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

Recent Submissions

  • Detection and Enumeration of Spore-Forming Bacteria in Powdered Dairy Products

    McHugh, Aoife J.; Feehily, Conor; Hill, Colin; Cotter, Paul D.; Department of Agriculture, Food and the Marine, Ireland (Frontiers, 2017-01-31)
    With the abolition of milk quotas in the European Union in 2015, several member states including Ireland, Luxembourg, and Belgium have seen year on year bi-monthly milk deliveries to dairies increase by up to 35%. Milk production has also increased outside of Europe in the past number of years. Unsurprisingly, there has been a corresponding increased focus on the production of dried milk products for improved shelf life. These powders are used in a wide variety of products, including confectionery, infant formula, sports dietary supplements and supplements for health recovery. To ensure quality and safety standards in the dairy sector, strict controls are in place with respect to the acceptable quantity and species of microorganisms present in these products. A particular emphasis on spore-forming bacteria is necessary due to their inherent ability to survive extreme processing conditions. Traditional microbiological detection methods used in industry have limitations in terms of time, efficiency, accuracy, and sensitivity. The following review will explore the common spore-forming bacterial contaminants of milk powders, will review the guidelines with respect to the acceptable limits of these microorganisms and will provide an insight into recent advances in methods for detecting these microbes. The various advantages and limitations with respect to the application of these diagnostics approaches for dairy food will be provided. It is anticipated that the optimization and application of these methods in appropriate ways can ensure that the enhanced pressures associated with increased production will not result in any lessening of safety and quality standards.
  • Mesophilic sporeformers identified in whey powder by using shotgun metagenomic sequencing

    McHugh, Aoife J.; Feehily, Conor; Tobin, John; Fenelon, Mark A.; Hill, Colin; Cotter, Paul D.; Department of Agriculture, Food and the Marine, Ireland; Science Foundation Ireland; 14/F/883; 11/P1/1137 (American Society for Microbiology, 2018-10-01)
    Spoilage and pathogenic spore-forming bacteria are a major cause of concern for producers of dairy products. Traditional agar-based detection methods employed by the dairy industry have limitations with respect to their sensitivity and specificity. The aim of this study was to identify low-abundance sporeformers in samples of a powdered dairy product, whey powder, produced monthly over 1 year, using novel culture-independent shotgun metagenomics-based approaches. Although mesophilic sporeformers were the main target of this study, in one instance thermophilic sporeformers were also targeted using this culture-independent approach. For comparative purposes, mesophilic and thermophilic sporeformers were also tested for within the same sample using culture-based approaches. Ultimately, the approaches taken highlighted differences in the taxa identified due to treatment and isolation methods. Despite this, low levels of transient, mesophilic, and in some cases potentially pathogenic sporeformers were consistently detected in powder samples. Although the specific sporeformers changed from one month to the next, it was apparent that 3 groups of mesophilic sporeformers, namely, Bacillus cereus, Bacillus licheniformis/Bacillus paralicheniformis, and a third, more heterogeneous group containing Brevibacillus brevis, dominated across the 12 samples. Total thermophilic sporeformer taxonomy was considerably different from mesophilic taxonomy, as well as from the culturable thermophilic taxonomy, in the one sample analyzed by all four approaches. Ultimately, through the application of shotgun metagenomic sequencing to dairy powders, the potential for this technology to facilitate the detection of undesirable bacteria present in these food ingredients is highlighted.
  • Evaluation of the Potential of Lactobacillus paracasei Adjuncts for Flavor Compounds Development and Diversification in Short-Aged Cheddar Cheese

    Stefanovic, Ewelina; Kilcawley, Kieran N; Roces, Clara; Rea, Mary C.; O’Sullivan, Maurice; Sheehan, Jeremiah J.; McAuliffe, Olivia; Teagasc Walsh Fellowship Programme; 2012040 (Frontiers, 2018-07-05)
    The non-starter microbiota of Cheddar cheese mostly comprises mesophilic lactobacilli, such as Lactobacillus casei, Lactobacillus paracasei, Lactobacillus rhamnosus, and Lactobacillus plantarum. These bacteria are recognized for their potential to improve Cheddar cheese flavor when used as adjunct cultures. In this study, three strains of L. paracasei (DPC2071, DPC4206, and DPC4536) were evaluated for their contribution to the enhancement and diversification of flavor in short-aged Cheddar cheese. The strains were selected based on their previously determined genomic diversity, variability in proteolytic enzyme activities and metabolic capability in cheese model systems. The addition of adjunct cultures did not affect the gross composition or levels of lipolysis of the cheeses. The levels of free amino acids (FAA) in cheeses showed a significant increase after 28 days of ripening. However, the concentrations of individual amino acids in the cheeses did not significantly differ except for some amino acids (aspartic acid, threonine, serine, and tryptophan) at Day 14. Volatile profile analysis revealed that the main compounds that differentiated the cheeses were of lipid origin, such as long chain aldehydes, acids, ketones, and lactones. This study demonstrated that the adjunct L. paracasei strains contributed to the development and diversification of compounds related to flavor in short-aged Cheddar cheeses.
  • Phages of non-dairy lactococci: isolation and characterization of ΦL47, a phage infecting the grass isolate Lactococcus lactis ssp. cremoris DPC6860

    Cavanagh, Daniel; Guinane, Catriona M.; Neve, Horst; Coffey, Aidan; Ross, R. Paul; Fitzgerald, Gerald F.; McAuliffe, Olivia; Irish Dairy Levy Research Trust; Teagasc Walsh Fellowship Programme (Frontiers, 2014-01-13)
    Lactococci isolated from non-dairy sources have been found to possess enhanced metabolic activity when compared to dairy strains. These capabilities may be harnessed through the use of these strains as starter or adjunct cultures to produce more diverse flavor profiles in cheese and other dairy products. To understand the interactions between these organisms and the phages that infect them, a number of phages were isolated against lactococcal strains of non-dairy origin. One such phage, ΦL47, was isolated from a sewage sample using the grass isolate L. lactis ssp. cremoris DPC6860 as a host. Visualization of phage virions by transmission electron microscopy established that this phage belongs to the family Siphoviridae and possesses a long tail fiber, previously unseen in dairy lactococcal phages. Determination of the lytic spectrum revealed a broader than expected host range, with ΦL47 capable of infecting 4 industrial dairy strains, including ML8, HP and 310, and 3 additional non-dairy isolates. Whole genome sequencing of ΦL47 revealed a dsDNA genome of 128, 546 bp, making it the largest sequenced lactococcal phage to date. In total, 190 open reading frames (ORFs) were identified, and comparative analysis revealed that the predicted products of 117 of these ORFs shared greater than 50% amino acid identity with those of L. lactis phage Φ949, a phage isolated from cheese whey. Despite their different ecological niches, the genomic content and organization of ΦL47 and Φ949 are quite similar, with both containing 4 gene clusters oriented in different transcriptional directions. Other features that distinguish ΦL47 from Φ949 and other lactococcal phages, in addition to the presence of the tail fiber and the genome length, include a low GC content (32.5%) and a high number of predicted tRNA genes (8). Comparative genome analysis supports the conclusion that ΦL47 is a new member of the 949 lactococcal phage group which currently includes the dairy Φ949.
  • Invited review: Whey proteins as antioxidants and promoters of cellular antioxidant pathways

    Corrochano, Alberto R.; Buckin, Vitaly; Kelly, Phil M.; Giblin, Linda; Department of Agriculture, Food and the Marine, Ireland; Teagasc Walsh Fellowship Programme; 13 F 454; 13 F 454-WheyGSH (Elsevier for American Dairy Science Association, 28/03/2018)
    Oxidative stress contributes to cell injury and aggravates several chronic diseases. Dietary antioxidants help the body to fight against free radicals and, therefore, avoid or reduce oxidative stress. Recently, proteins from milk whey liquid have been described as antioxidants. This review summarizes the evidence that whey products exhibit radical scavenging activity and reducing power. It examines the processing and treatment attempts to increase the antioxidant bioactivity and identifies 1 enzyme, subtilisin, which consistently produces the most potent whey fractions. The review compares whey from different milk sources and puts whey proteins in the context of other known food antioxidants. However, for efficacy, the antioxidant activity of whey proteins must not only survive processing, but also upper gut transit and arrival in the bloodstream, if whey products are to promote antioxidant levels in target organs. Studies reveal that direct cell exposure to whey samples increases intracellular antioxidants such as glutathione. However, the physiological relevance of these in vitro assays is questionable, and evidence is conflicting from dietary intervention trials, with both rats and humans, that whey products can boost cellular antioxidant biomarkers.
  • Physiological Gut Oxygenation Alters GLP‐1 Secretion from the Enteroendocrine Cell Line STC‐1

    Kondrashina, Alina; Papkovsky, Dmitri; Giblin, Linda; Enterprise Ireland; TC20130001 (Wiley, 29/09/2017)
    1 Scope Enteroendocrine cell lines are routinely assayed in simple buffers at ≈20% oxygen to screen foods for bioactives that boost satiety hormone levels. However, in vivo, enteroendocrine cells are exposed to different phases of food digestion and function at low oxygen concentration, ranging from 7.5% in the stomach to 0.5% in the colon–rectal junction. 2 Methods and results The objective of this study is to investigate the effect of physiologically relevant O2 concentrations of the gut on the production and secretion of the satiety hormone, glucagon‐like peptide 1 (GLP‐1), from the murine enteroendocrine cell line, secretin tumor cell line (STC‐1), in response to dairy macronutrients as they transit the gut. GLP‐1 exocytosis from STC‐1 cells is influenced by both oxygen concentration and by individual macronutrients. At low oxygen, STC‐1 cell viability is significantly improved for all macronutrient stimulations and cyclic adenosine monophosphate levels are dampened. GLP‐1 secretion from STC‐1 cells is influenced by both the phase of yogurt digestion and corresponding O2 concentration. Atmospheric oxygen at 4.5% combined with upper gastric digesta, which simulates ileum conditions, yields the highest GLP‐1 response. 3 Conclusion This demonstrates the importance of considering physiological oxygen levels and food digestion along gastrointestinal tract for reliable in vitro analysis of gut hormone secretion.
  • Sinapinic and protocatechuic acids found in rapeseed: isolation, characterisation and potential benefits for human health as functional food ingredients

    Quinn, Leah; Gray, Stephen G.; Meaney, Steven; Finn, Stephen; Kenny, Owen; Hayes, Maria (Teagasc (Agriculture and Food Development Authority), Ireland, 13/12/2017)
    Rapeseed is one of the world’s major oilseeds, and rapeseed oil is produced by pressing of the seeds. This process results in the production of a low-economic-value by-product, rapeseed meal, which is commonly used as animal feed. Rapeseed meal is rich in bioactive phenolic compounds, including sinapinic acid (SA) and protocatechuic acid (PCA). Isolation of these bioactive compounds from a by-product of rapeseed oil production is largely in agreement with the current concept of the circular economy and total utilisation of crop harvest using a biorefinery approach. In this review, current information concerning traditional and novel methods to isolate phenolic compounds – including SA and PCA – from rapeseed meal, along with in vitro and in vivo studies concerning the bioactivity of SA and PCA and their associated health effects, is collated. These health effects include anti-inflammatory, anti-cancer, anti-diabetes activities, along with histone deacetylase inhibition and protective cardiovascular, neurological and hepatic effects. The traditional extraction methods include use of solvents and/or enzymes. However, a need for simpler, more efficient methodologies has led to the development of novel extraction processes, including microwave-assisted, ultrasound-assisted, pulsed electric field and high-voltage electrical discharge extraction processes.
  • Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains

    Arboleya, Silvia; Bottacini, Francesca; O’Connell-Motherway, Mary; Ryan, C. A; Ross, R. P; van Sinderen, Douwe; Stanton, Catherine; Science Foundation Ireland; Department of Agriculture, Food and the Marine, Ireland; SFI/12/RC/2273; 10FDairy (Biomed Central, 08/01/2018)
    Background Bifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, thus indicative of a close symbiotic host-microbe relationship. Different mechanisms may be responsible for the high competitiveness of this taxon in its human host to allow stable establishment in the complex and dynamic intestinal microbiota environment. The objective of this study was to assess the genetic and metabolic diversity in a set of 20 B. longum strains, most of which had previously been isolated from infants, by performing whole genome sequencing and comparative analysis, and to analyse their carbohydrate utilization abilities using a gene-trait matching approach. Results We analysed their pan-genome and their phylogenetic relatedness. All strains clustered in the B. longum ssp. longum phylogenetic subgroup, except for one individual strain which was found to cluster in the B. longum ssp. suis phylogenetic group. The examined strains exhibit genomic diversity, while they also varied in their sugar utilization profiles. This allowed us to perform a gene-trait matching exercise enabling the identification of five gene clusters involved in the utilization of xylo-oligosaccharides, arabinan, arabinoxylan, galactan and fucosyllactose, the latter of which is an abundant human milk oligosaccharide (HMO). Conclusions The results showed high diversity in terms of genes and predicted glycosyl-hydrolases, as well as the ability to metabolize a large range of sugars. Moreover, we corroborate the capability of B. longum ssp. longum to metabolise HMOs. Ultimately, their intraspecific genomic diversity and the ability to consume a wide assortment of carbohydrates, ranging from plant-derived carbohydrates to HMOs, may provide an explanation for the competitive advantage and persistence of B. longum in the human gut microbiome.
  • Effect of pre-treatment on the generation of dipeptidyl peptidase-IV- and prolyl endopeptidase-inhibitory hydrolysates from bovine lung

    Lafarga, T.; Hayes, Maria; Department of Agriculture, Food and the Marine, Ireland; Teagasc Walsh Fellowship Programme; 11/F/043 (Teagasc (Agriculture and Food Development Authority), Ireland, 25/05/2017)
    The aim of this work was to study the effect of two different pre-treatments, high temperature (100 °C, 5 min) and high pressure (600 MPa, 3 min), on the potential of the enzymes papain, collagenase and Alcalase® to generate bioactive hydrolysates containing dipeptidyl peptidase-IV- (DPP-IV; EC 3.4.14.5) and prolyl endopeptidase- (PEP; EC 3.4.21.26) inhibitory peptides from bovine lung. Both pre-treatments resulted in an increase in the degree of hydrolysis over a 24 h period (P < 0.001) and significantly increased the DPP-IV- and PEP-inhibitory activities of the generated hydrolysates (P < 0.001). Generated hydrolysates included an Alcalase hydrolysate of pressure-treated bovine lung, which was the most active, and showed DPP-IV and PEP half-maximal inhibitory concentration (IC50) values of 1.43 ± 0.06 and 3.62 ± 0.07 mg/ mL, respectively. The major peptides contained in this hydrolysate were determined by liquid chromatography-tandem mass spectrometry, and results demonstrated that bovine lung is a good substrate for the release of bioactive peptides when proper pre-treatment and enzymatic treatment are applied.
  • Oral Delivery of Nisin in Resistant Starch Based Matrices Alters the Gut Microbiota in Mice

    Gough, Ronan; Cabrera-Rubio, Raul; O'Connor, Paula M.; Crispie, Fiona; Miao, Song; Hill, Colin; Ross, R. Paul; Cotter, Paul D.; Nilaweera, Kanishka N.; Rea, Mary C.; Department of Agriculture, Food and the Marine, Ireland; Teagasc Walsh Fellowship Programme; Science Foundation Ireland; BBSRC; Teagasc; 10/RD/TMFRC/701; 2012221; SFI/12/RC2273; SFI/16/BBSRC/3389; BB/P009875/1 (Frontiers, 15/06/2018)
    There is a growing recognition of the role the gastrointestinal microbiota plays in health and disease. Ingested antimicrobial proteins and peptides have the potential to alter the gastrointestinal microbiota; particularly if protected from digestion. Nisin is an antimicrobial peptide that is used as a food preservative. This study examined the ability of nisin to affect the murine microbiota when fed to mice in two different starch based matrices; a starch dough comprising raw starch granules and a starch gel comprising starch that was gelatinized and retrograded. The effects of the two starch matrices by themselves on the microbiota were also examined. Following 16S rRNA compositional sequencing, beta diversity analysis highlighted a significant difference (p = 0.001, n = 10) in the murine microbiota between the four diet groups. The differences between the two nisin containing diets were mainly attributable to differences in the nisin release from the starch matrices while the differences between the carriers were mainly attributable to the type of resistant starch they possessed. Indeed, the differences in the relative abundance of several genera in the mice consuming the starch dough and starch gel diets, in particular Akkermansia, the relative abundance of which was 0.5 and 11.9%, respectively (p = 0.0002, n = 10), points to the potential value of resistance starch as a modulator of beneficial gut microbes. Intact nisin and nisin digestion products (in particular nisin fragment 22–31) were detected in the feces and the nisin was biologically active. However, despite a three-fold greater consumption of nisin in the group fed the nisin in starch dough diet, twice as much nisin was detected in the feces of the group which consumed the nisin in starch gel diet. In addition, the relative abundance of three times as many genera from the lower gastrointestinal tract (GIT) were significantly different (p < 0.001, n = 10) to the control for the group fed the nisin in starch gel diet, implying that the starch gel afforded a degree of protection from digestion to the nisin entrapped within it.
  • Whey protein effects on energy balance link the intestinal mechanisms of energy absorption with adiposity and hypothalamic neuropeptide gene expression

    Nilaweera, Kanishka N.; Cabrera-Rubio, Raul; Speakman, John R.; O'Conor, Paula M.; McAuliffe, AnnMarie; guinane, Catriona M.; Lawton, Elaine; Crispie, Fiona; Aguillera, Monica; Stanley, Maurice; Boscaini, Serena; Joyce, Susan; Melgar, Silvia; Cryan, John F.; Cotter, Paul D.; BBSRC; Science Foundation Ireland; Teagasc; BB/P009875/1; SFI/16/BBSRC/3389 a; SFI/12/RC/2273 (American Physiological Society, 19/06/2017)
    We tested the hypothesis that dietary whey protein isolate (WPI) affects the intestinal mechanisms related to energy absorption and that the resulting energy deficit is compensated by changes in energy balance to support growth. C57BL/6 mice were provided a diet enriched with WPI with varied sucrose content, and the impact on energy balance-related parameters was investigated. As part of a high-sucrose diet, WPI reduced the hypothalamic expression of pro-opiomelanocortin gene expression and increased energy intake. The energy expenditure was unaffected, but epididymal weight was reduced, indicating an energy loss. Notably, there was a reduction in the ileum gene expression for amino acid transporter SLC6a19, glucose transporter 2, and fatty acid transporter 4. The composition of the gut microbiota also changed, where Firmicutes were reduced. The above changes indicated reduced energy absorption through the intestine. We propose that this mobilized energy in the adipose tissue and caused hypothalamic changes that increased energy intake, acting to counteract the energy deficit arising in the intestine. Lowering the sucrose content in the WPI diet increased energy expenditure. This further reduced epididymal weight and plasma leptin, whereupon hypothalamic ghrelin gene expression and the intestinal weight were both increased. These data suggest that when the intestine-adipose-hypothalamic pathway is subjected to an additional energy loss (now in the adipose tissue), compensatory changes attempt to assimilate more energy. Notably, WPI and sucrose content interact to enable the component mechanisms of this pathway.
  • Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains

    Arboleya, Silvia; Bottacini, Francesca; O’Connell-Motherway, Mary; Ryan, C. A; Ross, R. P; van Sinderen, Douwe; Stanton, Catherine; Science Foundation Ireland; Department of Agriculture, Food and the Marine, Ireland; SFI/12/RC/2273; 10FDairy (Biomed Central, 08/01/2018)
    Background Bifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, thus indicative of a close symbiotic host-microbe relationship. Different mechanisms may be responsible for the high competitiveness of this taxon in its human host to allow stable establishment in the complex and dynamic intestinal microbiota environment. The objective of this study was to assess the genetic and metabolic diversity in a set of 20 B. longum strains, most of which had previously been isolated from infants, by performing whole genome sequencing and comparative analysis, and to analyse their carbohydrate utilization abilities using a gene-trait matching approach. Results We analysed their pan-genome and their phylogenetic relatedness. All strains clustered in the B. longum ssp. longum phylogenetic subgroup, except for one individual strain which was found to cluster in the B. longum ssp. suis phylogenetic group. The examined strains exhibit genomic diversity, while they also varied in their sugar utilization profiles. This allowed us to perform a gene-trait matching exercise enabling the identification of five gene clusters involved in the utilization of xylo-oligosaccharides, arabinan, arabinoxylan, galactan and fucosyllactose, the latter of which is an abundant human milk oligosaccharide (HMO). Conclusions The results showed high diversity in terms of genes and predicted glycosyl-hydrolases, as well as the ability to metabolize a large range of sugars. Moreover, we corroborate the capability of B. longum ssp. longum to metabolise HMOs. Ultimately, their intraspecific genomic diversity and the ability to consume a wide assortment of carbohydrates, ranging from plant-derived carbohydrates to HMOs, may provide an explanation for the competitive advantage and persistence of B. longum in the human gut microbiome.
  • Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains

    Arboleya, Silvia; Bottacini, Francesca; O’Connell-Motherway, Mary; Ryan, C. A; Ross, R. P; van Sinderen, Douwe; Stanton, Catherine; Science Foundation Ireland; Department of Agriculture, Food and the Marine, Ireland; SFI/12/RC/2273; 10FDairy (Biomed Central, 08/01/2018)
    Background Bifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, thus indicative of a close symbiotic host-microbe relationship. Different mechanisms may be responsible for the high competitiveness of this taxon in its human host to allow stable establishment in the complex and dynamic intestinal microbiota environment. The objective of this study was to assess the genetic and metabolic diversity in a set of 20 B. longum strains, most of which had previously been isolated from infants, by performing whole genome sequencing and comparative analysis, and to analyse their carbohydrate utilization abilities using a gene-trait matching approach. Results We analysed their pan-genome and their phylogenetic relatedness. All strains clustered in the B. longum ssp. longum phylogenetic subgroup, except for one individual strain which was found to cluster in the B. longum ssp. suis phylogenetic group. The examined strains exhibit genomic diversity, while they also varied in their sugar utilization profiles. This allowed us to perform a gene-trait matching exercise enabling the identification of five gene clusters involved in the utilization of xylo-oligosaccharides, arabinan, arabinoxylan, galactan and fucosyllactose, the latter of which is an abundant human milk oligosaccharide (HMO). Conclusions The results showed high diversity in terms of genes and predicted glycosyl-hydrolases, as well as the ability to metabolize a large range of sugars. Moreover, we corroborate the capability of B. longum ssp. longum to metabolise HMOs. Ultimately, their intraspecific genomic diversity and the ability to consume a wide assortment of carbohydrates, ranging from plant-derived carbohydrates to HMOs, may provide an explanation for the competitive advantage and persistence of B. longum in the human gut microbiome.
  • Microbiota-related Changes in Bile Acid & Tryptophan Metabolism are Associated with Gastrointestinal Dysfunction in a Mouse Model of Autism

    Golubeva, Anna B.; Joyce, Susan A.; Moloney, Gerard; Burokas, Aurelijus; Sherwin, Eoin; Arboyelaya, Silvia; Flynn, Ian; Khochanskiy, Dmitry; Pérez, Angela M.; Peterson, Veronica; Rea, Kieran; MUrphy, Kiera; Makarova, Olga; Buravkov, Sergey; Hyland, Niall P.; Stanton, Catherine; Clarke, Gerard; Gahan, Cormac G>M>; Dinan, Timothy G.; Cryan, John F.; Science Foundation Ireland; SFI/12/RC/2273 (15/09/2017)
    Autism spectrum disorder (ASD) is one of the most prevalent neurodevelopmental conditions worldwide. There is growing awareness that ASD is highly comorbid with gastrointestinal distress and altered intestinal microbiome, and that host-microbiome interactions may contribute to the disease symptoms. However, the paucity of knowledge on gut-brain axis signaling in autism constitutes an obstacle to the development of precision microbiota-based therapeutics in ASD. To this end, we explored the interactions between intestinal microbiota, gut physiology and social behavior in a BTBR T+ Itpr3tf/J mouse model of ASD. Here we show that a reduction in the relative abundance of very particular bacterial taxa in the BTBR gut – namely, bile-metabolizing Bifidobacterium and Blautia species, - is associated with deficient bile acid and tryptophan metabolism in the intestine, marked gastrointestinal dysfunction, as well as impaired social interactions in BTBR mice. Together these data support the concept of targeted manipulation of the gut microbiota for reversing gastrointestinal and behavioral symptomatology in ASD, and offer specific plausible targets in this endeavor.
  • Bile acids at the cross-roads of gut microbiome–host cardiometabolic interactions

    Ryan, Paul M; Stanton, Catherine; Caplice, Noel M; Science Foundation Ireland; Enterprise Ireland; SFI/12/RC/2273; CF/2013/3030A/B (Biomed Central, 28/12/2017)
    While basic and clinical research over the last several decades has recognized a number of modifiable risk factors associated with cardiometabolic disease progression, additional and alternative biological perspectives may offer novel targets for prevention and treatment of this disease set. There is mounting preclinical and emerging clinical evidence indicating that the mass of metabolically diverse microorganisms which inhabit the human gastrointestinal tract may be implicated in initiation and modulation of cardiovascular and metabolic disease outcomes. The following review will discuss this gut microbiome–host metabolism axis and address newly proposed bile-mediated signaling pathways through which dysregulation of this homeostatic axis may influence host cardiovascular risk. With a central focus on the major nuclear and membrane-bound bile acid receptor ligands, we aim to review the putative impact of microbial bile acid modification on several major phenotypes of metabolic syndrome, from obesity to heart failure. Finally, attempting to synthesize several separate but complementary hypotheses, we will review current directions in preclinical and clinical investigation in this evolving field.
  • Insights into the Mode of Action of the Sactibiotic Thuricin CD

    Mathur, Harsh; Fallico, Vicenzo; O'Connor, Paula M.; Rea, Mary C.; Cotter, Paul D.; Hill, Colin; Ross, R. Paul (Frontiers, 20/04/2017)
    Thuricin CD is a two-component bacteriocin, consisting of the peptides Trnα and Trnβ, and belongs to the newly designated sactibiotic subclass of bacteriocins. While it is clear from studies conducted thus far that it is a narrow-spectrum bacteriocin, requiring the synergistic activity of the two peptides, the precise mechanism of action of thuricin CD has not been elucidated. This study used a combination of flow cytometry and traditional culture-dependent assays to ascertain the effects of the thuricin CD peptides on the morphology, physiology and viability of sensitive Bacillus firmus DPC6349 cells. We show that both Trnα and Trnβ are membrane-acting and cause a collapse of the membrane potential, which could not be reversed even under membrane-repolarizing conditions. Furthermore, the depolarizing action of thuricin CD is accompanied by reductions in cell size and granularity, producing a pattern of physiological alterations in DPC6349 cells similar to those triggered by the pore-forming single-component bacteriocin Nisin A, and two-component lacticin 3147. Taken together, these results lead us to postulate that the lytic activity of thuricin CD involves the insertion of thuricin CD peptides into the membrane of target cells leading to permeabilization due to pore formation and consequent flux of ions across the membrane, resulting in membrane depolarization and eventual cell death.
  • Genome Sequence of Staphylococcus saprophyticus DPC5671, a Strain Isolated from Cheddar Cheese

    Bertuzzi, Andrea; Guinane, Caitriona M.; Crispie, Fiona; Kilcawley, Kieran N; McSweeney, Paul L.H.; Rea, Mary C. (American Society for Microbiology, 20/04/2017)
    The draft genome sequence of Staphylococcus saprophyticus DPC5671, isolated from cheddar cheese, was determined. S. saprophyticus is a common Gram-positive bacterium detected on the surface of smear-ripened cheese and other fermented foods.
  • Algal Proteins: Extraction, Application, and Challenges Concerning Production

    Bleakley, Stephen; Hayes, Maria; Teagasc Walsh Fellowship Programme (MDPI, 26/04/2017)
    Population growth combined with increasingly limited resources of arable land and fresh water has resulted in a need for alternative protein sources. Macroalgae (seaweed) and microalgae are examples of under-exploited “crops”. Algae do not compete with traditional food crops for space and resources. This review details the characteristics of commonly consumed algae, as well as their potential for use as a protein source based on their protein quality, amino acid composition, and digestibility. Protein extraction methods applied to algae to date, including enzymatic hydrolysis, physical processes, and chemical extraction and novel methods such as ultrasound-assisted extraction, pulsed electric field, and microwave-assisted extraction are discussed. Moreover, existing protein enrichment methods used in the dairy industry and the potential of these methods to generate high value ingredients from algae, such as bioactive peptides and functional ingredients are discussed. Applications of algae in human nutrition, animal feed, and aquaculture are examined
  • Bacteriocin-Antimicrobial Synergy: A Medical and Food Perspective

    Mathur, Harsh; Field, Des; Rea, Mary C.; Cotter, Paul D.; Hill, Colin; Ross, R.Paul; Science Foundation Ireland; SFI/12/RC/2273 (Frontiers, 29/06/2017)
    The continuing emergence of multi-drug resistant pathogens has sparked an interest in seeking alternative therapeutic options. Antimicrobial combinatorial therapy is one such avenue. A number of studies have been conducted, involving combinations of bacteriocins with other antimicrobials, to circumvent the development of antimicrobial resistance and/or increase antimicrobial potency. Such bacteriocin-antimicrobial combinations could have tremendous value, in terms of reducing the likelihood of resistance development due to the involvement of two distinct mechanisms of antimicrobial action. Furthermore, antimicrobial synergistic interactions may also have potential financial implications in terms of decreasing the costs of treatment by reducing the concentration of an expensive antimicrobial and utilizing it in combination with an inexpensive one. In addition, combinatorial therapies with bacteriocins can broaden antimicrobial spectra and/or result in a reduction in the concentration of an antibiotic required for effective treatments to the extent that potentially toxic or adverse side effects can be reduced or eliminated. Here, we review studies in which bacteriocins were found to be effective in combination with other antimicrobials, with a view to targeting clinical and/or food-borne pathogens. Furthermore, we discuss some of the bottlenecks which are currently hindering the development of bacteriocins as viable therapeutic options, as well as addressing the need to exercise caution when attempting to predict clinical outcomes of bacteriocin-antimicrobial combinations.
  • Whole-Genome Shotgun Sequence of Salmonella bongori, First Isolated in Northwestern Italy

    Romano, Angelo; Bellio, Alberto; Macori, Guerrino; Cotter, Paul D; Manila Bianchi, Daniela; Gallina, Silvia; Decastelli, Lucia (American Society for Microbiology, 06/07/2017)
    This study describes the whole-genome shotgun sequence of Salmonella bongori 48:z35:–, originally isolated from a 1-year-old symptomatic patient in northwest Italy, a typically nonendemic area. The draft genome sequence contained 4.56 Mbp and the G+C content was 51.27%.

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