequency of identification and the need for future validation experiments is discussed. Key findings and conclusions This review identifies six pathways involved in beef colour including energy metabolism, heat shock and oxidative stress, myofibril structure, signalling, proteolysis and apoptosis. The data-mining of the list of the putative biomarkers showed that certain proteins, such as β-enolase (ENO3), Peroxiredoxin 6 (PRDX6), HSP27 (HSPB1), Phosphoglucomutase 1 (PGM1), Superoxide Dismutase [Cu-Zn] (SOD1) and μ-calpain (CAPN1) were consistently reported by multiple studies as being differentially expressed and having a significant role in beef colour. This integromics work proposes a list of 27 putative biomarkers of beef colour for validation using adapted high-throughput methods.
  • The harmonized INFOGEST in vitro digestion method: From knowledge to action

    Egger, Lotti; Ménard, Olivia; Delgado-Andrade, Cristina; Alvito, Paula; Assunção, Ricardo; Balance, Simon; Barberá, Reyes; Brodkorb, Andre; European Union; Fundação para a Ciência e Tecnologia; et al. (Elsevier BV, 2015-12)
    Within the active field of in vitro digestion in food research, the COST Action INFOGEST aimed to harmonize in vitro protocols simulating human digestion on the basis of physiologically inferred conditions. A harmonized static in vitro digestion (IVD) method was recently published as a primary output from this network. To validate this protocol, inter-laboratory trials were conducted within the INFOGEST network. A first study was performed using skim milk powder (SMP) as a model food and served to compare the different in-house digestion protocols used among the INFOGEST members. In a second inter-laboratory study applying the harmonized protocol, the degree of consistency in protein hydrolysis was investigated. Analysis of the hydrolyzed proteins, after the gastric and intestinal phases, showed that caseins were mainly hydrolyzed during the gastric phase, whereas β-lactoglobulin was, as previously shown, resistant to pepsin. Moreover, generation of free amino acids occurred mainly during the intestinal phase. The study also showed that a few critical steps were responsible for the remaining inter-laboratory variability. The largest deviations arose from the determination of pepsin activity. Therefore, this step was further clarified, harmonized, and implemented in a third inter-laboratory study. The present work gives an overview of all three inter-laboratory studies, showing that the IVD INFOGEST method has led to an increased consistency that enables a better comparability of in vitro digestion studies in the future.
  • Proteomic biomarkers of beef colour

    Gagaoua, Mohammed; Hughes, Joanne; Terlouw, E.M. Claudia; Warner, Robyn D.; Purslow, Peter P.; Lorenzo, José M.; Picard, Brigitte; Marie Skłodowska-Curie grant agreement; Meat Technology Ireland; 713654; et al. (Elsevier, 2020-05-28)
    Background Implementation of proteomics over the last decade has been an important step toward a better understanding of the complex biological systems underlying the conversion of muscle to meat. These sophisticated analytical tools have helped to reveal the biochemical pathways involved in fresh meat colour and have identified key protein biomarkers. Scope and approach Until recently, there have been no detailed or critical studies on the role of protein biomarkers in determining meat colour. This review presents an integromics of recent muscle proteomic studies to investigate pathways and mechanisms of beef colour. A database was created from 13 independent proteomic-based studies including data on five muscles and a list of 79 proteins which were significantly correlated with colour traits. The database was subjected to a multistep analysis including Gene Ontology annotations, pathway analysis and literature mining. This report discusses the key protein biomarkers and the biological pathways associated with fresh beef colour. Biomarkers were prioritised by the frequency of identification and the need for future validation experiments is discussed. Key findings and conclusions This review identifies six pathways involved in beef colour including energy metabolism, heat shock and oxidative stress, myofibril structure, signalling, proteolysis and apoptosis. The data-mining of the list of the putative biomarkers showed that certain proteins, such as β-enolase (ENO3), Peroxiredoxin 6 (PRDX6), HSP27 (HSPB1), Phosphoglucomutase 1 (PGM1), Superoxide Dismutase [Cu-Zn] (SOD1) and μ-calpain (CAPN1) were consistently reported by multiple studies as being differentially expressed and having a significant role in beef colour. This integromics work proposes a list of 27 putative biomarkers of beef colour for validation using adapted high-throughput methods.

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