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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  • Food for thought: The role of nutrition in the microbiota-gut–brain axis

    Oriach, Clara Seira; Robertson, Ruairi C.; Stanton, Catherine; Cryan, John F.; Dinan, Timothy G.; Science Foundation Ireland; Health Research Board of Ireland; Sea Change Strategy; NutraMara programme; SMART FOOD project; et al. (Elsevier BV, 2016-04)
    Recent research has provided strong evidence for the role of the commensal gut microbiota in brain function and behaviour. Many potential pathways are involved in this bidirectional communication between the gut microbiota and the brain such as immune mechanisms, the vagus nerve and microbial neurometabolite production. Dysbiosis of gut microbial function has been associated with behavioural and neurophysical deficits, therefore research focused on developing novel therapeutic strategies to treat psychiatric disorders by targeting the gut microbiota is rapidly growing. Numerous factors can influence the gut microbiota composition such as health status, mode of birth delivery and genetics, but diet is considered among the most crucial factors impacting on the human gut microbiota from infancy to old age. Thus, dietary interventions may have the potential to modulate psychiatric symptoms associated with gut–brain axis dysfunction. Further clinical and in vivo studies are needed to better understand the mechanisms underlying the link between nutrition, gut microbiota and control of behaviour and mental health.
  • Oligosaccharides Isolated from MGO™ Manuka Honey Inhibit the Adhesion of Pseudomonas aeruginosa, Escherichia Coli O157:H7 and Staphylococcus Aureus to Human HT-29 cells

    Lane, Johnathan A.; Calonne, Julie; Slattery, Helen; Hickey, Rita M. (MDPI AG, 2019-10-01)
    Historically, honey is known for its anti-bacterial and anti-fungal activities and its use for treatment of wound infections. Although this practice has been in place for millennia, little information exists regarding which manuka honey components contribute to the protective nature of this product. Given that sugar accounts for over 80% of honey and up to 25% of this sugar is composed of oligosaccharides, we have investigated the anti-infective activity of manuka honey oligosaccharides against a range of pathogens. Initially, oligosaccharides were extracted from a commercially-available New Zealand manuka honey—MGO™ Manuka Honey (Manuka Health New Zealand Ltd.)—and characterized by High pH anion exchange chromatography coupled with pulsed amperiometric detection. The adhesion of specific pathogens to the human colonic adenocarcinoma cell line, HT-29, was then assessed in the presence and absence of these oligosaccharides. Manuka honey oligosaccharides significantly reduced the adhesion of Escherichia coli O157:H7 (by 40%), Staphylococcus aureus (by 30%), and Pseudomonas aeruginosa (by 52%) to HT-29 cells. This activity was then proven to be concentration dependent and independent of bacterial killing. This study identifies MGO™ Manuka Honey as a source of anti-infective oligosaccharides for applications in functional foods aimed at lowering the incidence of infectious diseases.
  • The Effect of High Pressure Processing on Polyphenol Oxidase Activity, Phytochemicals and Proximate Composition of Irish Potato Cultivars

    Tsikrika, Konstantina; O’Brien, Nora; Rai, Dilip K.; Department of Agriculture, Food and Marine; 17/F/299 (MDPI AG, 2019-10-19)
    Polyphenol oxidase (PPO) activity, proximate composition, and phytochemicals were determined in four common Irish potato cultivars following a high pressure processing (HPP) at 600 MPa for 3 min. PPO activity was significantly (p < 0.05) lower in all HPP treated samples, while the overall proximate composition was not affected. The total phenolic content was significantly higher in the HPP treated samples. Chlorogenic acid levels significantly decreased with simultaneous increase of caffeic acid and p-coumaric acid levels upon HPP treatment. No significant changes were observed in rutin and ferulic acid levels, although their levels varied, depending on the potato cultivars, while the levels of cytotoxic glycoalkaloids (α-solanine and α-chaconine) remained unaltered.
  • Draft Genome Sequences of the Type Strains of Six Macrococcus Species

    Mazhar, Shahneela; Altermann, Eric; Hill, Colin; McAuliffe, Olivia; Teagasc Walsh Fellowship Programme; 2015055 (American Society for Microbiology, 2019-05-09)
    We report here the draft genome sequences of Macrococcus bovicus ATCC 51825T, Macrococcus carouselicus ATCC 51828T, Macrococcus equipercicus ATCC 51831T, Macrococcus brunensis CCM4811T, Macrococcus hajekii CCM4809T, and Macrococcus lamae CCM4815T. The availability of the genome sequences of these species will enable cross-species comparison, which could lead to a more comprehensive understanding of organisms of the Macrococcus genus.
  • Vangl2 disruption alters the biomechanics of late spinal neurulation leading to spina bifida in mouse embryos

    Galea, Gabriel L.; Nychyk, Oleksandr; Mole, Matteo A.; Moulding, Dale; Savery, Dawn; Nikolopoulou, Evanthia; Henderson, Deborah J.; Greene, Nicholas D. E.; Copp, Andrew J. (The Company of Biologists, 2018-03-12)
    Human mutations in the planar cell polarity component VANGL2 are associated with the neural tube defect spina bifida. Homozygous Vangl2 mutation in mice prevents initiation of neural tube closure, precluding analysis of its subsequent roles in neurulation. Spinal neurulation involves rostral-to-caudal ‘zippering’ until completion of closure is imminent, when a caudal-to-rostral closure point, ‘Closure 5’, arises at the caudal-most extremity of the posterior neuropore (PNP). Here, we used Grhl3Cre to delete Vangl2 in the surface ectoderm (SE) throughout neurulation and in an increasing proportion of PNP neuroepithelial cells at late neurulation stages. This deletion impaired PNP closure after the ∼25-somite stage and resulted in caudal spina bifida in 67% of Grhl3Cre/+Vangl2Fl/Fl embryos. In the dorsal SE, Vangl2 deletion diminished rostrocaudal cell body orientation, but not directional polarisation of cell divisions. In the PNP, Vangl2 disruption diminished mediolateral polarisation of apical neuroepithelial F-actin profiles and resulted in eversion of the caudal PNP. This eversion prevented elevation of the caudal PNP neural folds, which in control embryos is associated with formation of Closure 5 around the 25-somite stage. Closure 5 formation in control embryos is associated with a reduction in mechanical stress withstood at the main zippering point, as inferred from the magnitude of neural fold separation following zippering point laser ablation. This stress accommodation did not happen in Vangl2-disrupted embryos. Thus, disruption of Vangl2-dependent planar-polarised processes in the PNP neuroepithelium and SE preclude zippering point biomechanical accommodation associated with Closure 5 formation at the completion of PNP closure.
  • Draft Genome Sequences of Macrococcus caseolyticus, Macrococcus canis, Macrococcus bohemicus, and Macrococcus goetzii

    Mazhar, Shahneela; Altermann, Eric; Hill, Colin; McAuliffe, Olivia; Teagasc Walsh Fellowship Programme; 2015055 (American Society for Microbiology, 2019-05-09)
    Here, we present the draft genome sequences of 14 strains of 4 species of the genus Macrococcus. These strains were isolated from bovine milk and tongue samples obtained during a screening program.
  • Genome Sequence of Geobacillus stearothermophilus DSM 458, an Antimicrobial-Producing Thermophilic Bacterium, Isolated from a Sugar Beet Factory

    Egan, Kevin; Kelleher, Philip; Field, Des; Rea, Mary C.; Ross, R Paul; Cotter, Paul D.; Hill, Colin; Department of Agriculture, Food and the Marine; Science Foundation Ireland; DAFM 13/F/462; et al. (American Society for Microbiology, 2017-10-26)
    This paper reports the full genome sequence of the antimicrobial-producing bacterium Geobacillus stearothermophilus DSM 458, isolated in a sugar beet factory in Austria. In silico analysis reveals the presence of a number of novel bacteriocin biosynthetic genes.
  • Identification and characterisation of capidermicin, a novel bacteriocin produced by Staphylococcus capitis

    Lynch, David; O’Connor, Paula M.; Cotter, Paul D.; Hill, Colin; Field, Des; Begley, Máire; Cork Institute of Technology RISAM PhD scholarship (Public Library of Science (PLoS), 2019-10-16)
    One hundred human-derived coagulase negative staphylococci (CoNS) were screened for antimicrobial activity using agar-based deferred antagonism assays with a range of indicator bacteria. Based on the findings of the screen and subsequent well assays with cell free supernatants and whole cell extracts, one strain, designated CIT060, was selected for further investigation. It was identified as Staphylococcus capitis and herein we describe the purification and characterisation of the novel bacteriocin that the strain produces. This bacteriocin which we have named capidermicin was extracted from the cell-free supernatant of S. capitis CIT060 and purified to homogeneity using reversed-phase high performance liquid chromatography (RP-HPLC). Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometric (MS) analysis revealed that the capidermicin peptide has a mass of 5,464 Da. Minimal inhibitory concentration (MIC) experiments showed that capidermicin was active in the micro-molar range against all the Gram-positive bacteria that were tested. Antimicrobial activity was retained over a range of pHs (2–11) and temperatures (10–121°C x 15 mins). The draft genome sequence of S. capitis CIT060 was determined and the genes predicted to be involved in the biosynthesis of capidermicin were identified. These genes included the predicted capidermicin precursor gene, and genes that are predicted to encode a membrane transporter, an immunity protein and a transcriptional regulator. Homology searches suggest that capidermicin is a novel member of the family of class II leaderless bacteriocins.
  • The gut microbiota and the liver. Pathophysiological and clinical implications

    Quigley, Eamonn M.M.; Stanton, Catherine; Murphy, Eileen F. (Elsevier BV, 2012-11-06)
    The term microbiota is used to describe the complete population of microorganisms that populate a certain location, such as the gut, and is preferred to the term flora as the former incorporates not just bacteria but also archaea, viruses, and other microorganisms, such as protozoa. Though the potential role of the microbiota (through such concepts as ‘‘the putrefactive principle associated with faeces’’ and ‘‘intestinal toxins’’) in the pathogenesis of systemic disorders has been recognized since antiquity, a firm scientific basis for a role for the gut microbiome in liver disease did not emerge until the middle of the last century with the recognition of the relationship between hepatic coma and the absorption of nitrogenous substances from the intestine [1]. This was followed by the description of abundant coliforms in the small intestine of cirrhotics [2] and the role of bacteria was clinched by trials demonstrating that antibiotics led to clinical improvement in hepatic encephalopathy (HE) [3]. Subsequently, these same gut-derived bacteria were implicated in another complication of chronic liver disease and portal hypertension, spontaneous bacterial peritonitis. Most recently, more credence has been given to a suggestion that has lingered in the background for decades, namely, that the gut microbiota might play a role in the pathogenesis or progression of certain liver diseases, including alcoholic liver disease [4], non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steato-hepatitis (NASH) [5], total parenteral nutrition (TPN)/intestinal failure-related liver disease (IFALD) [6], and primary sclerosing cholangitis (PSC) [7], either through the direct effects of bacteria or their products, via inflammatory mediators such as tumor necrosis factor a (TNF), whose release had been triggered by constituents of the microbiota, or, as in the case of primary sclerosing cholangitis (PSC), through cross-reactivity between microbial antigens and human tissue components (e.g., atypical anti-nuclear cytoplasmic antibodies (p-ANCA), in PSC, recognize both tubulin beta isoform 5 in human neutrophils, and the bacterial cell division protein FtsZ) [8]. Indeed, inflammatory mediators have also been implicated in the development and maintenance of the hyperdynamic circulation that is a feature of portal hypertension [9], in impairing liver function and contributing to haemostatic failure [10]. It is in these contexts that modulation of the microbiota has emerged as a potential therapeutic strategy in the management of liver disease
  • Low numbers of ovarian follicles ≥3 mm in diameter are associated with low fertility in dairy cows

    Mossa, F.; Walsh, S.W.; Butler, Stephen T.; Berry, Donagh P.; Carter, F.; Lonergan, P.; Smith, G.W.; Ireland, J.J.; Evans, A.C.O. (American Dairy Science Association, 2012-05-01)
    The total number of ovarian follicles ≥3 mm in diameter (antral follicle count, AFC) during follicular waves varies among cattle of similar age, but AFC is highly repeatable within individuals. We hypothesized that lower AFC could be associated with reduced fertility in cattle. The AFC was assessed by ultrasonography for 2 d consecutively during the first wave of follicular growth of the estrous cycle, 4.6 ± 1.43 d (mean ± SD) after estrus, in 306 Holstein-Friesian dairy cows approximately 70 d postpartum. Cows were classified into 3 groups based on AFC: low (AFC ≤15), intermediate (AFC = 16 to 24), and high (AFC ≥25). During the cycle in which AFC was assessed and in subsequent cycles, cows were artificially inseminated (AI) following detection of estrus, and pregnancy status was assessed using ultrasonography. Cows with high AFC had 3.34 times greater odds of being pregnant at the end of the breeding season compared with cows with low AFC; the odds of a successful pregnancy at first service were 1.75 times greater in the intermediate compared with the low group. The predicted probability of a successful pregnancy by the end of the breeding period (length of breeding season was 86 ± 16.3 d) was 94, 88, and 84% for the high, intermediate, and low AFC groups, respectively. No difference was evident among groups in 21-d submission rate (proportion of all cows detected in estrus and submitted for AI in the first 21 d of the breeding season), but the interval from calving to conception was shorter in the high (109.5 ± 5.1 d) versus low (117.1 ± 4 d) group, and animals with intermediate AFC received fewer services during the breeding season (2.3 ± 0.1) compared with animals with low AFC (2.7 ± 0.1). Lactating cows with ≤15 ovarian follicles have lower reproductive performance compared with cows with higher numbers of follicles, but the existence of a positive association between high numbers of ovarian follicles and fertility is yet to be established.
  • Impact of direct and indirect heating systems in broiler units on environmental conditions and flock performance

    Smith, Shaun; Meade, Joseph; Gibbons, James; McGill, Kevina; Bolton, Declan J.; Whyte, Paul; Department of Agriculture, Food and the Marine; 11SF328 (Elsevier BV, 2016-11-11)
    This study compared the impact of three indirect heating systems to direct gas flame heaters on a selection of flock performance and environmental indicators in commercial broiler units. No statistically significant differences (P≥0.05) were found in flock mortality rates, bird weight, water consumption, stress response, carbon dioxide, ammonia, temperature, relative humidity, litter quality, within-flock Campylobacter levels or mean Campylobacter counts when flock data from any of the three indirect heating systems were compared to flocks reared in houses with direct heating systems. Differences in litter quality were observed between upper and lower litter layers in all houses, regardless of heating type, which may have implications for bird health and welfare. Carbon dioxide concentrations in houses with direct heating systems were significantly higher than those in houses with indirect heating systems during the first 10 days of bird life (P≤0.05). This was due to the increased use of heating systems during this period of the flock cycle. Differences in CO2 concentrations had no effect on flock performance, possibly due to the fact that concentrations did not exceed known safe levels. A statistically significant increase in stress response was observed in birds as a result of partial depopulation (thinning) within houses, irrespective of heating system type used (P≤0.05). Stress associated with thinning may have consequences for bird welfare and food safety. In conclusion, the results of our study suggest that indirect heating systems do not appear to negatively impact on flock performance, stress response, within-flock Campylobacter levels or mean Campylobacter counts and do not appear to significantly alter environmental conditions within broiler houses when compared to houses equipped with direct heating systems. Indirect systems are a viable alternative for heating broiler houses in terms of flock performance, bird welfare and food safety.
  • Defining optimal DEM resolutions and point densities for modelling hydrologically sensitive areas in agricultural catchments dominated by microtopography

    Thomas, I.A.; Jordan, P.; Shine, O.; Fenton, Owen; Mellander, Per-Erik; Dunlop, P.; Murphy, P.N.C.; Teagasc Walsh Fellowship Programme; Department of Agriculture, Food and the Marine (Elsevier BV, 2017-02)
    Defining critical source areas (CSAs) of diffuse pollution in agricultural catchments depends upon the accurate delineation of hydrologically sensitive areas (HSAs) at highest risk of generating surface runoff pathways. In topographically complex landscapes, this delineation is constrained by digital elevation model (DEM) resolution and the influence of microtopographic features. To address this, optimal DEM resolutions and point densities for spatially modelling HSAs were investigated, for onward use in delineating CSAs. The surface runoff framework was modelled using the Topographic Wetness Index (TWI) and maps were derived from 0.25 m LiDAR DEMs (40 bare-earth points m−2), resampled 1 m and 2 m LiDAR DEMs, and a radar generated 5 m DEM. Furthermore, the resampled 1 m and 2 m LiDAR DEMs were regenerated with reduced bare-earth point densities (5, 2, 1, 0.5, 0.25 and 0.125 points m−2) to analyse effects on elevation accuracy and important microtopographic features. Results were compared to surface runoff field observations in two 10 km2 agricultural catchments for evaluation. Analysis showed that the accuracy of modelled HSAs using different thresholds (5%, 10% and 15% of the catchment area with the highest TWI values) was much higher using LiDAR data compared to the 5 m DEM (70–100% and 10–84%, respectively). This was attributed to the DEM capturing microtopographic features such as hedgerow banks, roads, tramlines and open agricultural drains, which acted as topographic barriers or channels that diverted runoff away from the hillslope scale flow direction. Furthermore, the identification of ‘breakthrough’ and ‘delivery’ points along runoff pathways where runoff and mobilised pollutants could be potentially transported between fields or delivered to the drainage channel network was much higher using LiDAR data compared to the 5 m DEM (75–100% and 0–100%, respectively). Optimal DEM resolutions of 1–2 m were identified for modelling HSAs, which balanced the need for microtopographic detail as well as surface generalisations required to model the natural hillslope scale movement of flow. Little loss of vertical accuracy was observed in 1–2 m LiDAR DEMs with reduced bare-earth point densities of 2–5 points m−2, even at hedgerows. Further improvements in HSA models could be achieved if soil hydrological properties and the effects of flow sinks (filtered out in TWI models) on hydrological connectivity are also considered.
  • Collective unconscious: How gut microbes shape human behavior

    Dinan, Timothy G.; Stilling, Roman M.; Stanton, Catherine; Cryan, John F.; Science Foundation Ireland; Health Research Board of Ireland; European Union; SFI/12/RC/2273; HRA_POR/2011/23; HRA_POR/2012/32 (Elsevier BV, 2015-04)
    The human gut harbors a dynamic and complex microbial ecosystem, consisting of approximately 1 kg of bacteria in the average adult, approximately the weight of the human brain. The evolutionary formation of a complex gut microbiota in mammals has played an important role in enabling brain development and perhaps sophisticated social interaction. Genes within the human gut microbiota, termed the microbiome, significantly outnumber human genes in the body, and are capable of producing a myriad of neuroactive compounds. Gut microbes are part of the unconscious system regulating behavior. Recent investigations indicate that these microbes majorly impact on cognitive function and fundamental behavior patterns, such as social interaction and stress management. In the absence of microbes, underlying neurochemistry is profoundly altered. Studies of gut microbes may play an important role in advancing understanding of disorders of cognitive functioning and social interaction, such as autism.
  • Characterization of plant-derived lactococci on the basis of their volatile compounds profile when grown in milk

    Alemayehu, Debebe; Hannon, John A.; McAuliffe, Olivia; Ross, R Paul; Irish Dairy Levy Research Trust (Elsevier BV, 2014-02-17)
    A total of twelve strains of lactococci were isolated from grass and vegetables (baby corn and fresh green peas). Ten of the isolates were classified as Lactococcus lactis subsp. lactis and two as Lactococcus lactis subsp. cremoris based on 16S rDNA sequencing. Most of the plant-derived strains were capable of metabolising a wide range of carbohydrates in that they fermented D-mannitol, amygdalin, potassium gluconate, l-arabinose, d-xylose, sucrose and gentibiose. None of the dairy control strains (i.e. L. lactis subsp. cremoris HP, L. lactis subsp. lactis IL1403 and Lactococcus lactis 303) were able to utilize any of these carbohydrates. The technological potential of the isolates as flavour-producing lactococci was evaluated by analysing their growth in milk and their ability to produce volatile compounds using solid phase micro-extraction of the headspace coupled to gas chromatography–mass spectrometry (SPME GC–MS). Principal component analysis (PCA) of the volatile compounds clearly separated the dairy strains from the plant derived strains, with higher levels of most flavour rich compounds. The flavour compounds produced by the plant isolates among others included; fatty acids such as 2- and 3-methylbutanoic acids, and hexanoic acid, several esters (e.g. butyl acetate and ethyl butanoate) and ketones (e.g. acetoin, diacetyl and 2-heptanone), all of which have been associated with desirable and more mature flavours in cheese. As such the production of a larger number of volatile compounds is a distinguishing feature of plant-derived lactococci and might be a desirable trait for the production of dairy products with enhanced flavour and/or aroma.
  • Beneficial modulation of the gut microbiota

    Cotter, Paul D. (Elsevier BV, 2016-04-01)
    As the scientific community continues to develop an ever-greater understanding of the composition and function of the human gut microbiota, and the role of specific microbial populations in health and disease, attention has turned to the tools that are at our disposal with respect to altering these microbes in a beneficial way. The options available include the use of diet, probiotics/prebiotics, antimicrobials and, potentially, exercise. Here, our recent investigations of the relationship between protein, bacteriocin producing probiotics and exercise and the gut microbiota and, in turn, health will be described.
  • Marine Gelatine from Rest Raw Materials

    Milovanovic, Ivan; Hayes, Maria; Bord Iascaigh Mhara; DAFM/07/2017/PDFP (MDPI AG, 2018-11-27)
    In recent years, demand for consumption of marine foods, and especially fish, has substantially increased worldwide. The majority of collagen available is sourced from mammalian-derived products. Although fish derived gelatine is a viable alternative to mammalian sourced gelatine, there are certain limitations related to the use of fish gelatine that include odour, colour, functional properties, and consistency in its amino acid composition. Chemicals used for pre-treatment, as well as extraction conditions such as temperature and time, can influence the length of polypeptide chains that result and the functional properties of the gelatine. Compared to traditional sources, gelatines derived from fish show significant differences in chemical and physical properties, and great care should be paid to optimization of the production process in order to obtain a product with the best properties for intended applications. The focus of this review is to explore the feasibility of producing gelatine sourced from marine processing by-products using different pre-treatment and extraction strategies with the aim of improving the techno-functional properties of the final product and improving the clean-label status of gelatines. The bioactivities of gelatine hydrolysates are also discussed.
  • Recovery of Polyphenols from Brewer’s Spent Grains

    Birsan, Rares I.; Wilde, Peter; Waldron, Keith W.; Rai, Dilip K.; Teagasc Walsh Fellowship Programme; 2014027 (MDPI AG, 2019-09-07)
    The recovery of antioxidant polyphenols from light, dark and mix brewer’s spent grain (BSG) using conventional maceration, microwave and ultrasound assisted extraction was investigated. Total polyphenols were measured in the crude (60% acetone), liquor extracts (saponified with 0.75% NaOH) and in their acidified ethyl acetate (EtOAc) partitioned fractions both by spectrophotometry involving Folin–Ciocalteu reagent and liquid-chromatography-tandem mass spectrometry (LC-MS/MS) methods. Irrespective of the extraction methods used, saponification of BSG yielded higher polyphenols than in the crude extracts. The EtOAc fractionations yielded the highest total phenolic content (TPC) ranging from 3.01 ± 0.19 to 4.71 ± 0.28 mg gallic acid equivalent per g of BSG dry weight. The corresponding total polyphenols quantified by LC-MS/MS ranged from 549.9 ± 41.5 to 2741.1 ± 5.2 µg/g of BSG dry weight. Microwave and ultrasound with the parameters and equipment used did not improve the total polyphenol yield when compared to the conventional maceration method. Furthermore, the spectrophotometric quantification of the liquors overestimated the TPC, while the LC-MS/MS quantification gave a closer representation of the total polyphenols in all the extracts. The total polyphenols were in the following order in the EtOAc fractions: BSG light > BSG Mix > BSG dark, and thus suggested BSG light as a sustainable, low cost source of natural antioxidants that may be tapped for applications in food and phytopharmaceutical industries
  • Tracking the Dairy Microbiota from Farm Bulk Tank to Skimmed Milk Powder

    McHugh, Aoife J.; Feehily, Conor; Fenelon, Mark A.; Gleeson, David E; Hill, Colin; Cotter, Paul D.; Department of Agriculture, Food and the Marine; Science Foundation Ireland; European Union; 14/F/883; et al. (American Society for Microbiology, 2020-04-07)
    Microorganisms from the environment can enter the dairy supply chain at multiple stages, including production, milk collection, and processing, with potential implications for quality and safety. The ability to track these microorganisms can be greatly enhanced by the use of high-throughput DNA sequencing (HTS). Here HTS, both 16S rRNA gene amplicon and shotgun metagenomic sequencing were applied to investigate the microbiomes of fresh mid- and late-lactation milk collected from farm bulk tanks, collection tankers, milk silos, skimmed milk silos, a cream silo, and powder samples to investigate the microbial changes throughout a skim milk powder manufacturing process. 16S rRNA gene analysis established that the microbiota of raw milks from farm bulk tanks and in collection tankers were very diverse but that psychrotrophic genera associated with spoilage, Pseudomonas and Acinetobacter, were present in all samples. Upon storage within the whole-milk silo at the processing facility, the species Pseudomonas fluorescens and Acinetobacter baumannii became dominant. The skimmed milk powder generated during the mid-lactation period had a microbial composition that was very different from that of raw milk; specifically, two thermophilic genera, Thermus and Geobacillus, were enriched. In contrast, the microbiota of skimmed milk powder generated from late-lactation milk more closely resembled that of the raw milk and was dominated by spoilage-associated psychrotrophic bacteria. This study demonstrates that the dairy microbiota can differ significantly across different sampling days. More specifically, HTS can be used to trace microbial species from raw milks through processing to final powdered products.
  • Comparison of Staphylococcus Phage K with Close Phage Relatives Commonly Employed in Phage Therapeutics

    Ajuebor, Jude; Buttimer, Colin; Arroyo-Moreno, Sara; Chanishvili, Nina; Gabriel, Emma; O’Mahony, Jim; McAuliffe, Olivia; Neve, Horst; Franz, Charles; Coffey, Aidan; et al. (MDPI AG, 2018-04-25)
    The increase in antibiotic resistance in pathogenic bacteria is a public health danger requiring alternative treatment options, and this has led to renewed interest in phage therapy. In this respect, we describe the distinct host ranges of Staphylococcus phage K, and two other K-like phages against 23 isolates, including 21 methicillin-resistant S. aureus (MRSA) representative sequence types representing the Irish National MRSA Reference Laboratory collection. The two K-like phages were isolated from the Fersisi therapeutic phage mix from the Tbilisi Eliava Institute, and were designated B1 (vB_SauM_B1) and JA1 (vB_SauM_JA1). The sequence relatedness of B1 and JA1 to phage K was observed to be 95% and 94% respectively. In terms of host range on the 23 Staphylococcus isolates, B1 and JA1 infected 73.9% and 78.2% respectively, whereas K infected only 43.5%. Eleven open reading frames (ORFs) present in both phages B1 and JA1 but absent in phage K were identified by comparative genomic analysis. These ORFs were also found to be present in the genomes of phages (Team 1, vB_SauM-fRuSau02, Sb_1 and ISP) that are components of several commercial phage mixtures with reported wide host ranges. This is the first comparative study of therapeutic staphylococcal phages within the recently described genus Kayvirus.
  • Nisin in Combination with Cinnamaldehyde and EDTA to Control Growth of Escherichia coli Strains of Swine Origin

    Field, Des; Baghou, Inès; Rea, Mary; Gardiner, Gillian; Ross, R Paul; Hill, Colin; Science Foundation Ireland; 10/IN.1/B3027; SFI/12/RC/2273 (MDPI AG, 2017-12-12)
    Post-weaning diarrhoea (PWD) due to enterotoxigenic Escherichia coli (ETEC) is an economically important disease in pig production worldwide. Although antibiotics have contributed significantly to mitigate the economic losses caused by PWD, there is major concern over the increased incidence of antimicrobial resistance among bacteria isolated from pigs. Consequently, suitable alternatives that are safe and effective are urgently required. Many naturally occurring compounds, including the antimicrobial peptide nisin and a number of plant essential oils, have been widely studied and are reported to be effective as antimicrobial agents against pathogenic microorganisms. Here, we evaluate the potential of nisin in combination with the essential oil cinnamaldehyde and ethylenediaminetetraacetic acid (EDTA) to control the growth of E. coli strains of swine origin including two characterized as ETEC. The results reveal that the use of nisin (10 μM) with low concentrations of trans-cinnamaldehyde (125 μg/mL) and EDTA (0.25–2%) resulted in extended lag phases of growth compared to when either antimicrobial is used alone. Further analysis through kill curves revealed that an approximate 1-log reduction in E. coli cell counts was observed against the majority of targets tested following 3 h incubation. These results highlight the potential benefits of combining the natural antimicrobial nisin with trans-cinnamaldehyde and EDTA as a new approach for the inhibition of E. coli strains of swine origin.

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