The Teagasc Food Programme focuses on quality, safety and food product innovation. It is undertaken in collaboration with universities and research institutes in Ireland, the European Union and the USA. The Food Programme is internationally competitive from a scientific point of view while being targeted and applied to generate new opportunities for the Irish food industry The Teagasc Food Programme encompasses many aspects of food science and technology: Food Processing and Functionality, Food Safety, Foods for Health, Food Cultures, Food Quality and Structure, Meat and Meat Products, Prepared Consumer Foods. The Food Programme is run from the Teagasc Food Research Centres at Ashtown, Dublin 14 and Moorepark, Fermoy, Co. Cork

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Recent Submissions

  • Delivery of Curcumin Using Skim Milk or Oil in Water Emulsions: Effect of the Matrices on Cellular Uptake

    Guri, Anilda; Gülseren, İbrahim; Arranz, Elena; Corredig, Milena (Japan Oil Chemists' Society, 2018)
    To enhance the curcumin delivery in a variety of food grade matrices namely spray dried ethanolic curcumin in fresh skim milk (Spray dried Cu-SM), a fresh mixture of ethanolic curcumin and skim milk (Fresh Cu-SM) a powder mixture of curcumin and skim milk powder (Powder Cu-SMP) and oil in water emulsion (Emulsion) were studied. The cellular uptake of curcumin from the respective matrices was studied on Caco-2 cell monolayers. Spray dried Cu-SM showed higher encapsulation efficiency compared to a corresponding Powder Cu-SMP and an oil-in-water emulsion (40% oil) bearing curcumin. Furthermore, ethanolic administration of curcumin in spray dried form enhanced the cellular uptake of curcumin considerably higher than non-ethanolic samples (approx. 4 times). Overall, milk protein based vectors were found to perform better than emulsion samples. These findings highlighted the fact that curcumin uptake may be tailored by fine tuning of curcumin delivery vehicles which highlights possible application of powders as functional foods.
  • Novel Beverages of Yerba-Mate and Soy: Bioactive Compounds and Functional Properties

    Frizon, Cátia; Perussello, Camila; Sturion, José; Hoffmann-Ribani, Rosemary; CAPES Brazil (Coordination for the Improvement of Higher Education Personnel); Embrapa-Florestas (Colombo, PR, Brazil) (Multidisciplinary Digital Publishing Institute, 2018-03-06)
    In this paper, two high-nutrition commodities that are produced in great amounts in Brazil were joined in a single functional product. Yerba mate (Ilex paraguariensis) is rich in bioactive compounds, while soybean is a high-quality protein source. The objective of this paper was to assess the psychochemical characteristics of two yerba-mate progenies (planted–PL and native–NT leaves) and then confirm whether the functional and nutritional properties of the main ingredients were conveyed to the beverage produced. The main raw material, yerba-mate leaves, and the drinks were assessed for bioactive compounds, antioxidant capacity, physicochemical properties, and nutritional value. Planted leaves showed higher concentration of 5-CQA, caffeic acid and rutin than the native plant, whereas caffeine and theobromine were detected in larger amounts in native leaves. The nutritional profile of the drinks was compared to commercial beverages–either yerba-mate-based or soy-based. They indeed provide more protein, fiber, and fats than traditional yerba-mate beverages (chimarrão, tererê, and mate tea). Soy drinks currently marketed, for their turn, have similar caloric value and higher contents of lipid and protein as compared to our product, but are poor in fibers. NT drink (DPPH—IC50 92.83 and ABTS—8.18 μM Trolox/mL) had higher antioxidant activity than PL (IC50 147.06 and 5.63 μM Trolox/mL) due to the greater volume fraction of yerba-mate extract. NT beverage has more 5-CQA and caffeine in the same intake of tererê and traditional mate tea. This healthy beverage contributes to an increasing income to the food industry and yerba-mate producers, and environmental gains that are related to the exploration of natural resources.
  • DairyWater: striving for sustainability within the dairy processing industry in the Republic of Ireland

    Finnegan, William; Clifford, Eoghan; Goggins, Jamie; O'Leary, Niall; Dobson, Alan; Rowan, Neil; Xiao, Liwen; Miao, Song; Fitzhenry, Kelly; Leonard, Peter; et al. (Cambridge University Press (CUP), 2018-08-08)
    This Review describes the objectives and methodology of the DairyWater project as it aims to aid the Irish dairy processing industry in achieving sustainability as it expands. With the abolition of European milk quotas in March 2015, the Republic of Ireland saw a surge in milk production. The DairyWater project was established in anticipation of this expansion of the Irish dairy sector in order to develop innovative solutions for the efficient management of water consumption, wastewater treatment and the resulting energy use within the country's dairy processing industry. Therefore, the project can be divided into three main thematic areas: dairy wastewater treatment technologies and microbial analysis, water re-use and rainwater harvesting and environmental assessment. In order to ensure the project remains as relevant as possible to the industry, a project advisory board containing key industry stakeholders has been established. To date, a number of large scale studies, using data obtained directly from the Irish dairy industry, have been performed. Additionally, pilot-scale wastewater treatment (intermittently aerated sequencing batch reactor) and tertiary treatment (flow-through pulsed ultraviolet system) technologies have been demonstrated within the project. Further details on selected aspects of the project are discussed in greater detail in the subsequent cluster of research communications.
  • Dairy matrix effects: response to consumption of dairy fat differs when eaten within the cheese matrix—a randomized controlled trial

    Feeney, Emma L; Barron, Rebecca; Dible, Victoria; Hamilton, Zita; Power, Yvonne; Tanner, Linda; Flynn, Cal; Bouchier, Paul; Beresford, Tom; Noronha, Nessa; et al. (Oxford University Press (OUP), 2018-08-11)
    Background Dairy fat consumed as cheese has different effects on blood lipids than that consumed as butter. It is unknown whether the effect is specific to fat interaction with other cheese nutrients (calcium, casein proteins), or to the cheese matrix itself. Objective We aimed to test the effect of 6 wk daily consumption of ∼40 g dairy fat, eaten within macronutrient-matched food matrices, on markers of metabolic health, in overweight adults aged ≥50 y. Design The study was a 6-wk randomized parallel intervention; 164 volunteers (75 men) received ∼40 g of dairy fat/d, in 1 of 4 treatments: (A) 120 g full-fat Irish cheddar cheese (FFCC) (n = 46); (B) 120 g reduced-fat Irish cheddar cheese + butter (21 g) (RFC + B) (n = 45); (C) butter (49 g), calcium caseinate powder (30 g), and Ca supplement (CaCO3) (500 mg) (BCC) (n = 42); or (D) 120 g FFCC, for 6 wk (as per A) (n = 31). Group D first completed a 6-wk “run-in” period, where they excluded all dietary cheese before commencing the intervention. Results There was no difference in anthropometry, fasting glucose, or insulin between the groups at pre- or postintervention. However, a stepwise-matrix effect was observed between the groups for total cholesterol (TC) (P = 0.033) and LDL cholesterol (P = 0.026), with significantly lower postintervention TC (mean ± SD) (5.23 ± 0.88 mmol/L) and LDL cholesterol (2.97 ± 0.67 mmol/L) when all of the fat was contained within the cheese matrix (Group A), compared with Group C when it was not (TC: 5.57 ± 0.86 mmol/L; LDL cholesterol: 3.43 ± 0.78 mmol/L). Conclusion Dairy fat, eaten in the form of cheese, appears to differently affect blood lipids compared with the same constituents eaten in different matrices, with significantly lower total cholesterol observed when all nutrients are consumed within a cheese matrix This trial was registered at ISRCTN as ISRCTN86731958.
  • The Gut Microbiota of Marine Fish

    Egerton, Sian; Cullotoy, Sarah; Whooley, Jason; Stanton, Catherine; Ross, R. Paul; Irish Research Council (IRC); Biomarine Ingredients Ireland Ltd.; Science Foundation Ireland; Department of Agriculture, Food and the Marine (DAFM) in Ireland; Marine Institute; et al. (Frontiers, 2018-05-18)
    The body of work relating to the gut microbiota of fish is dwarfed by that on humans and mammals. However, it is a field that has had historical interest and has grown significantly along with the expansion of the aquaculture industry and developments in microbiome research. Research is now moving quickly in this field. Much recent focus has been on nutritional manipulation and modification of the gut microbiota to meet the needs of fish farming, while trying to maintain host health and welfare. However, the diversity amongst fish means that baseline data from wild fish and a clear understanding of the role that specific gut microbiota play is still lacking. We review here the factors shaping marine fish gut microbiota and highlight gaps in the research.
  • In silico Prediction and Exploration of Potential Bacteriocin Gene Clusters Within the Bacterial Genus Geobacillus

    Egan, Kevin; Field, Des; Ross, R. Paul; Cotter, Paul; Hill, Colin; Department of Agriculture, Fisheries and Food, Ireland; Science Foundation Ireland; 13/F/462; 10/IN.1/B3027; SFI/12/RC/2273 (Frontiers Media SA, 2018-09-20)
    The thermophilic, endospore-forming genus of Geobacillus has historically been associated with spoilage of canned food. However, in recent years it has become the subject of much attention due its biotechnological potential in areas such as enzyme and biofuel applications. One aspect of this genus that has not been fully explored or realized is its use as a source of novel forms of the ribosomally synthesized antimicrobial peptides known as bacteriocins. To date only two bacteriocins have been fully characterized within this genus, i.e., Geobacillin I and II, with only a small number of others partially characterized. Here we bioinformatically investigate the potential of this genus as a source of novel bacteriocins through the use of the in silico screening software BAGEL3, which scans publically available genomes for potential bacteriocin gene clusters. In this study we examined the association of bacteriocin gene presence with niche and phylogenetic position within the genus. We also identified a number of candidates from multiple bacteriocin classes which may be promising antimicrobial candidates when investigated in vitro in future studies.
  • The Lactobacillus casei Group: History and Health Related Applications

    Hill, Daragh; Sugrue, Ivan; Tobin, Conor; Hill, Colin; STANTON, CATHERINE; Ross, R. Paul; Teagasc Walsh Fellowships; Science Foundation Ireland; SFI/12/RC/2273 (Frontiers Media SA, 2018-09-10)
    The Lactobacillus casei group (LCG), composed of the closely related Lactobacillus casei, Lactobacillus paracasei, and Lactobacillus rhamnosus are some of the most widely researched and applied probiotic species of lactobacilli. The three species have been extensively studied, classified and reclassified due to their health promoting properties. Differentiation is often difficult by conventional phenotypic and genotypic methods and therefore new methods are being continually developed to distinguish the three closely related species. The group remain of interest as probiotics, and their use is widespread in industry. Much research has focused in recent years on their application for health promotion in treatment or prevention of a number of diseases and disorders. The LCG have the potential to be used prophylactically or therapeutically in diseases associated with a disturbance to the gut microbiota. The group have been extensively researched with regard to stress responses, which are crucial for their survival and therefore application as probiotics.
  • Extraction and Yield Optimisation of Fucose, Glucans and Associated Antioxidant Activities from Laminaria digitata by Applying Response Surface Methodology to High Intensity Ultrasound-Assisted Extraction

    Garcia-Vaquero, Marco; Rajauria, Gaurav; Tiwari, Brijesh; Sweeney, Torres; O’Doherty, John; Science Foundation Ireland; 14/IA/2548 (Multidisciplinary Digital Publishing Institute, 2018-07-30)
    The objectives of this study were to employ response surface methodology (RSM) to investigate and optimize the effect of ultrasound-assisted extraction (UAE) variables, temperature, time and amplitude on the yields of polysaccharides (fucose and total glucans) and antioxidant activities (ferric reducing antioxidant power (FRAP) and 1,1-diphenyl-2-picryl-hydrazyl radical scavenging activity (DPPH)) from Laminaria digitata, and to explore the suitability of applying the optimum UAE conditions for L. digitata to other brown macroalgae (L. hyperborea and Ascophyllum nodosum). The RSM with three-factor, four-level Box-Behnken Design (BBD) was used to study and optimize the extraction variables. A second order polynomial model fitted well to the experimental data with R2 values of 0.79, 0.66, 0.64, 0.73 for fucose, total glucans, FRAP and DPPH, respectively. The UAE parameters studied had a significant influence on the levels of fucose, FRAP and DPPH. The optimised UAE conditions (temperature = 76 °C, time = 10 min and amplitude = 100%) achieved yields of fucose (1060.7 ± 70.6 mg/100 g dried seaweed (ds)), total glucans (968.6 ± 13.3 mg/100 g ds), FRAP (8.7 ± 0.5 µM trolox/mg freeze-dried extract (fde)) and DPPH (11.0 ± 0.2%) in L. digitata. Polysaccharide rich extracts were also attained from L. hyperborea and A. nodosum with variable results when utilizing the optimum UAE conditions for L. digitata.
  • Isolation and characterization of an exopolysaccharide‐producing Leuconostoc citreum strain from artisanal cheese

    Domingos‐Lopes, M.F.P.; Lamosa, P.; Stanton, C.; Ross, R.P.; Silva, C.C.G.; FCT; FRCT; PTDC/AGR-ALI/104385/ 2008; M3.1.2/F/009/2011 (Wiley, 2018-10-18)
    High molar mass exopolysaccharides (EPS) produced from sucrose by lactic acid bacteria (LAB) are of great interest as natural additives to use in foods, medical and pharmaceutical industry. This study aimed to identify the EPS produced by Leuconostoc citreum L3C1E7 isolated from Pico cheese and characterize the strain for technological and probiotic potential. Purified EPS was isolated from the culture of L. citreum L3C1E7 by ethanol precipitation, with a yield of 520 mg ml−1. The EPS-producing strain had a mucoid phenotype and average molecular weight of 5·88 × 106 Da. The structural characterization of the purified EPS was determined by 1H, 13C and two-dimensional NMR spectroscopy. EPS was composed of alternating α-(1→6)-linked and α-(1→3)-linked D-glucopyranyl units, suggesting the existence of an alternan. The strain was slow acidifying, produced diacetyl and displayed high esterase/lipase and aminopeptidase activities, which promote the desirable flavours in dairy products. Moreover, L. citreum showed moderate resistance to the adverse conditions of the gastrointestinal (GI) tract and high adhesion to GI cells. This work provides a better understanding of EPS produced by L. citreum and the potential application of EPS-producing strain in food and/or as a probiotic culture.
  • A Prospective Metagenomic and Metabolomic Analysis of the Impact of Exercise and/or Whey Protein Supplementation on the Gut Microbiome of Sedentary Adults

    Cronin, Owen; Barton, Wiley; Skuse, Peter; Penney, Nicholas C.; Garcia-Perez, Isabel; Murphy, Eileen F.; Woods, Trevor; Nugent, Helena; Fanning, Aine; Melgar, Silvia; et al. (American Society for Microbiology, 2018-06-26)
    Many components of modern living exert influence on the resident intestinal microbiota of humans with resultant impact on host health. For example, exercise-associated changes in the diversity, composition, and functional profiles of microbial populations in the gut have been described in cross-sectional studies of habitual athletes. However, this relationship is also affected by changes in diet, such as changes in dietary and supplementary protein consumption, that coincide with exercise. To determine whether increasing physical activity and/or increased protein intake modulates gut microbial composition and function, we prospectively challenged healthy but sedentary adults with a short-term exercise regime, with and without concurrent daily whey protein consumption. Metagenomics- and metabolomics-based assessments demonstrated modest changes in gut microbial composition and function following increases in physical activity. Significant changes in the diversity of the gut virome were evident in participants receiving daily whey protein supplementation. Results indicate that improved body composition with exercise is not dependent on major changes in the diversity of microbial populations in the gut. The diverse microbial characteristics previously observed in long-term habitual athletes may be a later response to exercise and fitness improvement. IMPORTANCE The gut microbiota of humans is a critical component of functional development and subsequent health. It is important to understand the lifestyle and dietary factors that affect the gut microbiome and what impact these factors may have. Animal studies suggest that exercise can directly affect the gut microbiota, and elite athletes demonstrate unique beneficial and diverse gut microbiome characteristics. These characteristics are associated with levels of protein consumption and levels of physical activity. The results of this study show that increasing the fitness levels of physically inactive humans leads to modest but detectable changes in gut microbiota characteristics. For the first time, we show that regular whey protein intake leads to significant alterations to the composition of the gut virome.
  • RNA Phage Biology in a Metagenomic Era

    Callanan, Julie; Stockdale, Stephen; Shkoporov, Andrey; Draper, Lorraine; Ross, R.; Hill, Colin; Science Foundation Ireland (SFI); SFI/12/RC/2273 (Multidisciplinary Digital Publishing Institute, 2018-07-21)
    The number of novel bacteriophage sequences has expanded significantly as a result of many metagenomic studies of phage populations in diverse environments. Most of these novel sequences bear little or no homology to existing databases (referred to as the "viral dark matter"). Also, these sequences are primarily derived from DNA-encoded bacteriophages (phages) with few RNA phages included. Despite the rapid advancements in high-throughput sequencing, few studies enrich for RNA viruses, i.e., target viral rather than cellular fraction and/or RNA rather than DNA via a reverse transcriptase step, in an attempt to capture the RNA viruses present in a microbial communities. It is timely to compile existing and relevant information about RNA phages to provide an insight into many of their important biological features, which should aid in sequence-based discovery and in their subsequent annotation. Without comprehensive studies, the biological significance of RNA phages has been largely ignored. Future bacteriophage studies should be adapted to ensure they are properly represented in phageomic studies.
  • The Potential of Combined Emulsification and Spray Drying Techniques for Encapsulation of Polyphenols from Rosemary ( Rosmarinus officinalis L.) Leaves

    Bušić, Arijana; Komes, Draženka; Belščak-Cvitanović, Ana; Vojvodić Cebin, Aleksandra; Špoljarić, Igor; Mršić, Gordan; Miao, Song; National Natural Science Foundation of China; European Union; 31628016; et al. (PubMed, 2018-12)
    The present study evaluates the potential of encapsulation of polyphenolic antioxidants from rosemary (Rosmarinus officinalis L.) leaves by combining emulsification and spray drying techniques. To stabilize the emulsions and prepare samples suitable for use in dry products, double emulsions encapsulating rosemary polyphenolic extract and containing polyglycerol polyricinoleate (4%), whey protein isolates (2 and 4%) as emulsifiers, and maltodextrins (MDE 10 and 21) as enhancing coatings were subjected to spray drying. The obtained results show insignificant (p>0.05) effect of used maltodextrin type and protein content on mean particle size of double emulsions containing rosemary polyphenols. Morphology analyses showed that double emulsions were successfully prepared, spherical microcapsules were obtained after spray drying of double emulsions and double emulsion form was still preserved after rehydration of spray-dried microcapsules. Regardless of used maltodextrins, significantly (p>0.05) higher encapsulation efficiencies (EE) of total polyphenols (39.57 and 42.83%) in rehydrated samples were achieved when higher protein content (4% whey protein isolate) was used, indicating the major impact of protein content on EE of rosemary polyphenols. Also, using HPLC analysis, rosmarinic and caffeic acids, apigenin and luteolin derivatives were detected among specific polyphenols, where rosmarinic acid had notable encapsulation efficiency ranging from 62.15 to 67.43%. In this way, the obtained microcapsules encapsulating rosemary polyphenols could be easily blended with various dry mixtures, and serve for delivery in different functional products.
  • Omics-Based Insights into Flavor Development and Microbial Succession within Surface-Ripened Cheese

    Bertuzzi, A. S.; Walsh, A. M.; Sheehan, J. J.; Cotter, P. D.; Crispie, F.; McSweeney, P. L. H.; Kilcawley, K. N.; Rea, M. C.; Science Foundation Ireland; APC Microbiome Institute; et al. (American Society for Microbiology, 2018-02-27)
    In this study, a young Cheddar curd was used to produce two types of surface-ripened cheese, using two commercial smear-culture mixes of yeasts and bacteria. Whole-metagenome shotgun sequencing was used to screen the microbial population within the smear-culture mixes and on the cheese surface, with comparisons of microorganisms at both the species and the strain level. The use of two smear mixes resulted in the development of distinct microbiotas on the surfaces of the two test cheeses. In one case, most of the species inoculated on the cheese established themselves successfully on the surface during ripening, while in the other, some of the species inoculated were not detected during ripening and the most dominant bacterial species, Glutamicibacter arilaitensis, was not a constituent of the culture mix. Generally, yeast species, such as Debaryomyces hansenii and Geotrichum candidum, were dominant during the first stage of ripening but were overtaken by bacterial species, such as Brevibacterium linens and G. arilaitensis, in the later stages. Using correlation analysis, it was possible to associate individual microorganisms with volatile compounds detected by gas chromatography-mass spectrometry in the cheese surface. Specifically, D. hansenii correlated with the production of alcohols and carboxylic acids, G. arilaitensis with alcohols, carboxylic acids and ketones, and B. linens and G. candidum with sulfur compounds. In addition, metagenomic sequencing was used to analyze the metabolic potential of the microbial populations on the surfaces of the test cheeses, revealing a high relative abundance of metagenomic clusters associated with the modification of color, variation of pH, and flavor development. IMPORTANCE Fermented foods, in particular, surface-ripened cheese, represent a model to explain the metabolic interactions which regulate microbial succession in complex environments. This study explains the role of individual species in a heterogeneous microbial environment, i.e., the exterior of surface-ripened cheese. Through whole-metagenome shotgun sequencing, it was possible to investigate the metabolic potential of the resident microorganisms and show how variations in the microbial populations influence important aspects of cheese ripening, especially flavor development. Overall, in addition to providing fundamental insights, this research has considerable industrial relevance relating to the production of fermented food with specific qualities.
  • Mining bifidobacteria from the neonatal gastrointestinal tract for conjugated linolenic acid production

    Yang, Bo; Chen, Haiqin; Stanton, Catherine; Chen, Yong Q.; Zhang, Hao; Chen, Wei; National Natural Science Foundation of China; the Program for New Century Excellent Talents; the Program for Changjiang Scholars and Innovative Research Team in University; the National Natural Science Foundation of Jiangsu Province; et al. (Informa UK Limited, 2016-09-22)
    Conjugated linolenic acid (CLNA) is a family of isomers of linolenic acid with a number of healthassociated benefits, which has been attracting great interest. Microbial CLNA producers are potentially an alternative source of CLNA for human nutrition. In present study, 16 neonate feces were collected and used for Bifidobacteria isolation, from which 25 bifidobacteria isolates were obtained. The bifidobacteria isolates were identified using 16s rDNA sequencing as Bifidobacterium adolescentis, B. breve, B. longum and B. pseudocatenulatum. These isolates were further investigated for their ability to produce CLNA using linolenic acid as substrate via GC-MS. The results showed most of the isolates could convert free linolenic acid into c9,t11,c15-CLNA and t9,t11,c15-CLNA at different levels. B. pseudocatenulatum was the most effective CLNA producer, which converted 86.91% of linolenic acid to c9,t11,c15-CLNA and 3.59% of to t9,t11,c15-CLNA isomer and the isolate exhibited to accumulate CLNA during 72 h culturing in which most CLNA isomers were in the supernatant fluid. The results indicated that utilization of this isolate for CLNA production will eliminate the purification process.
  • Microbial Therapeutics Designed for Infant Health

    Watkins, Claire; STANTON, CATHERINE; Ryan, C. Anthony; Ross, R. Paul; Science Foundation Ireland (SFI); APC Microbiome Institute; Department of Agriculture Food and Marine (DAFM); INFANTMET (Ref. No. 10FDairy); ToddlerFood (Ref. No. 14F821) (Frontiers Media SA, 2017-10-26)
    Acknowledgment of the gut microbiome as a vital asset to health has led to multiple studies attempting to elucidate its mechanisms of action. During the first year of life, many factors can cause fluctuation in the developing gut microbiome. Host genetics, maternal health status, mode of delivery, gestational age, feeding regime, and perinatal antibiotic usage, are known factors which can influence the development of the infant gut microbiome. Thus, the microbiome of vaginally born, exclusively breastfed infants at term, with no previous exposure to antibiotics, either directly or indirectly from the mother, is to be considered the “gold standard.” Moreover, the use of prebiotics as an aid for the development of a healthy gut microbiome is equally as important in maintaining gut homeostasis. Breastmilk, a natural prebiotic source, provides optimal active ingredients for the growth of beneficial microbial species. However, early life disorders such as necrotising enterocolitis, childhood obesity, and even autism have been associated with an altered/disturbed gut microbiome. Subsequently, microbial therapies have been introduced, in addition to suitable prebiotic ingredients, which when administered, may aid in the prevention of a microbial disturbance in the gastrointestinal tract. The aim of this mini-review is to highlight the beneficial effects of different probiotic and prebiotic treatments in early life, with particular emphasis on the different conditions which negatively impact microbial colonisation at birth.
  • A Profile Hidden Markov Model to investigate the distribution and frequency of LanB-encoding lantibiotic modification genes in the human oral and gut microbiome

    Walsh, Calum J.; Guinane, Caitriona M.; O’ Toole, Paul W.; Cotter, Paul D.; Science Foundation Ireland; 11/PI/1137 (PeerJ, 2017-04-27)
    Background The human microbiota plays a key role in health and disease, and bacteriocins, which are small, bacterially produced, antimicrobial peptides, are likely to have an important function in the stability and dynamics of this community. Here we examined the density and distribution of the subclass I lantibiotic modification protein, LanB, in human oral and stool microbiome datasets using a specially constructed profile Hidden Markov Model (HMM). Methods The model was validated by correctly identifying known lanB genes in the genomes of known bacteriocin producers more effectively than other methods, while being sensitive enough to differentiate between different subclasses of lantibiotic modification proteins. This approach was compared with two existing methods to screen both genomic and metagenomic datasets obtained from the Human Microbiome Project (HMP). Results Of the methods evaluated, the new profile HMM identified the greatest number of putative LanB proteins in the stool and oral metagenome data while BlastP identified the fewest. In addition, the model identified more LanB proteins than a pre-existing Pfam lanthionine dehydratase model. Searching the gastrointestinal tract subset of the HMP reference genome database with the new HMM identified seven putative subclass I lantibiotic producers, including two members of the Coprobacillus genus. Conclusions These findings establish custom profile HMMs as a potentially powerful tool in the search for novel bioactive producers with the power to benefit human health, and reinforce the repertoire of apparent bacteriocin-encoding gene clusters that may have been overlooked by culture-dependent mining efforts to date.
  • Feeding the microbiota: transducer of nutrient signals for the host

    Shanahan, Fergus; van Sinderen, Douwe; O’Toole, Paul W; STANTON, CATHERINE (BMJ, 2017-06-29)
    Advances in microbiome science cast light on traditional concepts on nutritional science, and are poised for clinical translation. Epidemiologic observations which linked lifestyle factors to risk of disease are being re-interpreted with mechanistic insight based on improved understanding of the microbiota. Examples include the role of dietary fibre in disease prevention, the deleterious effects of highly restricted diets, and the contribution of the microbiota to over- and undernutrition. While the microbiota transduces nutrient signals for the host, food and habitual diet shape the composition of the gut microbiota at every stage of life. The composition and diversity of food intake determines which microbes will colonise, flourish, persist, or become extinct. Disruption of the developing microbiota in infancy contributes to the risk of immune and metabolic disease in later life, whereas loss of microbes in the elderly due to monotonous diets has been linked with unhealthy ageing and frailty. This should influence modern dietary advice regarding prevention and management of chronic non-communicable inflammatory and metabolic disorders, and will inform the design of infant and future food formula. The microbiota profile is also emerging as a biomarker to predict responsiveness to dietary interventions and promises to make personalised nutrition a reality.
  • Recent advances in microbial fermentation for dairy and health

    Hill, Daragh; Sugrue, Ivan; Arendt, Elke; Hill, Colin; STANTON, CATHERINE; Ross, R Paul; Teagasc Walsh Fellowships; Science Foundation Ireland (SFI); SFI/12/RC/2273 (F1000 Research Ltd, 2017-05-26)
    Microbial fermentation has been used historically for the preservation of foods, the health benefits of which have since come to light. Early dairy fermentations depended on the spontaneous activity of the indigenous microbiota of the milk. Modern fermentations rely on defined starter cultures with desirable characteristics to ensure consistency and commercial viability. The selection of defined starters depends on specific phenotypes that benefit the product by guaranteeing shelf life and ensuring safety, texture, and flavour. Lactic acid bacteria can produce a number of bioactive metabolites during fermentation, such as bacteriocins, biogenic amines, exopolysaccharides, and proteolytically released peptides, among others. Prebiotics are added to food fermentations to improve the performance of probiotics. It has also been found that prebiotics fermented in the gut can have benefits that go beyond helping probiotic growth. Studies are now looking at how the fermentation of prebiotics such as fructo-oligosaccharides can help in the prevention of diseases such as osteoporosis, obesity, and colorectal cancer. The potential to prevent or even treat disease through the fermentation of food is a medically and commercially attractive goal and is showing increasing promise. However, the stringent regulation of probiotics is beginning to detrimentally affect the field and limit their application.
  • In vitro enzyme inhibitory effects of green and brown Australian seaweeds and potential impact on metabolic syndrome

    Shannon, Emer; Conlon, Michael; Hayes, Maria; European Union; Teagasc; 754380 (Springer Science and Business Media LLC, 2023-02-03)
    Hypertension, type-2-diabetes (T2D) and obesity are contributory risk factors for the development of metabolic syndrome. Peptides, polyphenols and polysaccharides may inhibit enzymes involved in the disease pathways of this disorder. Peptide hydrolysates (PEP), polyphenol (PP) and polysaccharide (PS) extracts generated from the Australian seaweeds Phyllospora comosa (Labillardière) C. Agardh, Ecklonia radiata (C. Agardh) J. Agardh, and Ulva ohnoi M. Hiraoka & S. Shimada were screened in vitro for their potential to inhibit enzymes important in the control of diseases associated with metabolic syndrome. These enzymes include angiotensin-I-converting enzyme (ACE-1; EC which affects the development of hypertension in mammals, α-amylase (EC and lipase (EC which play a role in the development of T2D and dietary lipid absorption, respectively. The inhibitory activity of each seaweed extract was determined using established in vitro colorimetric methods with mammalian-derived enzymes and their respective substrates. The ACE-1 half-maximal inhibitory (IC50) concentrations of generated bioactive extracts ranged from 167.52 ± 3.17 µg mL−1 (U. ohnoi PEP) to 713.84 ± 12.45 µg mL−1 (E. radiata PS). None of the extracts screened displayed IC50 values comparable to the positive control drug Captopril (8.87 ± 0.04 µg mL−1). IC50 values determined for extracts that inhibited α-amylase ranged from 58.31 ± 1.41 µg mL−1 (P. comosa PP) to 515.24 ± 10.53 µg mL−1 (E. radiata PEP). All PS and PP had significantly lower IC50 values than the α-amylase inhibitor control, Acarbose (89.90 ± 0.15 µg mL−1). Lipase IC50 values determined for extracts ranged from 52.14 ± 2.77 µg mL−1 (P. comosa PP) to 876.30 ± 34.92 µg mL−1 (E. radiata PEP). All PP had significantly lower IC50 values than the lipase inhibitory drug Orlistat (70.83 ± 0.07 µg mL−1). To the authors’ knowledge there are no published values for the inhibitory potential of P. comosa, E. radiata or U. ohnoi extracts against the enzymes ACE-1, α-amylase, or lipase. These findings demonstrate the functional food potential of P. comosa, E. radiata and U. ohnoi polyphenols, polysaccharides and peptides.
  • Bioinformatic approaches for studying the microbiome of fermented food

    Walsh, Liam H.; Coakley, Mairéad; Walsh, Aaron M.; O’Toole, Paul W.; Cotter, Paul; European Union; Science Foundation Ireland; Department of Agriculture, Food and the Marine; Enterprise Ireland; 818368; et al. (Informa UK Limited, 2022-10-26)
    High-throughput DNA sequencing-based approaches continue to revolutionise our understanding of microbial ecosystems, including those associated with fermented foods. Metagenomic and metatranscriptomic approaches are state-of-the-art biological profiling methods and are employed to investigate a wide variety of characteristics of microbial communities, such as taxonomic membership, gene content and the range and level at which these genes are expressed. Individual groups and consortia of researchers are utilising these approaches to produce increasingly large and complex datasets, representing vast populations of microorganisms. There is a corresponding requirement for the development and application of appropriate bioinformatic tools and pipelines to interpret this data. This review critically analyses the tools and pipelines that have been used or that could be applied to the analysis of metagenomic and metatranscriptomic data from fermented foods. In addition, we critically analyse a number of studies of fermented foods in which these tools have previously been applied, to highlight the insights that these approaches can provide.

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