• Key factors influencing economic relationships and communication in European agri-food chains

      Henchion, Maeve; McIntyre, Bridin; Downey, Gerard (Teagasc, 2008-09)
      The project considered meat and cereal commodities in six EU countries. In total thirteen agri-food chains were examined: five pig-to-pigmeat chains, three cattle-to-beef chains, two barley-to-beer chains and three cereals-to-bakery product chains. The pig-to-pigmeat and cattle-to-beef chains were examined in Ireland.
    • Lactic Acid Bacteria and Bifidobacteria with Potential to Design Natural Biofunctional Health-Promoting Dairy Foods

      Linares, Daniel M.; Gómez, Carolina; Renes, Erica; Fresno, José M.; Tornadijo, María E.; Ross, R Paul; Stanton, Catherine; Science Foundation Ireland (Frontiers, 2017-05-18)
      Consumer interest in healthy lifestyle and health-promoting natural products is a major driving force for the increasing global demand of biofunctional dairy foods. A number of commercial sources sell synthetic formulations of bioactive substances for use as dietary supplements. However, the bioactive-enrichment of health-oriented foods by naturally occurring microorganisms during dairy fermentation is in increased demand. While participating in milk fermentation, lactic acid bacteria can be exploited in situ as microbial sources for naturally enriching dairy products with a broad range of bioactive components that may cover different health aspects. Several of these bioactive metabolites are industrially and economically important, as they are claimed to exert diverse health-promoting activities on the consumer, such as anti-hypertensive, anti-inflammatory, and anti-diabetic, anti-oxidative, immune-modulatory, anti-cholesterolemic, or microbiome modulation. This review aims at discussing the potential of these health-supporting bacteria as starter or adjunct cultures for the elaboration of dairy foods with a broad spectrum of new functional properties and added value.
    • Lactobacillus ruminis strains cluster according to their mammalian gut source

      O’Donnell, Michelle M.; Harris, Hugh M B; Lynch, Denise B; Ross, R Paul; O’Toole, Paul W.; Science Foundation Ireland; 07/IN.1/B1780 (Biomed Central, 01/04/2015)
      Background Lactobacillus ruminis is a motile Lactobacillus that is autochthonous to the human gut, and which may also be isolated from other mammals. Detailed characterization of L. ruminis has previously been restricted to strains of human and bovine origin. We therefore sought to expand our bio-bank of strains to identify and characterise isolates of porcine and equine origin by comparative genomics. Results We isolated five strains from the faeces of horses and two strains from pigs, and compared their motility, biochemistry and genetic relatedness to six human isolates and three bovine isolates including the type strain 27780T. Multilocus sequence typing analysis based on concatenated sequence data for six individual loci separated the 16 L. ruminis strains into three clades concordant with human, bovine or porcine, and equine sources. Sequencing the genomes of four additional strains of human, bovine, equine and porcine origin revealed a high level of genome synteny, independent of the source animal. Analysis of carbohydrate utilization, stress survival and technological robustness in a combined panel of sixteen L. ruminis isolates identified strains with optimal survival characteristics suitable for future investigation as candidate probiotics. Under laboratory conditions, six human isolates of L. ruminis tested were aflagellate and non-motile, whereas all 10 strains of bovine, equine and porcine origin were motile. Interestingly the equine and porcine strains were hyper-flagellated compared to bovine isolates, and this hyper-flagellate phenotype correlated with the ability to swarm on solid medium containing up to 1.8% agar. Analysis by RNA sequencing and qRT-PCR identified genes for the biosynthesis of flagella, genes for carbohydrate metabolism and genes of unknown function that were differentially expressed in swarming cells of an equine isolate of L. ruminis. Conclusions We suggest that Lactobacillus ruminis isolates have potential to be used in the functional food industry. We have also identified a MLST scheme able to distinguish between strains of L. ruminis of different origin. Genes for non-digestible oligosaccharide metabolism were identified with a putative role in swarming behaviour.
    • Lactoferrin affects the adherence and invasion of Streptococcus dysgalactiae spp. dysgalactiae in mammary epithelial cells

      O'Halloran, Fiona; Beecher, Christine; Chaurin, Valerie; Sweeney, Torres; Giblin, Linda; Department of Agriculture, Food and the Marine; Irish Dairy Levy Research Trust; Teagasc Walsh Fellowship Programme; 06RDTMFRC437; 06RDTMFRC445 (Elsevier, 24/03/2016)
      Streptococcus dysgalactiae ssp. dysgalactiae is an important causative agent of bovine mastitis worldwide. Lactoferrin is an innate immune protein that is associated with many functions including immunomodulatory, antiproliferative, and antimicrobial properties. This study aimed to investigate the interactions between lactoferrin and a clinical bovine mastitis isolate, Strep. dysgalactiae ssp. dysgalactiae DPC5345. Initially a deliberate in vivo bovine intramammary challenge was performed with Strep. dysgalactiae DPC5345. Results demonstrated a significant difference in lactoferrin mRNA levels in milk cells between the control and infused quarters 7 h postinfusion. Milk lactoferrin levels in the Strep. dysgalactiae DPC5345 infused quarters were significantly increased compared with control quarters at 48 h postinfusion. In vitro studies demonstrated that lactoferrin had a bacteriostatic effect on the growth of Strep. dysgalactiae DPC5345 and significantly decreased the ability of the bacteria to internalize into HC-11 mammary epithelial cells. Confocal microscopy images of HC-11 cells exposed to Strep. dysgalactiae and lactoferrin further supported this effect by demonstrating reduced invasion of bacteria to HC-11 cells. The combined data suggest that a bovine immune response to Strep. dysgalactiae infection includes a significant increase in lactoferrin expression in vivo, and based on in vitro data, lactoferrin limits mammary cell invasion of this pathogen by binding to the bacteria and preventing its adherence.
    • Lactoferrin affects the adherence and invasion of Streptococcus dysgalactiae ssp. dysgalactiae in mammary epithelial cells

      O'Halloran, Fiona; Beecher, Christine; Chaurin, Valerie; Sweeney, Torres; Giblin, Linda (Elsevier, 24/03/2016)
      Streptococcus dysgalactiae ssp. dysgalactiae is an important causative agent of bovine mastitis worldwide. Lactoferrin is an innate immune protein that is associated with many functions including immunomodulatory, antiproliferative, and antimicrobial properties. This study aimed to investigate the interactions between lactoferrin and a clinical bovine mastitis isolate, Strep. dysgalactiae ssp. dysgalactiae DPC5345. Initially a deliberate in vivo bovine intramammary challenge was performed with Strep. dysgalactiae DPC5345. Results demonstrated a significant difference in lactoferrin mRNA levels in milk cells between the control and infused quarters 7 h postinfusion. Milk lactoferrin levels in the Strep. dysgalactiae DPC5345 infused quarters were significantly increased compared with control quarters at 48 h postinfusion. In vitro studies demonstrated that lactoferrin had a bacteriostatic effect on the growth of Strep. dysgalactiae DPC5345 and significantly decreased the ability of the bacteria to internalize into HC-11 mammary epithelial cells. Confocal microscopy images of HC-11 cells exposed to Strep. dysgalactiae and lactoferrin further supported this effect by demonstrating reduced invasion of bacteria to HC-11 cells. The combined data suggest that a bovine immune response to Strep. dysgalactiae infection includes a significant increase in lactoferrin expression in vivo, and based on in vitro data, lactoferrin limits mammary cell invasion of this pathogen by binding to the bacteria and preventing its adherence.
    • Listeria monocytogenes in Milk Products

      Jordan, Kieran; Hunt, Karen; Dalmasso, Marion (Springer International Publishing, 2016-04-13)
      Milk and milk products are frequently identified as vectors for transmission of Listeria monocytogenes. Milk can be contaminated at farm level either by indirect external contamination from the farm environment or less frequently by direct contamination of the milk from infection in the animal. Pasteurisation of milk will kill L. monocytogenes, but post-pasteurisation contamination, consumption of unpasteurised milk and manufacture of unpasteurised milk products can lead to milk being the cause of outbreaks of listeriosis. Therefore, there is a concern that L. monocytogenes in milk could lead to a public health risk. To protect against this risk, there is a need for awareness surrounding the issues, hygienic practices to reduce the risk and adequate sampling and analysis to verify that the risk is controlled. This review will highlight the issues surrounding L. monocytogenes in milk and milk products, including possible control measures. It will therefore create awareness about L. monocytogenes, contributing to protection of public health.
    • Listeriolysin S, a Novel Peptide Haemolysin Associated with a Subset of Lineage I Listeria monocytogenes

      Cotter, Paul D.; Draper, Lorraine A.; Lawton, Elaine M.; Daly, Karen M.; Groeger, David S.; Casey, Patrick G.; Ross, R Paul; Hill, Colin; Science Foundation Ireland; 06/IN.1/B98 (PLOS, 12/09/2008)
      Streptolysin S (SLS) is a bacteriocin-like haemolytic and cytotoxic virulence factor that plays a key role in the virulence of Group A Streptococcus (GAS), the causative agent of pharyngitis, impetigo, necrotizing fasciitis and streptococcal toxic shock syndrome. Although it has long been thought that SLS and related peptides are produced by GAS and related streptococci only, there is evidence to suggest that a number of the most notorious Gram-positive pathogenic bacteria, including Listeria monocytogenes, Clostridium botulinum and Staphylococcus aureus, produce related peptides. The distribution of the L. monocytogenes cluster is particularly noteworthy in that it is found exclusively among a subset of lineage I strains; i.e., those responsible for the majority of outbreaks of listeriosis. Expression of these genes results in the production of a haemolytic and cytotoxic factor, designated Listeriolysin S, which contributes to virulence of the pathogen as assessed by murine- and human polymorphonuclear neutrophil–based studies. Thus, in the process of establishing the existence of an extended family of SLS-like modified virulence peptides (MVPs), the genetic basis for the enhanced virulence of a proportion of lineage I L. monocytogenes may have been revealed.
    • Live animal measurements, carcass composition and plasma hormone and metabolite concentrations in male progeny of sires differing in genetic merit for beef production

      Clarke, A. M.; Drennan, Michael J; McGee, Mark; Kenny, David A.; Evans, Ross D; Berry, Donagh P. (Cambridge University Press, 2009-07)
      In genetic improvement programmes for beef cattle, the effect of selecting for a given trait or index on other economically important traits, or their predictors, must be quantified to ensure no deleterious consequential effects go unnoticed. The objective was to compare live animal measurements, carcass composition and plasma hormone and metabolite concentrations of male progeny of sires selected on an economic index in Ireland. This beef carcass index (BCI) is expressed in euros and based on weaning weight, feed intake, carcass weight and carcass conformation and fat scores. The index is used to aid in the genetic comparison of animals for the expected profitability of their progeny at slaughter. A total of 107 progeny from beef sires of high (n = 11) or low (n = 11) genetic merit for the BCI were compared in either a bull (slaughtered at 16 months of age) or steer (slaughtered at 24 months of age) production system, following purchase after weaning (8 months of age) from commercial beef herds. Data were analysed as a 2 × 2 factorial design (two levels of genetic merit by two production systems). Progeny of high BCI sires had heavier carcasses, greater (P < 0.01) muscularity scores after weaning, greater (P < 0.05) skeletal scores and scanned muscle depth pre-slaughter, higher (P < 0.05) plasma insulin concentrations and greater (P < 0.01) animal value (obtained by multiplying carcass weight by carcass value, which was based on the weight of meat in each cut by its commercial value) than progeny of low BCI sires. Regression of progeny performance on sire genetic merit was also undertaken across the entire data set. In steers, the effect of BCI on carcass meat proportion, calculated carcass value (c/kg) and animal value was positive (P < 0.01), while a negative association was observed for scanned fat depth pre-slaughter and carcass fat proportion (P < 0.01), but there was no effect in bulls. The effect of sire expected progeny difference (EPD) for carcass weight followed the same trends as BCI. Muscularity scores, carcass meat proportion and calculated carcass value increased, whereas scanned fat depth, carcass fat and bone proportions decreased with increasing sire EPD for conformation score. The opposite association was observed for sire EPD for fat score. Results from this study show that selection using the BCI had positive effects on live animal muscularity, carcass meat proportion, proportions of high-value cuts and carcass value in steer progeny, which are desirable traits in beef production.
    • Longitudinal Study of Two Irish Dairy Herds: Low Numbers of Shiga Toxin-Producing Escherichia coli O157 and O26 Super-Shedders Identified

      Murphy, Brenda P.; McCabe, Evonne; Murphy, Mary; Buckley, James F.; Crowley, Dan; Fanning, Seamus; Duffy, Geraldine; Department of Agriculture, Food and the Marine, Ireland; 11/F/051 (Frontiers, 2016-11-18)
      A 12-month longitudinal study was undertaken on two dairy herds to ascertain the Shiga-toxin producing Escherichia coli (STEC) O157 and O26 shedding status of the animals and its impact (if any) on raw milk. Cattle are a recognized reservoir for these organisms with associated public health and environmental implications. Animals shedding E. coli O157 at >10,000 CFU/g of feces have been deemed super-shedders. There is a gap in the knowledge regarding super-shedding of other STEC serogroups. A cohort of 40 lactating cows from herds previously identified as positive for STEC in a national surveillance project were sampled every second month between August, 2013 and July, 2014. Metadata on any potential super-shedders was documented including, e.g., age of the animal, number of lactations and days in lactation, nutritional condition, somatic cell count and content of protein in milk to assess if any were associated with risk factors for super-shedding. Recto-anal mucosal swabs (RAMS), raw milk, milk filters, and water samples were procured for each herd. The swabs were examined for E. coli O157 and O26 using a quantitative real time PCR method. Counts (CFU swab-1) were obtained from a standard calibration curve that related real-time PCR cycle threshold (Ct) values against the initial concentration of O157 or O26 in the samples. Results from Farm A: 305 animals were analyzed; 15 E. coli O157 (5%) were recovered, 13 were denoted STEC encoding either stx1 and/or stx2 virulence genes and 5 (2%) STEC O26 were recovered. One super-shedder was identified shedding STEC O26 (stx1&2). Farm B: 224 animals were analyzed; eight E. coli O157 (3.5%) were recovered (seven were STEC) and 9 (4%) STEC O26 were recovered. Three super-shedders were identified, one was shedding STEC O157 (stx2) and two STEC O26 (stx2). Three encoded the adhering and effacement gene (eae) and one isolate additionally encoded the haemolysin gene (hlyA). All four super-shedders were only super-shedding once during the 1-year sampling period. The results of this study show, low numbers of super-shedders in the herds examined, with high numbers of low and medium shedding. Although four super-shedding animals were identified, no STEC O157 or O26 were recovered from any of the raw milk, milk filter, or water samples. The authors conclude that this study highlights the need for further surveillance to assess the potential for environmental contamination and food chain security.
    • Managing new food product development.

      Daly, Eimear; European Union (Teagasc, 2002-10)
      The future success of the Irish food industry depends on the ability of companies to develop new skills in a rapidly changing market environment. One such skill is the management of new product development. This report illustrates the impact that training in the product development process had on a range of small to medium enterprises. Training was delivered as a series of interactive workshops covering the key stages of the new product development process. Each company also received up to 7 days consultancy support to facilitate implementation of the learning.
    • Marine Functional Foods Research Initiative (NutraMara)

      Troy, Declan; Tiwari, Brijesh; Hayes, Maria; Ross, R Paul; Stanton, Catherine; Johnson, Mark; Stengel, Dagmar; O'Doherty, John V.; Fitzgerald, Richard J.; McSorley, Emeir; Kerry, Joseph; Marine Institute; Marine Institute; MFFRI/07/01; MFFRI/07/01 (Marine Institute, 2017-12)
      The NutraMara – Marine Functional Foods Research Initiative was conceived by Sea Change - A Marine Knowledge, Research and Innovation Strategy for Ireland 2007-2013. The goal was to develop a collaborative funding mechanism that would create new research capacity and build the capabilities required to maximise the potential of Ireland’s extensive marine bioresources. By supporting a strong interdisciplinary research team, capable of exploring marine animals and plants as a sustainable source of materials for use as functional ingredients and foods, the vision for NutraMara was to position Ireland to the fore in use of marine bioresources as health beneficial ingredients. Commencing in 2008 and supported by funds of €5.2 million from the Marine Institute and the Department of Agriculture, Food and the Marine, the research programme was led by Teagasc as the head of a multi-institutional consortium. The NutraMara consortium comprises marine bioresources and bioscience expertise, with food science and technology expertise from University College Cork; University College Dublin; the National University of Ireland Galway; the University of Limerick and Ulster University. Research effort was directed towards exploring Ireland’s marine bioresources – including macro- and microalgae, finfish and shellfish from wild and cultured sources: and discards from processing fish as sources of novel ingredients with bioactive characteristics. This discovery activity involved the collection of over 600 samples from 39 species of algae and fish and the analysis of 5,800 extracts, which resulted in 3,000 positive “hits” for bioactivity. The NutraMara consortium has built a strong research capacity to identify, characterise and evaluate marine-origin bioactives for use as/in functional foods. It further built the capacity to develop model foods enhanced with these marine-origin functional ingredients; providing insights to the processing challenges associated with producing functional ingredients from marine organisms. The consortium was actively engaged in research activities designed to identify and assess bioactive compounds from available marine resources, including polyphenols, proteins/peptides, amino acids, polysaccharides, polyunsaturated fatty acids and materials with antioxidant, probiotic or prebiotic properties. A key component of NutraMara’s activities was the development of human capital. The recruitment of M.Sc. and PhD students and their integration within a dynamic research environment that has strong links to industry, provided lasting expertise and capabilities, which are relevant to the needs of Ireland’s food and marine sectors. NutraMara research led to the awarding of eighteen PhDs and recruitment of 21 post-doctoral researchers over the eight year research programme. In excess of 80 peer reviewed publications resulted from this research and more publications are planned. A further 100 posters and conference presentations were also delivered by NutraMara researchers and Principal Investigators. The development and implementation of training and exchange programmes aimed at providing early stage researchers with inter-disciplinary skills that are critical to their development as researchers, enhanced the research capacity of institutions, the industry sectors and the country as a whole. Principal Investigators involved in leading the NutraMara research programme have secured additional research grants of almost €6 million from national and international sources and are engaged in extensive research collaboration involving marine and food research expertise; an activity which did not exist prior to NutraMara. The dissemination of knowledge and transfer of research results to industry were key activities in the research programme. The research outputs and visibility of NutraMara activity nationally resulted in 10 companies engaging in research and development activity with the consortium. Regular workshops and conferences organised by NutraMara attracted close to five hundred participants from Ireland and overseas. Members of the NutraMara core PI group have contributed to the formulation of new national foods and marine research policy and national research agenda, both during the national prioritisation exercise and in sectoral research strategies. This final project report describes the process by which research targets were identified, and the results of extensive screening and evaluation of compounds extracted from marine bioresources. It also highlights the development of new protocols designed to extract compounds in ways that are food friendly. Evaluating the functional properties, bioactivity and bioavailability of high potential marine compounds involved in vitro and in vivo testing. Pilot animal and human intervention studies yielded further insight to the potential and challenges in developing marine functional ingredients. As a result of work completed within the NutraMara consortium, Ireland is well positioned to continue to contribute to the development of ingredients derived from marine organisms and in doing so support the on-going development of Ireland’s food sector.
    • The market for speciality foods in Ireland

      Meehan, Hilary; Murphy, Aidan; O'Reilly, Seamus; Bogue, Joe (Teagasc, 2001-05)
      The speciality food sector has experienced above average industry growth over recent years. Most speciality foods are produced in limited quantities using non-industrial artisan techniques. The majority of speciality food producing businesses were set up in the last fifteen years, have a turnover below €635,000, are based in a rural region and employ less than ten people. The most important markets for Irish speciality food producers are the export market, food service and multiple retailers.
    • The market potential for in-conversion organic products in Ireland

      Cowan, Cathal; Connolly, Liam; Howlett, Brendan; Meehan, Hilary; Ryan, Jane; Mahon, Denise; McIntyre, Bridin; Fanning, Martin; Downey, Gerard; European Union; QLK-2000-01112 (Teagasc, 01/08/2005)
      This report deals with the market for and financial feasibility of converting from conventional to organic food production in Ireland. All members of the organic supply chain were included in the study i.e. farmers, intermediaries, retailers and consumers, to examine the potential of a market for conversion grade produce. Conversion products are those produced in the second year of the conversion phase from conventional to organic farming. Products do not attain full organic status until this is completed.
    • Measuring the lean content of carcasses using TOBEC

      Allen, Paul; McGeehin, Brian (Teagasc, 2001-05)
      This project examined the potential of two objective methods of measuring the lean and fat content of meat carcasses and cuts. Total Body Electrical Conductivity (TOBEC) and Bioelectrical Impedance Analysis (BIA) are both based on the different conductivity of lean and fat tissues. TOBEC measures the absorption by a carcass or cut of electrical energy from an electromagnetic field whereas BIA measures the resistance to the flow of an electrical current. TOBEC is a large and relatively expensive piece of equipment that is fully automated. BIA is small and relatively low cost but requires an operator.
    • Mechanical Grading of beef carcasses

      Allen, Paul; Finnerty, Nicholas; European Union; European Union (Teagasc, 2001-10)
      Three beef carcass classification systems that use Video Image Analysis (VIA) technology were tested in two trials at Dawn Meats Midleton, Co. Cork. The VIA systems were BCC2, manufactured by SFK Technology, Denmark, VBS2000, manufactured by E+V, Germany, and VIAscan, manufactured by Meat and Livestock Australia. The first trial, conducted over a 6-week period in July/August 1999, calibrated the VIA systems on a large sample of carcasses and validated these calibrations on a further sample obtained at the same time. The second trial, conducted in the first two weeks of March 2000, was a further validation trial. The reference classification scores were determined by a panel of three experienced classifiers using the EUROP grid with 15 subclasses for conformation class and 15 sub-classes for fat. In the first trial the accuracy of the VIA systems at predicting saleable meat yield in steer carcasses was also assessed.
    • 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, 01/10/2018)
      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.
    • Methods for antibiotic residues in food

      O'Keeffe, Mandy J.; Walshe, Michaela; Horne, Elizabeth; O'Keeffe, Michael; Foran, Shane; Lardner, Caroline; Daly, Tracy; Kane, Marian (Teagasc, 2001-04)
      A comprehensive capability to test for residues of veterinary drugs is an important support for the Irish food industry. There is a requirement for food manufacturers to demonstrate the compliance of their products with stringent customer specifications. In addition, legislative requirements are becoming more exacting both in terms of the range of substances covered and the lower residue levels to which test systems must measure.
    • Methods for veterinary drug residue analysis in food

      O'Keeffe, Michael (Teagasc, 1999-02)
      A comprehensive capability to test for residues of veterinary drugs is an important support for the Irish food industry. There is a requirement for food manufacturers to demonstrate the compliance of their products with stringent customer specifications. In addition, legislative requirements are becoming more exacting both in terms of the range of substances covered and the lower residue levels to which test systems must measure.
    • Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir

      Walsh, Aaron M.; Crispie, Fiona; Kilcawley, Kieran N.; O’Sullivan, Orla; O’Sullivan, Maurice G.; Claesson, Marcus J.; Cottera, Paul D.; Science Foundation Ireland; SFI/12/RC/2273; SFI/11/PI/1137; SFI/13/SIRG/2160 (2018-11-05)
      Kefir is a putatively health-promoting dairy beverage that is produced when a kefir grain, consisting of a consortium of microorganisms, is added to milk to initiate a natural fermentation. Here, a detailed analysis was carried out to determine how the microbial population, gene content, and flavor of three kefirs from distinct geographic locations change over the course of 24-h fermentations. Metagenomic sequencing revealed that Lactobacillus kefiranofaciens was the dominant bacterial species in kefir during early stages of fermentations but that Leuconostoc mesenteroides became more prevalent in later stages. This pattern is consistent with an observation that genes involved in aromatic amino acid biosynthesis were absent from L. kefiranofaciens but were present in L. mesenteroides. Additionally, these shifts in the microbial community structure, and associated pathways, corresponded to changes in the levels of volatile compounds. Specifically, Acetobacter spp. correlated with acetic acid; Lactobacillus spp. correlated with carboxylic acids, esters and ketones; Leuconostoc spp. correlated with acetic acid and 2,3-butanedione; and Saccharomyces spp. correlated with esters. The correlation data suggest a causal relationship between microbial taxa and flavor that is supported by observations that addition of L. kefiranofaciens NCFB 2797 increased the levels of esters and ketones whereas addition of L. mesenteroides 213M0 increased the levels of acetic acid and 2,3-butanedione. Finally, we detected genes associated with probiotic functionalities in the kefir microbiome. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein and can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods. IMPORTANCE Traditional fermented foods represent relatively low-complexity microbial environments that can be used as model microbial communities to understand how microbes interact in natural environments. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein. In the process, the link between individual species, and associated pathways, with flavor compounds is revealed and several genes that could be responsible for the purported gut health-associated benefits of consuming kefir are identified. Ultimately, in addition to providing an important fundamental insight into microbial interactions, this information can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods.
    • The microbiological safety and quality of foods processed by the "sous vide" system as a method of commercial catering

      Bolton, Declan J.; Department of Agriculture, Food and the Marine, Ireland (Teagasc, Ballsbridge, Dublin 4, 1998-08)
      The objective of this project was to improve the quality and safety of sous vide foods by investigating the responses of the food-poisoning microorganisms to the processing and storage conditions used in this technology. The major food poisoning bacteria of concern in sous vide foods are strains of Clostridium botulinum, Bacillus cereus, verotoxigenic Escherichia coli O157:H7 (VTEC), Salmonella spp., Listeria monocytogenes and Yersinia enterocolitica.