Now showing items 1-20 of 820

    • Next-Generation Food Research: Use of Meta-Omic Approaches for Characterizing Microbial Communities Along the Food Chain

      Yap, Min; Ercolini, Danilo; Álvarez-Ordóñez, Avelino; O'Toole, Paul W.; O'Sullivan, Orla; Cotter, Paul D.; Irish Dairy Levy; Science Foundation Ireland; European Commission; SFI/12/RC/2273; et al. (Annual Reviews, 2021-10-22)
      Microorganisms exist along the food chain and impact the quality and safety of foods in both positive and negative ways. Identifying and understanding the behavior of these microbial communities enable the implementation of preventative or corrective measures in public health and food industry settings. Current culture-dependent microbial analyses are time-consuming and target only specific subsets of microbes. However, the greater use of culture-independent meta-omic approaches has the potential to facilitate a thorough characterization of the microbial communities along the food chain. Indeed, these methods have shown potential in contributing to outbreak investigation, ensuring food authenticity, assessing the spread ofantimicrobial resistance, tracking microbial dynamics during fermentation and processing, and uncovering the factors along the food chain that impact food quality and safety. This review examines the community-based approaches, and particularly the application of sequencing-based meta-omics strategies, for characterizing microbial communities along the food chain.
    • Irish research response to dairy quality in an era of change

      O'Brien, Bernadette J.; Beresford, Tom; Cotter, Paul D.; Gleeson, D.; Kelly, A.; Kilcawley, Kieran; Magan, J.; McParland, Sinead; Murphy, E.; O’Callaghan, Tom; et al. (Teagasc, 2022-02-26)
      The Irish dairy sector is recognised for its very significant contribution to the national economic status; it is now worth ∼€5 billion annually and represents the largest food and drink export category, which, in turn, represents one of the four largest manufacturing industries in the country. Given anticipated further growth in global demand for dairy products and the positive attributes and capabilities that Ireland has to meet that demand, in terms of pasture-based production and cost competitiveness, it is incumbent for the sector to attain the highest quality milk and dairy products. The combined collaborative approach between research and industry has ensured significant progress and enabled Ireland to remain at the forefront globally in terms of production of quality milk and dairy products. This paper highlights some specific scientific platforms and technologies currently shaping the industry in this regard and discusses current research activity as well as anticipating key requirements for future progress. While research, and farm and processing plant management have accomplished very significant advances in milk and dairy product quality, some overarching emerging challenges include product substitution and sustainability. Some key pillars for the future have been identified on which a strong, efficient dairy sector can be maintained and progressed. Specifically, the use of evidence-based information and real-time measures in prediction and decision-making will be a crucial pillar for the dairy sector of the future. This can promote an approach of proactive maintenance and optimisation of production through improved predictability and control of manufacturing processes.
    • Meta-analysis of cheese microbiomes highlights contributions to multiple aspects of quality

      Walsh, Aaron M.; Macori, Guerrino; Kilcawley, Kieran N.; Cotter, Paul D.; Science Foundation Ireland; European Commission; Department of Agriculture, Food and Marine; SFI/12/RC/2273P1; SFI/12/RC/2273P2; 818368; et al. (Springer Science and Business Media LLC, 2020-08-13)
      A detailed understanding of the cheese microbiome is key to the optimization of flavour, appearance, quality and safety. Accordingly, we conducted a high-resolution meta-analysis of cheese microbiomes and corresponding volatilomes. Using 77 new samples from 55 artisanal cheeses from 27 Irish producers combined with 107 publicly available cheese metagenomes, we recovered 328 metagenome-assembled genomes, including 47 putative new species that could influence taste or colour through the secretion of volatiles or biosynthesis of pigments. Additionally, from a subset of samples, we found that differences in the abundances of strains corresponded with levels of volatiles. Genes encoding bacteriocins and other antimicrobials, such as pseudoalterin, were common, potentially contributing to the control of undesirable microorganisms. Although antibiotic-resistance genes were detected, evidence suggested they are not of major concern with respect to dissemination to other microbiomes. Phages, a potential cause of fermentation failure, were abundant and evidence for phage-mediated gene transfer was detected. The anti-phage defence mechanism CRISPR was widespread and analysis thereof, and of anti-CRISPR proteins, revealed a complex interaction between phages and bacteria. Overall, our results provide new and substantial technological and ecological insights into the cheese microbiome that can be applied to further improve cheese production.
    • Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples

      McHugh, Aoife J.; Yap, Min; Crispie, Fiona; Feehily, Conor; Hill, Colin; Cotter, Paul D.; Department of Agriculture, Food and the Marine; Science Foundation Ireland; European Commission; 14/F/883; et al. (Springer Science and Business Media LLC, 2021-02-15)
      Efficient and accurate identification of microorganisms throughout the food chain can potentially allow the identification of sources of contamination and the timely implementation of control measures. High throughput DNA sequencing represents a potential means through which microbial monitoring can be enhanced. While Illumina sequencing platforms are most typically used, newer portable platforms, such as the Oxford Nanopore Technologies (ONT) MinION, offer the potential for rapid analysis of food chain microbiomes. Initial assessment of the ability of rapid MinION-based sequencing to identify microbes within a simple mock metagenomic mixture is performed. Subsequently, we compare the performance of both ONT and Illumina sequencing for environmental monitoring of an active food processing facility. Overall, ONT MinION sequencing provides accurate classification to species level, comparable to Illumina-derived outputs. However, while the MinION-based approach provides a means of easy library preparations and portability, the high concentrations of DNA needed is a limiting factor.
    • Seasonality and Geography Have a Greater Influence than the Use of Chlorine-Based Cleaning Agents on the Microbiota of Bulk Tank Raw Milk

      Yap, Min; Gleeson, David; O’Toole, Paul W.; O'Sullivan, Orla; Cotter, Paul D.; Irish Dairy Levy (American Society for Microbiology, 2021-10-28)
      Cleaning of the production environment is vital to ensure the safety and quality of dairy products. Although cleaning with chlorine-based agents is widely adopted, it has been associated with detrimental effects on milk quality and safety, which has garnered increasing interest in chlorine-free cleaning. However, the influence of these methods on the milk microbiota is not well documented. This study investigated the factors that influence the raw milk microbiota, with a focus on the differences when chlorine-based and chlorine-free cleaning of milking equipment are used. Bulk tank raw milk was sampled during three sampling months (April, August, and November), from farms across Ireland selected to capture the use of different cleaning methods, i.e., exclusively chlorine-based (n = 51) and chlorine-free cleaning (n = 92) and farms that used chlorine-free agents for the bulk tank and chlorine-based cleaning agents for the rest of the equipment (n = 28). Shotgun metagenomic analysis revealed the significant influence of seasonal and geographic factors on the bulk tank milk microbiota, indicated by differences in diversity, taxonomic composition, and functional characteristics. Taxonomic and functional profiles of samples collected in November clustered separately from those of samples collected in other months. In contrast, cleaning methods only accounted for 1% of the variation in the bulk tank milk bacterial community, and samples collected from farms using chlorine-based versus chlorine-free cleaning did not differ significantly, suggesting that the chlorine-free approaches used did not negatively impact microbiological quality. This study shows the value of shotgun metagenomics in advancing our knowledge of the raw milk microbiota.
    • Development and validation of a quantitative method for 15 antiviral drugs in poultry muscle using liquid chromatography coupled to tandem mass spectrometry

      Douillet, Clément; Moloney, Mary; Di Rocco, Melissa; Elliott, Christopher; Danaher, Martin; European Union; Chinese Ministry of Science and Technology; 727864 (Elsevier BV, 2022-02)
      The objective of this work was to develop a quantitative multi-residue method for analysing antiviral drug residues and their metabolites in poultry meat samples. Antiviral drugs are not licensed for the treatment of influenza in food producing animals. However, there have been some reports indicating their illegal use in poultry. In this study, a method was developed for the analysis of 15 antiviral drug residues in poultry muscle (chicken, duck, quail and turkey) using liquid chromatography coupled to tandem mass spectrometry. This included 13 drugs against influenza and associated metabolites, but also two drugs employed for the treatment of herpes (acyclovir and ganciclovir). The method required the development of a novel chromatographic separation using a hydrophilic interaction chromatographic (HILIC) BEH amide column, which was necessary to retain the highly polar compounds. The analytes were detected using a triple quadrupole mass spectrometer operating in positive electrospray ionization mode. A range of different sample preparation protocols suitable for polar compounds were evaluated. The most effective procedure was based on a simple acetonitrile-based protein precipitation step followed by a further dilution in a methanol/water solution. The confirmatory method was validated according to the EU 2021/808 guidelines on different species including chicken, duck, turkey and quail. The validation was performed using various calibration curves ranging from 0.1 µg kg−1to 200 µg kg−1, according to the analyte. Depending on the analyte sensitivity, decision limits achieved ranged from 0.12 µg kg−1 for arbidol to 34.7 µg kg−1 for ribavirin. Overall, the reproducibility precision values ranged from 2.8% to 22.7% and the recoveries from 84% to 127%. The method was applied to 120 commercial poultry samples from the Irish market, which were all found to be residue-free.
    • Enhancing muscle fatty acid profile by pasture finishing within a dairy-origin calf-to-steer beef production system and its potential to authenticate the dietary history of the cattle

      Moloney, Aidan; Keane, Michael G.; Monahan, F. J.; O'Callaghan, Tom (Teagasc, 2021-11-18)
      The influence of modifying a traditional 24-mo dairy steer calf to beef production system on the fatty acid composition of the longissimus muscle and its potential to authenticate beef provenance was examined. Fifty-four male calves (n = 18 per sire breed), progeny of Holstein-Friesian cows mated with Holstein-Friesian (HF), Aberdeen Angus (AA) and Belgian Blue (BB) bulls were at pasture from March until August of their second year when they were assigned to a 3 (breed types) × 3 (finishing strategies) factorial experiment. The three finishing strategies were (i) pasture only for a further 94 d prior to slaughter (21 mo of age) (Grass), (ii) concentrates ad libitum indoors for 94 d prior to slaughter (21 mo of age) (EC) and (iii) pasture only for a further 94 d followed by concentrates ad libitum indoors for 98 d prior to slaughter (24 mo of age) (LC). Compared to EC, muscle from Grass had a lower intramuscular fat concentration and omega-6: omega-3 polyunsaturated fatty acid (PUFA) ratio and higher proportion of conjugated linoleic acid. A longer period at pasture pre-concentrate finishing increased the concentration of omega-3 PUFA which was still lower than in Grass. To maximise the omega-3 PUFA concentration, a late-maturing breed is more appropriate while to maximise conjugated linoleic acid, an early-maturing breed is more appropriate and both should be finished on grass. Chemometric analysis confirmed that the fatty acid profile can authenticate “Grass-Finished” beef per se and has potential to distinguish “Concentrate-Finished” beef based on the length of grazing prior to finishing, but not distinguish between sire breeds.
    • Effect of applying crust-freezing after skin-packaging on the natural microflora of Atlantic salmon (Salmo salar) during storage at low temperatures

      Pedrós-Garrido, S.; Condón-Abanto, S.; Calanche, J.B.; Beltrán, J.A.; Lyng, J.G.; Bolton, Declan; Brunton, Nigel; Whyte, P.; Department of Agriculture, Food and the Marine; 13F458 (Teagasc, 2021-03-26)
      The aim of the present study was to evaluate the effect of crust-freezing (CF) on fresh salmon fillets in skin-packaging during storage at −2.0°C. After CF, all treated samples and untreated controls were stored in a refrigerated cabinet for 20 d. Sampling was carried out at days 0, 2, 6, 8, 10, 14 and 20 in order to analyse total volatile basic nitrogen (TVB-N) and levels of mesophilic and psychrophilic viable counts (MVC and PVC). Enterobacteriaceae (ENT), lactic acid bacteria (LAB), H2S-producing bacteria (SPB) and Pseudomonas spp. (PSE). No significant differences in TVB-N were found between samples except for those taken on day 20 where TVB-N levels of CF samples were lower than controls. Our results suggest that ENT might be the limiting microbial group to determine the end of shelf-life. Thus, if this group is used as an indicator of acceptability, the shelf-life of salmon can be extended from 8 to 20 d when skin-packed and then treated with CF.
    • A preliminary study of Salmonella spp., Listeria monocytogenes, Escherichia coli O157, Enterococcus faecalis and Clostridium spp. in Irish cattle

      Russell, L.; Galindo, C.P.; Whyte, P.; Bolton, Declan; Department of Agriculture, Food and the Marine; Teagasc Walsh Scholarship Programme; 14/SF/487; 2014239 (Teagasc, 2021-06-03)
      Although Salmonella spp., Escherichia coli O157, Listeria monocytogenes, Enterococcus faecalis and Clostridium spp. present a significant food safety and/or spoilage issue for the beef sector, there are limited data on their prevalence in Irish cattle. The objectives of this preliminary study were to investigate the distribution (percentage of farms positive) of Salmonella spp., E. coli O157, L. monocytogenes, E. faecalis and Clostridium spp. and the overall prevalence (%) of these bacteria in cattle on a small cohort of Irish beef farms. A total of 121 fresh bovine faecal samples were obtained on 10 randomly selected beef farms in the Northeast of Ireland and tested for the target pathogens using standard culture-based methods. Presumptive positives were confirmed using previously published polymerase chain reaction (PCR) methods. Salmonella were not detected in any of the samples. E. coli O157, L. monocytogenes, E. faecalis and Clostridium spp. were present on 50%, 40%, 100% and 100% of farms, respectively, with overall (all farms) prevalence rates in cattle of 9%, 8.2%, 61.9% and 87.6%, respectively. This study suggests that E. coli O157 may be more prevalent than previously thought and L. monocytogenes, E. faecalis and Clostridium spp. are widespread in Irish beef animals.
    • Gerry Downey: an authentic spectroscopist

      Davies, A. N.; Downey, Gerard (2021-12-16)
      This year has seen the retirement of Gerry Downey from active service with the Irish National Agriculture and Food Research Institute, Teagasc1 in Dublin. As one of Europe’s leading innovative spectroscopic chemometricians and a great positive personality to have as a project partner, we thought it appropriate to dedicate a column to Gerry’s career, however embarrassed he may be about the idea!
    • The Sensory Quality and Volatile Profile of Dark Chocolate Enriched with Encapsulated Probiotic Lactobacillus plantarum Bacteria

      Mirković, Milica; Seratlić, Sanja; Kilcawley, Kieran; Mannion, David; Mirković, Nemanja; Radulović, Zorica; Ministry of Education, Science and Technological Development of Serbia; 046009; 046010 (MDPI AG, 2018-08-06)
      Cocoa and dark chocolate have a wide variety of powerful antioxidants and other nutrients that can positively affect human health. Probiotic dark chocolate has the potential to be a new product in the growing number of functional foods. In this study, encapsulated potential probiotic Lactobacillus plantarum 564 and commercial probiotic Lactobacillus plantarum 299v were added in the production of dark chocolate. The results show very good survival of probiotic bacteria after production and during storage, reaching 108 cfu/g in the first 60 days and over 106 cfu/g up to 180 days. No statistically significant difference (p > 0.05) in chemical composition and no major differences in the volatile profiles between control and experimental chocolate samples were observed, indicating no impact of probiotic bacteria on compositional and sensory characteristics of dark chocolate. The sensory evaluation of control and both probiotic dark chocolate samples showed excellent sensory quality after 60 and 180 days of storage, demonstrating that probiotics did not affect aroma, texture and appearance of chocolate. Due to a high viability of bacterial cells and acceptable sensory properties, it can be concluded that encapsulated probiotics Lb. plantarum 564 and Lb. plantarum 299v could be successfully used in the production of probiotic dark chocolate.
    • Screening of Contaminants of Emerging Concern in Microalgae Food Supplements

      Martín-Girela, Isabel; Albero, Beatriz; Tiwari, Brijesh K.; Miguel, Esther; Aznar, Ramón; European Union; EAPA_338/2016 (MDPI AG, 2020-05-20)
      The frenetic lifestyle in the developed countries has driven us to be deficient in some nutrients, which may be overcome by supplements. Microalgae, like spirulina (Arthrospira platensis) and chlorella (Chlorella ssp.) are widely used as supplements due to their high contents of macroand micronutrients. Chlorella and spirulina can be grown naturally in a range of water bodies, showing their high adaptability to harsh environments. They are mainly produced in countries with poor water quality and sometimes inexistent water legislation, which can be a vector of micropollutant introduction into the food chain. Thus, a method for the simultaneous determination of 31 emerging contaminants commonly found as micropollutants in freshwater (pharmaceutical and personal care products, hormones, flame retardants and biocides) in two microalgae is presented. Target contaminants were extracted from the microalgae employing ultrasound-assisted matrix solid-phase dispersion followed by gas chromatography-mass spectrometry analysis. The method was validated for chlorella and spirulina with recoveries ranging from 70% to 111% at concentrations of 25 and 100 ng·g −1 , and good linearity in the range from 5 to 400 ng·g −1 with limits of detection below 2.5 ng·g −1 , in both microalgae. The method validated was applied to a range of microalgae supplement foods and the results proved that the compounds studied were below limits of detection.
    • Transcriptional control of central carbon metabolic flux in Bifidobacteria by two functionally similar, yet distinct LacI-type regulators

      Lanigan, Noreen; Kelly, Emer; Arzamasov, Aleksandr A.; Stanton, Catherine; Rodionov, Dmitry A.; van Sinderen, Douwe; Science Foundation Ireland; Department of Agriculture, Food and the Marine; Russian Science Foundation; SFI/12/RC/2273-P1; et al. (Springer Science and Business Media LLC, 2019-11-28)
      Bifdobacteria resident in the gastrointestinal tract (GIT) are subject to constantly changing environmental conditions, which require rapid adjustments in gene expression. Here, we show that two predicted LacI-type transcription factors (TFs), designated AraQ and MalR1, are involved in regulating the central, carbohydrate-associated metabolic pathway (the so-called phosphoketolase pathway or bifd shunt) of the gut commensal Bifdobacterium breve UCC2003. These TFs appear to not only control transcription of genes involved in the bifd shunt and each other, but also seem to commonly and directly afect transcription of other TF-encoding genes, as well as genes related to uptake and metabolism of various carbohydrates. This complex and interactive network of AraQ/MalR1-mediated gene regulation provides previously unknown insights into the governance of carbon metabolism in bifdobacteria.
    • Gamma-aminobutyric acid-producing lactobacilli positively affect metabolism and depressive-like behaviour in a mouse model of metabolic syndrome

      Patterson, E.; Ryan, P. M.; Wiley, N.; Carafa, I.; Sherwin, E.; Moloney, G.; Franciosi, E.; Mandal, R.; Wishart, D. S.; Tuohy, K.; et al. (Springer Science and Business Media LLC, 2019-11-08)
      Metabolic and neuroactive metabolite production represents one of the mechanisms through which the gut microbiota can impact health. One such metabolite, gamma-aminobutyric acid (GABA), can modulate glucose homeostasis and alter behavioural patterns in the host. We previously demonstrated that oral administration of GABA-producing Lactobacillus brevis DPC6108 has the potential to increase levels of circulating insulin in healthy rats. Therefore, the objective of this study was to assess the efcacy of endogenous microbial GABA production in improving metabolic and behavioural outcomes in a mouse model of metabolic dysfunction. Diet-induced obese and metabolically dysfunctional mice received one of two GABA-producing strains, L. brevis DPC6108 or L. brevis DSM32386, daily for 12 weeks. After 8 and 10 weeks of intervention, the behavioural and metabolic profles of the mice were respectively assessed. Intervention with both L. brevis strains attenuated several abnormalities associated with metabolic dysfunction, causing a reduction in the accumulation of mesenteric adipose tissue, increased insulin secretion following glucose challenge, improved plasma cholesterol clearance and reduced despair-like behaviour and basal corticosterone production during the forced swim test. Taken together, this exploratory dataset indicates that intervention with GABA-producing lactobacilli has the potential to improve metabolic and depressive- like behavioural abnormalities associated with metabolic syndrome in mice.
    • Metabolome and microbiome profiling of a stress-sensitive rat model of gut-brain axis dysfunction

      Bassett, Shalome A.; Young, Wayne; Fraser, Karl; Dalziel, Julie E.; Webster, Jim; Ryan, Leigh; Fitzgerald, Patrick; Stanton, Catherine; Dinan, Timothy G.; Cryan, John F.; et al. (Springer Science and Business Media LLC, 2019-10-01)
      Stress negatively impacts gut and brain health. Individual diferences in response to stress have been linked to genetic and environmental factors and more recently, a role for the gut microbiota in the regulation of stress-related changes has been demonstrated. However, the mechanisms by which these factors infuence each other are poorly understood, and there are currently no established robust biomarkers of stress susceptibility. To determine the metabolic and microbial signatures underpinning physiological stress responses, we compared stress-sensitive Wistar Kyoto (WKY) rats to the normoanxious Sprague Dawley (SD) strain. Here we report that acute stress-induced strain-specifc changes in brain lipid metabolites were a prominent feature in WKY rats. The relative abundance of Lactococcus correlated with the relative proportions of many brain lipids. In contrast, plasma lipids were signifcantly elevated in response to stress in SD rats, but not in WKY rats. Supporting these fndings, we found that the greatest diference between the SD and WKY microbiomes were the predicted relative abundance of microbial genes involved in lipid and energy metabolism. Our results provide potential insights for developing novel biomarkers of stress vulnerability, some of which appear genotype specifc.
    • Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome

      Pasolli, Edoardo; De Filippis, Francesca; Mauriello, Italia E.; Cumbo, Fabio; Walsh, Aaron M.; Leech, John; Cotter, Paul D.; Segata, Nicola; Ercolini, Danilo; European Union; et al. (Springer Science and Business Media LLC, 2020-05-25)
      Lactic acid bacteria (LAB) are fundamental in the production of fermented foods and several strains are regarded as probiotics. Large quantities of live LAB are consumed within fermented foods, but it is not yet known to what extent the LAB we ingest become members of the gut microbiome. By analysis of 9445 metagenomes from human samples, we demonstrate that the prevalence and abundance of LAB species in stool samples is generally low and linked to age, lifestyle, and geography, with Streptococcus thermophilus and Lactococcus lactis being most prevalent. Moreover, we identify genome-based differences between food and gut microbes by considering 666 metagenome-assembled genomes (MAGs) newly reconstructed from fermented food microbiomes along with 154,723 human MAGs and 193,078 reference genomes. Our large-scale genome-wide analysis demonstrates that closely related LAB strains occur in both food and gut environments and provides unprecedented evidence that fermented foods can be indeed regarded as a possible source of LAB for the gut microbiome.
    • Immunoglobulin G from bovine milk primes intestinal epithelial cells for increased colonization of bifidobacteria

      Morrin, Sinead T.; McCarthy, Geoffrey; Kennedy, Deirdre; Marotta, Mariarosaria; Irwin, Jane A.; Hickey, Rita M.; Teagasc Walsh Fellowship Programme; 2014058 (Springer Science and Business Media LLC, 2020-06-18)
      A bovine colostrum fraction (BCF) was recently shown to enhance the adherence of several commensal organisms to intestinal epithelial cells through modulating the epithelial cell surface. In this study, the main components of the BCF were examined to investigate the active component/s responsible for driving the changes in the intestinal cells. The adherence of various bifdobacteria to HT-29 cells was increased when the intestinal cells were pre-incubated with immunoglobulin G (IgG). Modulation of the intestinal cells by IgG was concentration dependent with 16 mg/ mL IgG resulting in a 43-fold increase in the adhesion of Bifdobacterium longum NCIMB 8809 to HT-29 cells. Periodate treatment of colostral IgG prior to performing the colonization studies resulted in a reduction in the adhesion of the strain to the intestinal cells demonstrating that the glycans of IgG may be important in modulating the intestinal cells for enhanced commensal adhesion. IgG isolated from mature milk also resulted in signifcant increases in adhesion of the Bifdobacterium strains tested albeit at reduced levels (3.9-fold). The impact of IgG on the HT-29 cells was also visualised via scanning electron microscopy. This study builds a strong case for the inclusion of IgG ingredients sourced from cow’s milk in functional foods aimed at increasing numbers of health promoting bacteria in the human gut.
    • Viromes of one year old infants reveal the impact of birth mode on microbiome diversity

      McCann, Angela; Ryan, Feargal J.; Stockdale, Stephen R.; Dalmasso, Marion; Blake, Tony; Ryan, C. Anthony; STANTON, CATHERINE; Mills, Susan; Ross, Paul R.; Hill, Colin; et al. (PeerJ, 2018-05-07)
      Establishing a diverse gut microbiota after birth is being increasingly recognised as important for preventing illnesses later in life. It is well established that bacterial diversity rapidly increases post-partum; however, few studies have examined the infant gut virome/phageome during this developmental period. We performed a metagenomic analysis of 20 infant faecal viromes at one year of age to determine whether spontaneous vaginal delivery (SVD) or caesarean section (CS) influenced viral composition. We find that birth mode results in distinctly different viral communities, with SVD infants having greater viral and bacteriophage diversity. We demonstrate that CrAssphage is acquired early in life, both in this cohort and two others, although no difference in birth mode is detected. A previous study has shown that bacterial OTU’s (operational taxonomic units) identified in the same infants could not discriminate between birth mode at 12 months of age. Therefore, our results indicate that vertical transmission of viral communities from mother to child may play a role in shaping the early life microbiome, and that birth mode should be considered when studying the early life gut virome.
    • The response of foodborne pathogens to osmotic and desiccation stresses in the food chain

      Burgess, Catherine; Gianotti, Andrea; Gruzdev, Nadia; Holah, John; Knøchel, Susanne; Lehner, Angelika; Margas, Edyta; Esser, Stephan Schmitz; Sela (Saldinger), Shlomo; Tresse, Odile; et al. (Elsevier BV, 2016-03)
      In combination with other strategies, hyperosmolarity and desiccation are frequently used by the food processing industry as a means to prevent bacterial proliferation, and particularly that of foodborne pathogens, in food products. However, it is increasingly observed that bacteria, including human pathogens, encode mechanisms to survive and withstand these stresses. This review provides an overview of the mechanisms employed by Salmonella spp., Shiga toxin producing E. coli, Cronobacter spp., Listeria monocytogenes and Campylobacter spp. to tolerate osmotic and desiccation stresses and identifies gaps in knowledge which need to be addressed to ensure the safety of low water activity and desiccated food products.
    • Effect of storage, food processing and novel extraction technologies on onions flavonoid content: A review

      Ren, Feiyue; Nian, Yingqun; Perussello, Camila A.; Department of Agriculture, Food and Marine; FIRM 06/NITARFC6 (Elsevier, 2020-06-30)
      Onions play an important part in the daily diet for most populations around the world owing to their nutritional composition and their unique capacity to naturally flavor dishes. Onions contain quercetin and its derivatives - the predominant flavonoid in onions that exert a great contribution to the effective bioactive properties of onion, including its derived products. The present paper comprehensively reviewed flavonoids (with a specific focus on quercetin in onions): their chemical composition, distribution, bioactivities in onion, and impacting factors with a focus on how they can be affected by various post-harvest conditions (storage and food processing). In addition, research on the extraction of flavonoid compounds from onions using a number of novel technologies was also reviewed.