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.


Food Biosciences

Recent Submissions

  • Complete Genome Sequence of the Gamma-Aminobutyric Acid-Producing Strain Streptococcus thermophilus APC151

    Linares, Daniel M.; Arboleya, Silvia; Ross, R. Paul; Stanton, Catherine; Science Foundation Ireland (SFI); SFI/12/RC/2273 (American Society for Microbiology, 2017-04-27)
    Here is presented the whole-genome sequence of Streptococcus thermophilus APC151, isolated from a marine fish. This bacterium produces gamma-aminobutyric acid (GABA) in high yields and is biotechnologically suitable to produce naturally GABAenriched biofunctional yogurt. Its complete genome comprises 2,097 genes and 1,839,134 nucleotides, with an average GC content of 39.1%.
  • Separation of the effects of denaturation and aggregation on whey-casein protein interactions during the manufacture of a model infant formula

    Joyce, Aoife M.; Brodkorb, André; Kelly, Alan L.; O’Mahony, James A.; Irish Department of Agriculture, Food and the Marine; 10/RD/ProSurf/TMFRC/723 (Springer Science and Business Media LLC, 2016-10-10)
    Denaturation and aggregation of whey protein have been extensively studied but there is limited knowledge of their effects on processing properties of infant milk formulae (IMF) systems. In this study, the separate effects of denaturation and aggregation of whey protein on the physicochemical characteristics during processing of a model IMF were examined. Whey protein solutions (8%, w/w, protein) were pre-heated for 2 min at 72 or 85 °C, followed by addition of 2.2 mM calcium (Ca) (H-BCa), or at 85 °C after addition of the same level of Ca (H-ACa), to give pre-treated whey protein for inclusion in three model IMF systems, encoded as H-72-BCa, H-85-BCa and H-85-ACa, respectively. Unheated control samples without (UH-C) and with (UH-C-Ca) added Ca were also prepared. Model IMF systems (5.2%, w/w, protein, 60:40 whey protein:casein ratio, pH 6.8) were then prepared incorporating these pre-treated whey protein ingredients and subjected to lab-scale high-temperature short-time (HTST) heating at 85 °C for 2 min; whey protein denaturation was >81.2% in all samples after HTST. Aggregation of whey protein resulted in a significantly (P < 0.05) higher viscosity in sample H-85-ACa (8.3 mPa.s) compared to UH-C (4.0 mPa.s), and measurement of Ca ion concentration on heating showed that Ca ions enhanced whey protein aggregation, resulting in larger mean protein particle size. The results also suggest that pre-heating of whey protein had a preventative effect on aggregation of protein during HTST of IMF. This study clearly showed that aggregation is more influential than denaturation in determining viscosity development during HTST treatment of IMF, and that such viscosity development can be controlled by altering protein-protein interactions using, for example, pre-heat treatment of whey protein ingredients.
  • Forgotten fungi—the gut mycobiome in human health and disease

    Huseyin, Chloe E.; O’Toole, Paul W.; Cotter, Paul D.; Scanlan, Pauline D.; Science Foundation Ireland (SFI); Science Foundation Ireland-Royal Society University Research Fellowship; SFI/12/RC/2273 (Oxford University Press (OUP), 2017-04-18)
    The human body is home to a complex and diverse microbial ecosystem that plays a central role in host health. This includes a diversity of fungal species that is collectively referred to as our ‘mycobiome’. Although research into the mycobiome is still in its infancy, its potential role in human disease is increasingly recognised. Here we review the existing literature available on the human mycobiota with an emphasis on the gut mycobiome, including how fungi interact with the human host and other microbes. In doing so, we provide a comprehensive critique of the methodologies available to research the human mycobiota as well as highlighting the latest research findings from mycological surveys of different groups of interest including infants, obese and inflammatory bowel disease cohorts. This in turn provides new insights and directions for future studies in this burgeoning research area.
  • Glycomacropeptide Reduces Intestinal Epithelial Cell Barrier Dysfunction and Adhesion of Entero-Hemorrhagic and Entero-Pathogenic Escherichia coli in Vitro

    Feeney, Shane; Ryan, Joseph; Kilcoyne, Michelle; Joshi, Lokesh; Hickey, Rita; Teagasc Walsh Fellowship; Department of Agriculture and Food, Ireland; 10/RD/NUIG/707 (Multidisciplinary Digital Publishing Institute, 2017-10-27)
    In recent years, the potential of glycosylated food components to positively influence health has received considerable attention. Milk is a rich source of biologically active glycoconjugates which are associated with antimicrobial, immunomodulatory, anti-adhesion, anti-inflammatory and prebiotic properties. Glycomacropeptide (GMP) is the C-terminal portion of kappa-casein that is released from whey during cheese-making by the action of chymosin. Many of the biological properties associated with GMP, such as anti-adhesion, have been linked with the carbohydrate portion of the protein. In this study, we investigated the ability of GMP to inhibit the adhesion of a variety of pathogenic Escherichia coli strains to HT-29 and Caco-2 intestinal cell lines, given the importance of E. coli in causing bacterial gastroenteritis. GMP significantly reduced pathogen adhesion, albeit with a high degree of species specificity toward enteropathogenic E. coli (EPEC) strains O125:H32 and O111:H2 and enterohemorrhagic E. coli (EHEC) strain 12900 O157:H7. The anti-adhesive effect resulted from the interaction of GMP with the E. coli cells and was also dependent on GMP concentration. Pre-incubation of intestinal Caco-2 cells with GMP reduced pathogen translocation as represented by a decrease in transepithelial electrical resistance (TEER). Thus, GMP is an effective in-vitro inhibitor of adhesion and epithelial injury caused by E. coli and may have potential as a biofunctional ingredient in foods to improve gastrointestinal health.
  • Boarfish (Capros aper): review of a new capture fishery and its valorization potential

    Egerton, Sian; Culloty, Sarah; Whooley, Jason; STANTON, CATHERINE; Ross, R. Paul; Irish Research Council (IRC); Biomarine Ingredients Ireland Ltd. via the IRC Enterprise Partnership Scheme (Oxford University Press (OUP), 2017-04-18)
    The world’s fish stocks, although renewable, are a finite resource. European capture fisheries have remained stagnant in terms of volume for many years. To remain profitable, fishers are looking for new opportunities to diversify, reduce costs, and maximize profits. The targeted fishing of boarfish (Capros aper) in Europe is an excellent example of such adaptation. Using this fishery as a case study, we highlight how established fisheries are adapting to changes faced by the industry. We begin by compiling the knowledge to date on the taxonomy, biology, and ecology of the understudied boarfish and go on to provide a comprehensive overview of its expansion as a targeted fishery in Europe, examining the range of valorization options currently being investigated.
  • Metagenome-based surveillance and diagnostic approaches to studying the microbial ecology of food production and processing environments

    Doyle, Conor J.; O'Toole, Paul W.; Cotter, Paul D.; Teagasc Walsh Fellowship; internal Teagasc funding; 2013030; RMIS6364 (Wiley, 2017-09-14)
    Metagenomic-based analyses have the potential to revolutionize our understanding of the microbiology of food production and processing environments. By adopting such approaches, it will be possible to more accurately determine sources of microbial contamination, identify critical control points for such contaminants, and select practices that optimize quality and safety. This mini-review will discuss the merits of adopting metagenostic-based approaches, highlight novel insights that they have provided to date and consider how they could be further implemented.
  • Impacts of Seasonal Housing and Teat Preparation on Raw Milk Microbiota: a High-Throughput Sequencing Study

    Doyle, Conor J.; Gleeson, David; O'Toole, Paul W.; Cotter, Paul D.; Teagasc Walsh Fellowship; internal Teagasc funding; 2013030; RMIS6364 (American Society for Microbiology, 2017-01-15)
    In pasture-based systems, changes in dairy herd habitat due to seasonality results in the exposure of animals to different environmental niches. These niches contain distinct microbial communities that may be transferred to raw milk, with potentially important food quality and safety implications for milk producers. It is postulated that the extent to which these microorganisms are transferred could be limited by the inclusion of a teat preparation step prior to milking. High-throughput sequencing on a variety of microbial niches on farms was used to study the patterns of microbial movement through the dairy production chain and, in the process, to investigate the impact of seasonal housing and the inclusion/exclusion of a teat preparation regime on the raw milk microbiota from the same herd over two sampling periods, i.e., indoor and outdoor. Beta diversity and network analyses showed that environmental and milk microbiotas separated depending on whether they were sourced from an indoor or outdoor environment. Within these respective habitats, similarities between the milk microbiota and that of teat swab samples and, to a lesser extent, fecal samples were apparent. Indeed, SourceTracker identified the teat surface as the most significant source of contamination, with herd feces being the next most prevalent source of contamination. In milk from cows grazing outdoors, teat prep significantly increased the numbers of total bacteria present. In summary, sequence-based microbiota analysis identified possible sources of raw milk contamination and highlighted the influence of environment and farm management practices on the raw milk microbiota.
  • Bacteriophages and Bacterial Plant Diseases

    Buttimer, Colin; McAuliffe, Olivia; Ross, R. P.; Hill, Colin; O’Mahony, Jim; Coffey, Aidan; CIT Rísam Ph.D. Scholarship (Frontiers Media SA, 2017-01-20)
    Losses in crop yields due to disease need to be reduced in order to meet increasing global food demands associated with growth in the human population. There is a well-recognized need to develop new environmentally friendly control strategies to combat bacterial crop disease. Current control measures involving the use of traditional chemicals or antibiotics are losing their efficacy due to the natural development of bacterial resistance to these agents. In addition, there is an increasing awareness that their use is environmentally unfriendly. Bacteriophages, the viruses of bacteria, have received increased research interest in recent years as a realistic environmentally friendly means of controlling bacterial diseases. Their use presents a viable control measure for a number of destructive bacterial crop diseases, with some phage-based products already becoming available on the market. Phage biocontrol possesses advantages over chemical controls in that tailor-made phage cocktails can be adapted to target specific disease-causing bacteria. Unlike chemical control measures, phage mixtures can be easily adapted for bacterial resistance which may develop over time. In this review, we will examine the progress and challenges for phage-based disease biocontrol in food crops.
  • Things Are Getting Hairy: Enterobacteria Bacteriophage vB_PcaM_CBB

    Buttimer, Colin; Hendrix, Hanne; Oliveira, Hugo; Casey, Aidan; Neve, Horst; McAuliffe, Olivia; Ross, R. Paul; Hill, Colin; Noben, Jean-Paul; O'Mahony, Jim; et al. (Frontiers Media SA, 2017-01-24)
    Enterobacteria phage vB_PcaM_CBB is a “jumbo” phage belonging to the family Myoviridae. It possesses highly atypical whisker-like structures along the length of its contractile tail. It has a broad host range with the capability of infecting species of the genera Erwinia, Pectobacterium, and Cronobacter. With a genome of 355,922 bp, excluding a predicted terminal repeat of 22,456 bp, phage CBB is the third largest phage sequenced to date. Its genome was predicted to encode 554 ORFs with 33 tRNAs. Based on prediction and proteome analysis of the virions, 29% of its predicted ORFs could be functionally assigned. Protein comparison shows that CBB shares between 33–38% of its proteins with Cronobacter phage GAP32, coliphages PBECO4 and 121Q as well as Klebsiella phage vB_KleM_Rak2. This work presents a detailed and comparative analysis of vB_PcaM_CBB of a highly atypical jumbo myoviridae phage, contributing to a better understanding of phage diversity and biology.
  • Predicted Release and Analysis of Novel ACE-I, Renin, and DPP-IV Inhibitory Peptides from Common Oat (Avena sativa) Protein Hydrolysates Using in Silico Analysis

    Bleakley, Stephen; Hayes, Maria; O’ Shea, Nora; Gallagher, Eimear; Lafarga, Tomas; Teagasc Walsh Fellowship; Irish Department of Agriculture, Food and Marine (DAFM); Spanish Ministry of Economy, Industry, and Competitiveness; 2016073; FIRM 11/SF/317; et al. (Multidisciplinary Digital Publishing Institute, 2017-12-04)
    The renin-angiotensin-aldosterone system (RAAS) plays an important role in regulating hypertension by controlling vasoconstriction and intravascular fluid volume. RAAS itself is largely regulated by the actions of renin (EC and the angiotensin-I-converting enzyme (ACE-I; EC The enzyme dipeptidyl peptidase-IV (DPP-IV; EC also plays a role in the development of type-2 diabetes. The inhibition of the renin, ACE-I, and DPP-IV enzymes has therefore become a key therapeutic target for the treatment of hypertension and diabetes. The aim of this study was to assess the bioactivity of different oat (Avena sativa) protein isolates and their ability to inhibit the renin, ACE-I, and DPP-IV enzymes. In silico analysis was carried out to predictthe likelihood of bioactive inhibitory peptides occurring from oat protein hydrolysates following in silico hydrolysis with the proteases papain and ficin. Nine peptides, including FFG, IFFFL, PFL, WWK, WCY, FPIL, CPA, FLLA, and FEPL were subsequently chemically synthesised, and their bioactivities were confirmed using in vitro bioassays. The isolated oat proteins derived from seven different oat varieties were found to inhibit the ACE-I enzyme by between 86.5 ± 10.7% and 96.5 ± 25.8%, renin by between 40.5 ± 21.5% and 70.9 ± 7.6%, and DPP-IV by between 3.7 ± 3.9% and 46.2 ± 28.8%. The activity of the synthesised peptides was also determined.
  • A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding

    Vartia, Salla; Villanueva-Cañas, José L.; Finarelli, John; Farrell, Edward D.; Collins, Patrick C.; Hughes, Graham M.; Carlsson, Jeanette E. L.; Gauthier, David T.; McGinnity, Philip; Cross, Thomas F.; et al. (The Royal Society, 2016-01)
    This study examines the potential of next-generation sequencing based ‘genotyping-by-sequencing’ (GBS) of microsatellite loci for rapid and cost-effective genotyping in large-scale population genetic studies. The recovery of individual genotypes from large sequence pools was achieved by PCR-incorporated combinatorial barcoding using universal primers. Three experimental conditions were employed to explore the possibility of using this approach with existing and novel multiplex marker panels and weighted amplicon mixture. The GBS approach was validated against microsatellite data generated by capillary electrophoresis. GBS allows access to the underlying nucleotide sequences that can reveal homoplasy, even in large datasets and facilitates cross laboratory transfer. GBS of microsatellites, using individual combinatorial barcoding, is potentially faster and cheaper than current microsatellite approaches and offers better and more data.
  • Draft Genome Sequence of Lactobacillus casei DPC6800, an Isolate with the Potential to Diversify Flavor in Cheese

    Stefanovic, Ewelina; Casey, Aidan; Cotter, Paul; Cavanagh, Daniel; Fitzgerald, Gerald; McAuliffe, Olivia; Dairy Research Ireland; Teagasc; 6156; 6224 (American Society for Microbiology, 2016-04-28)
    Lactobacillus casei is a nonstarter lactic acid bacterium commonly present in various types of cheeses. It is believed that strains of this species have a significant impact on the development of cheese flavor. The draft genome sequence of L. casei DPC6800, isolated from a semi-hard Dutch cheese, is reported.
  • Thermus and the Pink Discoloration Defect in Cheese

    Quigley, Lisa; O’Sullivan, Daniel J.; Daly, David; O’Sullivan, Orla; Burdikova, Zuzana; Vana, Rostislav; Beresford, Tom P.; Ross, R. Paul; Fitzgerald, Gerald F.; McSweeney, Paul L. H.; et al. (American Society for Microbiology, 2016-06-28)
    A DNA sequencing-based strategy was applied to study the microbiology of Continental-type cheeses with a pink discoloration defect. The basis for this phenomenon has remained elusive, despite decades of research. The bacterial composition of cheese containing the defect was compared to that of control cheese using 16S rRNA gene and shotgun metagenomic sequencing as well as quantitative PCR (qPCR). Throughout, it was apparent that Thermus, a carotenoid-producing genus, was present at higher levels in defect-associated cheeses than in control cheeses. Prompted by this finding and data confirming the pink discoloration to be associated with the presence of a carotenoid, a culture-based approach was employed, and Thermus thermophilus was successfully cultured from defect-containing cheeses. The link between Thermus and the pinking phenomenon was then established through the cheese defect equivalent of Koch’s postulates when the defect was recreated by the reintroduction of a T. thermophilus isolate to a test cheese during the manufacturing process. IMPORTANCE Pink discoloration in cheese is a defect affecting many cheeses throughout the world, leading to significant financial loss for the dairy industry. Despite decades of research, the cause of this defect has remained elusive. The advent of high-throughput, next-generation sequencing has revolutionized the field of food microbiology and, with respect to this study, provided a means of testing a possible microbial basis for this defect. In this study, a combined 16S rRNA, whole-genome sequencing, and quantitative PCR approach was taken. This resulted in the identification of Thermus, a carotenoid-producing thermophile, in defect-associated cheeses and the recreation of the problem in cheeses to which Thermus was added. This finding has the potential to lead to new strategies to eliminate this defect, and our method represents an approach that can be employed to investigate the role of microbes in other food defects of unknown origin.
  • The Omega-3 Polyunsaturated Fatty Acid Docosahexaenoic Acid (DHA) Reverses Corticosterone-Induced Changes in Cortical Neurons

    Pusceddu, Matteo M.; Nolan, Yvonne M.; Green, Holly F.; Robertson, Ruairi C.; STANTON, CATHERINE; Kelly, Philip; Cryan, John F.; Dinan, Timothy G.; Food Institutional Research Measure; Science Foundation Ireland; et al. (Oxford University Press (OUP), 2015-12-12)
    Background: Chronic exposure to the glucocorticoid hormone corticosterone exerts cellular stress-induced toxic effects that have been associated with neurodegenerative and psychiatric disorders. Docosahexaenoic acid is a polyunsaturated fatty acid that has been shown to be of benefit in stress-related disorders, putatively through protective action in neurons. Methods: We investigated the protective effect of docosahexaenoic acid against glucocorticoid hormone corticosterone-induced cellular changes in cortical cell cultures containing both astrocytes and neurons. Results: We found that glucocorticoid hormone corticosterone (100, 150, 200 μM) at different time points (48 and 72 hours) induced a dose- and time-dependent reduction in cellular viability as assessed by methyl thiazolyl tetrazolium. Moreover, glucocorticoid hormone corticosterone (200 μM, 72 hours) decreased the percentage composition of neurons while increasing the percentage of astrocytes as assessed by βIII-tubulin and glial fibrillary acidic protein immunostaining, respectively. In contrast, docosahexaenoic acid treatment (6 μM) increased docosahexaenoic acid content and attenuated glucocorticoid hormone corticosterone (200 μM)-induced cell death (72 hours) in cortical cultures. This translates into a capacity for docosahexaenoic acid to prevent neuronal death as well as astrocyte overgrowth following chronic exposure to glucocorticoid hormone corticosterone. Furthermore, docosahexaenoic acid (6 μM) reversed glucocorticoid hormone corticosterone-induced neuronal apoptosis as assessed by terminal deoxynucleotidyl transferase-mediated nick-end labeling and attenuated glucocorticoid hormone corticosterone-induced reductions in brain derived neurotrophic factor mRNA expression in these cultures. Finally, docosahexaenoic acid inhibited glucocorticoid hormone corticosterone-induced downregulation of glucocorticoid receptor expression on βIII- tubulin-positive neurons. Conclusions: This work supports the view that docosahexaenoic acid may be beneficial in ameliorating stress-related cellular changes in the brain and may be of value in psychiatric disorders.
  • N-3 Polyunsaturated Fatty Acids through the Lifespan: Implication for Psychopathology

    Pusceddu, Matteo M.; Kelly, Philip; STANTON, CATHERINE; Cryan, John F.; Dinan, Timothy G.; Mead Johnson Nutrition; Cremo; Suntory Wellness Danone-Nutritia; 4D Pharma; Yakult; et al. (Oxford University Press (OUP), 2016-09-08)
    Objective: The impact of lifetime dietary habits and their role in physical, mental, and social well-being has been the focus of considerable recent research. Omega-3 polyunsaturated fatty acids as a dietary constituent have been under the spotlight for decades. Omega-3 polyunsaturated fatty acids constitute key regulating factors of neurotransmission, neurogenesis, and neuroinflammation and are thereby fundamental for development, functioning, and aging of the CNS. Of note is the fact that these processes are altered in various psychiatric disorders, including attention deficit hyperactivity disorder, depression, and Alzheimer’s disease. Design: Relevant literature was identified through a search of MEDLINE via PubMed using the following words, “n-3 PUFAs,” “EPA,” and “DHA” in combination with “stress,” “cognition,” “ADHD,” “anxiety,” “depression,” “bipolar disorder,” “schizophrenia,” and “Alzheimer.” The principal focus was on the role of omega-3 polyunsaturated fatty acids throughout the lifespan and their implication for psychopathologies. Recommendations for future investigation on the potential clinical value of omega-3 polyunsaturated fatty acids were examined. Results: The inconsistent and inconclusive results from randomized clinical trials limits the usage of omega-3 polyunsaturated fatty acids in clinical practice. However, a body of literature demonstrates an inverse correlation between omega-3 polyunsaturated fatty acid levels and quality of life/ psychiatric diseases. Specifically, older healthy adults showing low habitual intake of omega-3 polyunsaturated fatty acids benefit most from consuming them, showing improved age-related cognitive decline. Conclusions: Although further studies are required, there is an exciting and growing body of research suggesting that omega-3 polyunsaturated fatty acids may have a potential clinical value in the prevention and treatment of psychopathologies.
  • Gut microbiota, obesity and diabetes

    Patterson, E; Ryan, PM; Cryan, John F; Dinan, Timothy G; Ross, R Paul; Fitzgerald, Gerald F; Stanton, Catherine; Teagasc Walsh Fellowship; Science Foundation Ireland (SFI); SFI/12/RC/2273 (BMJ Journals, 2016-02-24)
    The central role of the intestinal microbiota in the progression and, equally, prevention of metabolic dysfunction is becoming abundantly apparent. The symbiotic relationship between intestinal microbiota and host ensures appropriate development of the metabolic system in humans. However, disturbances in composition and, in turn, functionality of the intestinal microbiota can disrupt gut barrier function, a trip switch for metabolic endotoxemia. This low-grade chronic inflammation, brought about by the influx of inflammatory bacterial fragments into circulation through a malfunctioning gut barrier, has considerable knock-on effects for host adiposity and insulin resistance. Conversely, recent evidence suggests that there are certain bacterial species that may interact with host metabolism through metabolite-mediated stimulation of enteric hormones and other systems outside of the gastrointestinal tract, such as the endocannabinoid system. When the abundance of these keystone species begins to decline, we see a collapse of the symbiosis, reflected in a deterioration of host metabolic health. This review will investigate the intricate axis between the microbiota and host metabolism, while also addressing the promising and novel field of probiotics as metabolic therapies.
  • Lactobacillus reuteri FYNLJ109L1 Attenuating Metabolic Syndrome in Mice via Gut Microbiota Modulation and Alleviating Inflammation

    Yang, Bo; Zheng, Fuli; STANTON, CATHERINE; Ross, Reynolds Paul; Zhao, Jianxin; Zhang, Hao; Chen, Wei; National Natural Science Foundation of China; Nos. 32021005, 31820103010; Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province (Multidisciplinary Digital Publishing Institute, 2021-09-02)
    Metabolic syndrome is caused by an excessive energy intake in a long-term, high-fat and/or high-sugar diet, resulting in obesity and a series of related complications, which has become a global health concern. Probiotics intervention can regulate the gut microbiota and relieve the systemic and chronic low-grade inflammation, which is an alternative to relieving metabolic syndrome. The aim of this work was to explore the alleviation of two different Lactobacillusreuteri strains on metabolic syndrome. Between the two L. reuteri strains, FYNLJ109L1 had a better improvement effect on blood glucose, blood lipid, liver tissue damage and other related indexes than NCIMB 30242. In particular, FYNLJ109L1 reduced weight gain, food intake and fat accumulation. Additionally, it can regulate the gut microbiota, increase IL-10, and reduce IL-6 and tumor necrosis factor-α (TNF-α), as well as liver injury, and further reduce insulin resistance and regulate lipid metabolism disorders. In addition, it could modulate the gut microbiota, particularly a decreased Romboutsia and Clostridium sensu stricto-1, and an increased Acetatifactor. The results indicated that FYNLJ109L1 could improve metabolic syndrome significantly via alleviating inflammation and gut microbiota modulation.
  • Recreating pink defect in cheese with different strains of Thermus bacteria

    Yeluri Jonnala, Bhagya R; McSweeney, Paul L H; Cotter, Paul D; Sheehan, Jeremiah J (Wiley, 2021-07-15)
    Pink discoloration defects in cheese manifests as the appearance of pink patches within cheese blocks and has recently been associated with Thermus thermophilus. Swiss-type cheeses were prepared at pilot scale using thermophilic starter cultures, Propionibacterium freudenreichii, and one of Thermus thermophilus HB27, Thermus scotoductus SE1 or Thermus thermophilus DPC6866 or a control without Thermus. Significantly, a higher level of redness was observed in cheeses with Thermus thermophilus HB27 relative to the other cheeses and suggests that the development of the pink defect is dependent on the strain of Thermus present and on other, as yet unknown, factors that require further study.
  • Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants

    Hill, Cian J.; Brown, Jillian R. M.; Lynch, Denise B.; Jeffery, Ian B.; Ryan, C. Anthony; Ross, R. Paul; STANTON, CATHERINE; O’Toole, Paul W.; Department of Agriculture, Food and Marine; Science Foundation Ireland; et al. (Springer Science and Business Media LLC, 2016-05-10)
    Background Alterations in intestinal microbiota have been correlated with a growing number of diseases. Investigating the faecal microbiota is widely used as a non-invasive and ethically simple proxy for intestinal biopsies. There is an urgent need for collection and transport media that would allow faecal sampling at distance from the processing laboratory, obviating the need for same-day DNA extraction recommended by previous studies of freezing and processing methods for stool. We compared the faecal bacterial DNA quality and apparent phylogenetic composition derived using a commercial kit for stool storage and transport (DNA Genotek OMNIgene GUT) with that of freshly extracted samples, 22 from infants and 20 from older adults. Results Use of the storage vials increased the quality of extracted bacterial DNA by reduction of DNA shearing. When infant and elderly datasets were examined separately, no differences in microbiota composition were observed due to storage. When the two datasets were combined, there was a difference according to a Wilcoxon test in the relative proportions of Faecalibacterium, Sporobacter, Clostridium XVIII, and Clostridium XlVa after 1 week’s storage compared to immediately extracted samples. After 2 weeks’ storage, Bacteroides abundance was also significantly different, showing an apparent increase from week 1 to week 2. The microbiota composition of infant samples was more affected than that of elderly samples by storage, with significantly higher Spearman distances between paired freshly extracted and stored samples (p < 0.001). When the microbiota profiles were analysed at the operational taxonomic unit (OTU) level, three infant datasets in the study did not cluster together, while only one elderly dataset did not. The lower microbiota diversity of the infant gut microbiota compared to the elderly gut microbiota (p < 0.001) means that any alteration in the infant datasets has a proportionally larger effect. Conclusions The commercial storage vials appear to be suitable for high diversity microbiota samples, but may be less appropriate for lower diversity samples. Differences between fresh and stored samples mean that where storage is unavoidable, a consistent storage regime should be used. We would recommend extraction ideally within the first week of storage.
  • Adaptation to abiotic conditions drives local adaptation in bacteria and viruses coevolving in heterogeneous environments

    Gorter, Florien A.; Scanlan, Pauline D.; Buckling, Angus; NERC, AXA research fund; BBSRC; the Royal Society (The Royal Society, 2016-02)
    Parasite local adaptation, the greater performance of parasites on their local compared with foreign hosts, has important consequences for the maintenance of diversity and epidemiology. While the abiotic environment may significantly affect local adaptation, most studies to date have failed either to incorporate the effects of the abiotic environment, or to separate them from those of the biotic environment. Here, we tease apart biotic and abiotic components of local adaptation using the bacterium Pseudomonas fluorescens and its viral parasite bacteriophage F2. We coevolved replicate populations of bacteria and phages at three different temperatures, and determined their performance against coevolutionary partners from the same and different temperatures. Crucially, we measured performance at different assay temperatures, which allowed us to disentangle adaptation to biotic and abiotic habitat components. Our results show that bacteria and phages are more resistant and infectious, respectively, at the temperature at which they previously coevolved, confirming that local adaptation to abiotic conditions can play a crucial role in determining parasite infectivity and host resistance. Our work underlines the need to assess host–parasite interactions across multiple relevant abiotic environments, and suggests that microbial adaption to local temperatures can create ecological barriers to dispersal across temperature gradients.

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