• Carbohydrate catabolic flexibility in the mammalian intestinal commensal Lactobacillus ruminis revealed by fermentation studies aligned to genome annotations

      O'Donnell, Michelle M.; Forde, Brian M; Neville, B. Anne; Ross, R Paul; O'Toole, Paul W. (Biomed Central, 30/08/2011)
      Background: Lactobacillus ruminis is a poorly characterized member of the Lactobacillus salivarius clade that is part of the intestinal microbiota of pigs, humans and other mammals. Its variable abundance in human and animals may be linked to historical changes over time and geographical differences in dietary intake of complex carbohydrates. Results: In this study, we investigated the ability of nine L. ruminis strains of human and bovine origin to utilize fifty carbohydrates including simple sugars, oligosaccharides, and prebiotic polysaccharides. The growth patterns were compared with metabolic pathways predicted by annotation of a high quality draft genome sequence of ATCC 25644 (human isolate) and the complete genome of ATCC 27782 (bovine isolate). All of the strains tested utilized prebiotics including fructooligosaccharides (FOS), soybean-oligosaccharides (SOS) and 1,3:1,4-β-D-gluco-oligosaccharides to varying degrees. Six strains isolated from humans utilized FOS-enriched inulin, as well as FOS. In contrast, three strains isolated from cows grew poorly in FOS-supplemented medium. In general, carbohydrate utilisation patterns were strain-dependent and also varied depending on the degree of polymerisation or complexity of structure. Six putative operons were identified in the genome of the human isolate ATCC 25644 for the transport and utilisation of the prebiotics FOS, galacto-oligosaccharides (GOS), SOS, and 1,3:1,4-β-D-Gluco-oligosaccharides. One of these comprised a novel FOS utilisation operon with predicted capacity to degrade chicory-derived FOS. However, only three of these operons were identified in the ATCC 27782 genome that might account for the utilisation of only SOS and 1,3:1,4-β-D-Gluco-oligosaccharides. Conclusions: This study has provided definitive genome-based evidence to support the fermentation patterns of nine strains of Lactobacillus ruminis, and has linked it to gene distribution patterns in strains from different sources. Furthermore, the study has identified prebiotic carbohydrates with the potential to promote L. ruminis growth in vivo.
    • A case of bovine raw milk contamination with Listeria monocytogenes

      Hunt, Karen; Drummond, Niall; Murphy, Mary; Butler, Francis; Buckley, James F.; Jordan, Kieran; Teagasc Walsh Fellowship Programme; Department of Agriculture, Food and the Marine, Ireland; European Union (Biomed Central, 06/07/2012)
      During routine sampling of bulk raw milk on a dairy farm, the pathogenic bacteria Listeria monocytogenes was found to be a contaminant, at numbers < 100 cfu/ml. A strain with an indistinguishable pulsed-field gel electrophoresis pattern was isolated from the bulk milk two months later. Environmental swabs taken at the dairy environment were negative for the presence of L. monocytogenes, indicating a possible case of excretion of the L. monocytogenes directly into the milk. Milk samples were collected from the individual cows and analysed, resulting in the identification of L. monocytogenes excretion (at 280 cfu/ml) from one of the 4 mammary quarters of one dairy cow out of 180. When the infected cow was isolated from the herd, no L. monocytogenes was detected from the remaining herd. The pulsed-field gel electrophoresis pattern of the strain from the individual cow was indistinguishable from that originally isolated from the bulk milk. The infected cow did not show any clinical signs of disease, nor did the appearance of the milk have any physical abnormalities. Antibiotic treatment of the infected mammary quarter was found to be ineffective. This study shows that there can be risks associated with direct contamination of raw milk with L. monocytogenes.
    • Catabolic flexibility of mammalian-associated lactobacilli

      O'Donnell, Michelle M.; O'Toole, Paul W.; Ross, R Paul (Biomed Central, 16/05/2013)
      Metabolic flexibility may be generally defined as “the capacity for the organism to adapt fuel oxidation to fuel availability”. The metabolic diversification strategies used by individual bacteria vary greatly from the use of novel or acquired enzymes to the use of plasmid-localised genes and transporters. In this review, we describe the ability of lactobacilli to utilise a variety of carbon sources from their current or new environments in order to grow and survive. The genus Lactobacillus now includes more than 150 species, many with adaptive capabilities, broad metabolic capacity and species/strain variance. They are therefore, an informative example of a cell factory capable of adapting to new niches with differing nutritional landscapes. Indeed, lactobacilli naturally colonise and grow in a wide variety of environmental niches which include the roots and foliage of plants, silage, various fermented foods and beverages, the human vagina and the mammalian gastrointestinal tract (GIT; including the mouth, stomach, small intestine and large intestine). Here we primarily describe the metabolic flexibility of some lactobacilli isolated from the mammalian gastrointestinal tract, and we also describe some of the food-associated species with a proven ability to adapt to the GIT. As examples this review concentrates on the following species - Lb. plantarum, Lb. acidophilus, Lb. ruminis, Lb. salivarius, Lb. reuteri and Lb. sakei, to highlight the diversity and inter-relationships between the catabolic nature of species within the genus.
    • Characterisation and application of fruit by-products as novel ingredients in gluten-free products

      O'Shea, Norah; Department of Agriculture, Food and the Marine, Ireland (2014-01)
      Literature has revealed that “waste” left from the processing of fruit can still contain a substantial quantity of macro and minor nutrients. The aim of this thesis was to ascertain the nutritional and structural properties and potential uses of two fruit by-products [apple pomace (Malus domestica Cv. “Karmijn de Sonnaville”) and orange pomace (Citrus sinensis L. Cv. “Valencia”)] in glutenfree bread and extruded snack formulations. The physicochemical and nutritional properties of the fruit by-products were initially studied. Apple pomace contained a high level of fibre and pectin. The isolated pectin was demonstrated to have a high level of methylation which developed viscous pastes. Orange pomace also had high levels of fibre and pectin, and it was an abundant source of minerals such as potassium and magnesium. Orange pomace had a poor gelling ability. The flour obtained after milling dried orange pomace was used in the formulation of gluten-free bread with the aid of a response surface design. Due to the fibrous properties of orange pomace flour, proofing and water addition were also studied. When added at levels greater than 6%, the loaf volume decreased. The number of cells per slice also decreased with increasing orange pomace addition. Inclusion of orange pomace at levels of up to 4% increased crumb softness. An optimised formulation and proofing time was derived using the optimisation tool; these consisted of 5.5% orange pomace, 94.6% water inclusion and with 49 minutes proofing. These optimised parameters doubled the total dietary fibre content of the bread compared to the original control. The pasting properties, rheology, microstructure and sensory characteristics of the optimised formulation (batter and bread) were investigated. Pasting results showed how orange pomace inclusions reduced the final viscosity of the batter, hence reducing the occurrence of starch gelatinisation. Rheological properties such as the storage modulus (G') and complex modulus (G*) increased in the orange pomace batter compared to the control batter. This demonstrates how the orange pomace as an ingredient improved the robustness of the formulation. Sensory panellists scored the orange pomace bread comparably to the control bread. Milled apple pomace was studied as a potential novel ingredient in an extruded snack. As extrusion requires the trialling of a number of extruder parameters, a response surface design was again used to develop an optimised snack. The parameters studied were apple pomace addition, die head temperature and screw speed. Screw speed had the most significant impact on extrudate characteristics. As screw speed increased the favourable extrudate characteristics such as radical expansion ratio, porosity and specific volume decreased. The inclusion of apple pomace had a negative effect on extrudate characteristics at levels greater than 8% addition. Including apple pomace reduced the hardness and increased the crispiness of the snack. Using the optimisation tool, the optimised and validated formulation and extrusion process contained the following parameters: 7.7% apple pomace, 150oC die head temperature and a screw speed of 69 rpm.
    • Characterization of functional properties of proteins from Ganxet beans (Phaseolus vulgaris L. var. Ganxet) isolated using an ultrasound-assisted methodology

      Lafarga, Tomas; Alvarez, Carlos; Bobo, Gloria; Aguilo-Aguayo, Ingrid; Generalitat de Catalunya; Juan de la Cierva contract award; Postdoctoral Senior Grant Ramon y Cajal; FJCI-2016-29541; RYC-2016-19949 (Elsevier, 2018-08-17)
      This study investigated different methods of extraction of protein from Ganxet beans (Phaseolus vulgaris L. var. Ganxet) and evaluated the functional properties of these valuable proteins. Overall, ultrasound processing (40 kHz, 250 W) resulted in higher yields and increased percentages of material solubilized and proteins recovered. The highest percentage of recovered protein was obtained after extraction using 0.4 M NaOH followed by ultrasound processing for 60 min and was calculated as 78.73 ± 4.88% (p < 0.05). Extraction using 0.4 M NaOH followed by sonication for 60 min resulted in the highest yield and percentage of solubilized material calculated as 37.98 ± 0.02 and 54.58 ± 0.19%, respectively (p < 0.05). The water- and oil-holding capacities of the Ganxet protein concentrate were calculated as 2.33 ± 0.12 and 2.69 ± 0.32 g of water or oil per g of protein concentrate, respectively. The highest emulsifying capacity was observed at pH 8.0 and was calculated as 69.4 ± 0.8%.
    • Characterization of plant-derived lactococci on the basis of their volatile compounds profile when grown in milk

      Alemayehu, Debebe; Hannon, John A.; McAuliffe, Olivia; Ross, R Paul; Irish Dairy Levy Research Trust (Elsevier, 2013-12-03)
      A total of twelve strains of lactococci were isolated from grass and vegetables (baby corn and fresh green peas). Ten of the isolates were classified as Lactococcus lactis subsp. lactis and two as Lactococcus lactis subsp. cremoris based on 16S rDNA sequencing. Most of the plant-derived strains were capable of metabolising a wide range of carbohydrates in that they fermented D-mannitol, amygdalin, potassium gluconate, l-arabinose, d-xylose, sucrose and gentibiose. None of the dairy control strains (i.e. L. lactis subsp. cremoris HP, L. lactis subsp. lactis IL1403 and Lactococcus lactis 303) were able to utilize any of these carbohydrates. The technological potential of the isolates as flavour-producing lactococci was evaluated by analysing their growth in milk and their ability to produce volatile compounds using solid phase micro-extraction of the headspace coupled to gas chromatography–mass spectrometry (SPME GC–MS). Principal component analysis (PCA) of the volatile compounds clearly separated the dairy strains from the plant derived strains, with higher levels of most flavour rich compounds. The flavour compounds produced by the plant isolates among others included; fatty acids such as 2- and 3-methylbutanoic acids, and hexanoic acid, several esters (e.g. butyl acetate and ethyl butanoate) and ketones (e.g. acetoin, diacetyl and 2-heptanone), all of which have been associated with desirable and more mature flavours in cheese. As such the production of a larger number of volatile compounds is a distinguishing feature of plant-derived lactococci and might be a desirable trait for the production of dairy products with enhanced flavour and/or aroma.
    • Characterization of plant-derived lactococci on the basis of their volatile compounds profile when grown in milk

      Alemayehu, Debebe; Hannon, John A.; McAuliffe, Olivia; Ross, R Paul; Irish Dairy Levy Research Trust (Elsevier BV, 2014-02-17)
      A total of twelve strains of lactococci were isolated from grass and vegetables (baby corn and fresh green peas). Ten of the isolates were classified as Lactococcus lactis subsp. lactis and two as Lactococcus lactis subsp. cremoris based on 16S rDNA sequencing. Most of the plant-derived strains were capable of metabolising a wide range of carbohydrates in that they fermented D-mannitol, amygdalin, potassium gluconate, l-arabinose, d-xylose, sucrose and gentibiose. None of the dairy control strains (i.e. L. lactis subsp. cremoris HP, L. lactis subsp. lactis IL1403 and Lactococcus lactis 303) were able to utilize any of these carbohydrates. The technological potential of the isolates as flavour-producing lactococci was evaluated by analysing their growth in milk and their ability to produce volatile compounds using solid phase micro-extraction of the headspace coupled to gas chromatography–mass spectrometry (SPME GC–MS). Principal component analysis (PCA) of the volatile compounds clearly separated the dairy strains from the plant derived strains, with higher levels of most flavour rich compounds. The flavour compounds produced by the plant isolates among others included; fatty acids such as 2- and 3-methylbutanoic acids, and hexanoic acid, several esters (e.g. butyl acetate and ethyl butanoate) and ketones (e.g. acetoin, diacetyl and 2-heptanone), all of which have been associated with desirable and more mature flavours in cheese. As such the production of a larger number of volatile compounds is a distinguishing feature of plant-derived lactococci and might be a desirable trait for the production of dairy products with enhanced flavour and/or aroma.
    • Characterization of Pro-Inflammatory Flagellin Proteins Produced by Lactobacillus ruminis and Related Motile Lactobacilli

      Neville, B. Anne; Forde, Brian M; Claesson, Marcus J.; Darby, Trevor; Coghlan, Avril; Nally, Kenneth; Ross, R Paul; O'Toole, Paul W.; Science Foundation Ireland; Irish Research Council for Science, Engineering and Technology; et al. (PLOS, 10/07/2012)
      Lactobacillus ruminis is one of at least twelve motile but poorly characterized species found in the genus Lactobacillus. Of these, only L. ruminis has been isolated from mammals, and this species may be considered as an autochthonous member of the gastrointestinal microbiota of humans, pigs and cows. Nine L. ruminis strains were investigated here to elucidate the biochemistry and genetics of Lactobacillus motility. Six strains isolated from humans were non-motile while three bovine isolates were motile. A complete set of flagellum biogenesis genes was annotated in the sequenced genomes of two strains, ATCC25644 (human isolate) and ATCC27782 (bovine isolate), but only the latter strain produced flagella. Comparison of the L. ruminis and L. mali DSM20444T motility loci showed that their genetic content and gene-order were broadly similar, although the L. mali motility locus was interrupted by an 11.8 Kb region encoding rhamnose utilization genes that is absent from the L. ruminis motility locus. Phylogenetic analysis of 39 motile bacteria indicated that Lactobacillus motility genes were most closely related to those of motile carnobacteria and enterococci. Transcriptome analysis revealed that motility genes were transcribed at a significantly higher level in motile L. ruminis ATCC27782 than in non-motile ATCC25644. Flagellin proteins were isolated from L. ruminis ATCC27782 and from three other Lactobacillus species, while recombinant flagellin of aflagellate L. ruminis ATCC25644 was expressed and purified from E. coli. These native and recombinant Lactobacillus flagellins, and also flagellate L. ruminis cells, triggered interleukin-8 production in cultured human intestinal epithelial cells in a manner suppressed by short interfering RNA directed against Toll-Like Receptor 5. This study provides genetic, transcriptomic, phylogenetic and immunological insights into the trait of flagellum-mediated motility in the lactobacilli.
    • Characterization of protein hydrolysates from blue whiting (Micromesistius poutassou) and their application in beverage fortification

      Egerton, Sian; Culloty, Sarah; Whooley, Jason; Stanton, Catherine; Ross, R Paul; Irish Research Council; Biomarine Ingredients Ireland Ltd.; The APC Microbiome Institute; EPSPG/2015/57; SFI/12/RC/2273 (Elsevier, 2017-10-21)
      Enzymatic hydrolysis of fish proteins has been employed as a principle method for converting under-utilised fish into valuable products for the pharmaceutical and health food industries. In this study, six commercial enzymes were tested for their ability to make fish protein hydrolysate powders from whole blue whiting. The chemical and functional properties of these powders were compared. The powders all had high solubility (>80%) across a wide pH range in water and their solubility improved further within a vitamin-tea beverage matrix (>85%). Varying degrees of anti-oxidant activities were recorded for the powders using three model systems (DPPH, ferrous chelating and reducing power). This study demonstrates that commercial enzymes are useful for the extraction and alteration of fish protein from a low value source to produce highly digestible, low molecular weight peptide powders that could be used as a fortifying health ingredient, especially in beverages.
    • Cholestasis induced by bile duct ligation promotes changes in the intestinal microbiome in mice.

      Cabrera-Rubio, Raul; Patterson, Angela M; Cotter, Paul D.; Beraza, Naiara; Biotechnology and Biological Sciences Research Council; BB/J004529/1; BBS/E/F/00044509; BB/R012490/1; BBS/E/F/000PR10355; BB/CCG1860/1 (Nature, 2019-08-23)
      Increasing evidence point to the relevance of intestinal disfunction and changes in the microbiome composition during chronic liver disease. More specifically, recent studies have highlighted that cholestatic diseases associate with a reduction in the microbiome diversity in patients. Still, the dynamics of the changes in the microbiome composition observed, as well as their implication in contributing to the pathogenesis of this disease remain largely undefined. Hence, experimental mouse models resembling the human pathogenesis are crucial to move forward our understanding on the mechanisms underpinning cholestatic disease and to enable the development of effective therapeutics. Our results show that the bile duct ligation (BDL) experimental model of cholestasis leads to rapid and significant changes in the microbiome diversity, with more than 100 OTUs being significantly different in faecal samples obtained from WT mice at 3 days and 7 days after BDL when compared to control animals. Changes in the microbial composition in mice after BDL included the enrichment of Akkermansia, Prevotella, Bacteroides and unclassified Ruminococcaceae in parallel with a drastic reduction of the presence of Faecalibacterium prausnitzii. In conclusion, our results support that bile duct ligation induces changes in the microbiome that partly resemble the gut microbial changes observed during human cholestatic disease.
    • Choosing Healthy Eating for Infant Health (CHErIsH) study: protocol for a feasibility study

      Matvienko-Sikar, Karen; Toomey, Elaine; Queally, Michelle; Flannery, Caragh; O Neill, Kate; Dinan, Ted G; Doherty, Edel; Harrington, Janas M; Hayes, Catherine; Heary, Caroline; et al. (BMJ, 2019-08-22)
      Introduction: Cildhood obesity is a public health challenge. There is evidence for associations between parents’ feeding behaviours and childhood obesity risk. Primary care provides a unique opportunity for delivery of infant feeding interventions for childhood obesity prevention. Implementation strategies are needed to support infant feeding intervention delivery. The Choosing Healthy Eating for Infant Health (CHErIsH) intervention is a complex infant feeding intervention delivered at infant vaccination visits, alongside a healthcare professional (HCP)-level implementation strategy to support delivery. Methods and analysis: This protocol provides a description of a non-randomised feasibility study of an infant feeding intervention and implementation strategy, with an embedded process evaluation and economic evaluation. Intervention participants will be parents of infants aged ≤6 weeks at recruitment, attending a participating HCP in a primary care practice. The intervention will be delivered at the infant’s 2, 4, 6, 12 and 13 month vaccination visits and involves brief verbal infant feeding messages and additional resources, including a leaflet, magnet, infant bib and sign-posting to an information website. The implementation strategy encompasses a local opinion leader, HCP training delivered prior to intervention delivery, electronic delivery prompts and additional resources, including a training manual, poster and support from the research team. An embedded mixed-methods process evaluation will examine the acceptability and feasibility of the intervention, the implementation strategy and study processes including data collection. Qualitative interviews will explore parent and HCP experiences and perspectives of delivery and receipt of the intervention and implementation strategy. Self-report surveys will examine fidelity of delivery and receipt, and acceptability, suitability and comprehensiveness of the intervention, implementation strategy and study processes. Data from electronic delivery prompts will also be collected to examine implementation of the intervention. A cost–outcome description will be conducted to measure costs of the intervention and the implementation strategy.
    • Chronic intermittent hypoxia disrupts cardiorespiratory homeostasis and gut microbiota composition in adult male guinea-pigs

      Lucking, Eric F.; O'Connor, Karen M.; Strain, Conall R.; Fouhy, Fiona; Bastiaanssen, Thomaz F.S.; Burns, David P.; Golubeva, Anna V.; Stanton, Catherine; Clarke, Gerard; Cryan, John F.; et al. (Elsevier, 2018-11-13)
      Background: Carotid body (peripheral oxygen sensor) sensitisation is pivotal in the development of chronic intermittent hypoxia (CIH)-induced hypertension. We sought to determine if exposure to CIH, modelling human sleep apnoea, adversely affects cardiorespiratory control in guinea-pigs, a species with hypoxia-insensitive carotid bodies. We reasoned that CIH-induced disruption of gut microbiota would evoke cardiorespiratory morbidity. Methods: Adult male guinea-pigs were exposed to CIH (6.5% O2 at nadir, 6 cycles.hour−1) for 8 h.day−1 for 12 consecutive days. Findings: CIH-exposed animals established reduced faecal microbiota species richness, with increased relative abundance of Bacteroidetes and reduced relative abundance of Firmicutes bacteria. Urinary corticosterone and noradrenaline levels were unchanged in CIH-exposed animals, but brainstem noradrenaline concentrations were lower compared with sham. Baseline ventilation was equivalent in CIH-exposed and sham animals; however, respiratory timing variability, sigh frequency and ventilation during hypoxic breathing were all lower in CIH-exposed animals. Baseline arterial blood pressure was unaffected by exposure to CIH, but β-adrenoceptor-dependent tachycardia and blunted bradycardia during phenylephrine-induced pressor responses was evident compared with sham controls. Interpretation: Increased carotid body chemo-afferent signalling appears obligatory for the development of CIH-induced hypertension and elevated chemoreflex control of breathing commonly reported in mammals, with hypoxia-sensitive carotid bodies. However, we reveal that exposure to modest CIH alters gut microbiota richness and composition, brainstem neurochemistry, and autonomic control of heart rate, independent of carotid body sensitisation, suggesting modulation of breathing and autonomic homeostasis via the microbiota-gut-brainstem axis. The findings have relevance to human sleep-disordered breathing.
    • CLA-producing adjunct cultures improve the nutritional value of sheep cheese fat

      Renes, Erica; Gomez-Cortés, Pilar; de la Fuente, Miguel Ángel; Linares, Daniel M.; Tornadijo, María E.; Fresno, José M.; University of León; Juan de la Cierva research contract (Elsevier, 2018-09-10)
      The influence of the autochthonous CLA-producing Lactobacillus plantarum TAUL 1588 and Lactobacillus casei subsp. casei SS 1644 strains and the ripening time on the fatty acid (FA) content and sensory characteristics of sheep cheese were investigated. Three cheese types with different cultures and the control cheese were produced in duplicate and ripened for 8 months. 86 individual FA were determined by gas chromatography. Ripening time (2, 90, 180 and 240 days) did not have a significant effect (P > .05) on the FA content. However, the presence of both Lactobacillus CLA-producing strains led to a decrease of the saturated FA content and to 1.30, 1.19 and 1.27 times higher levels of vaccenic acid, CLA and omega-3, respectively, when compared to the control cheese. This combination allowed obtaining sheep milk cheeses with a healthier FA content, without appreciable changes on sensory characteristics. This work could be a promising approach to increase the bioactive fatty acid content of cheeses.
    • Cold Atmospheric Plasma Stimulates Clathrin-Dependent Endocytosis to Repair Oxidised Membrane and Enhance Uptake of Nanomaterial in Glioblastoma Multiforme Cells

      He, Zhonglei; Liu, Kangze; Scally, Laurence; Manaloto, Eline; Gunes, Sebnem; Ng, Sing Wei; Maher, Marcus; Tiwari, Brijesh; Byrne, Hugh J.; Bourke, Paula; et al. (Springer Science and Business Media LLC, 2020-04-24)
      Cold atmospheric plasma (CAP) enhances uptake and accumulation of nanoparticles and promotes synergistic cytotoxicity against cancer cells. However, the mechanisms are not well understood. In this study, we investigate the enhanced uptake of theranostic nanomaterials by CAP. Numerical modelling of the uptake of gold nanoparticle into U373MG Glioblastoma multiforme (GBM) cells predicts that CAP may introduce a new uptake route. We demonstrate that cell membrane repair pathways play the main role in this stimulated new uptake route, following non-toxic doses of dielectric barrier discharge CAP. CAP treatment induces cellular membrane damage, mainly via lipid peroxidation as a result of reactive oxygen species (ROS) generation. Membranes rich in peroxidised lipids are then trafficked into cells via membrane repairing endocytosis. We confirm that the enhanced uptake of nanomaterials is clathrin-dependent using chemical inhibitors and silencing of gene expression. Therefore, CAP-stimulated membrane repair increases endocytosis and accelerates the uptake of gold nanoparticles into U373MG cells after CAP treatment. We demonstrate the utility of CAP to model membrane oxidative damage in cells and characterise a previously unreported mechanism of membrane repair to trigger nanomaterial uptake. This knowledge will underpin the development of new delivery strategies for theranostic nanoparticles into cancer cells.
    • Collective unconscious: How gut microbes shape human behavior

      Dinan, Timothy G.; Stilling, Roman M.; Stanton, Catherine; Cryan, John F.; Science Foundation Ireland; Health Research Board; European Union; SFI/12/RC/2273; HRA_POR/2011/23; HRA_POR/2012/32; et al. (Elsevier, 2015-03-03)
      The human gut harbors a dynamic and complex microbial ecosystem, consisting of approximately 1 kg of bacteria in the average adult, approximately the weight of the human brain. The evolutionary formation of a complex gut microbiota in mammals has played an important role in enabling brain development and perhaps sophisticated social interaction. Genes within the human gut microbiota, termed the microbiome, significantly outnumber human genes in the body, and are capable of producing a myriad of neuroactive compounds. Gut microbes are part of the unconscious system regulating behavior. Recent investigations indicate that these microbes majorly impact on cognitive function and fundamental behavior patterns, such as social interaction and stress management. In the absence of microbes, underlying neurochemistry is profoundly altered. Studies of gut microbes may play an important role in advancing understanding of disorders of cognitive functioning and social interaction, such as autism.
    • Collective unconscious: How gut microbes shape human behavior

      Dinan, Timothy G.; Stilling, Roman M.; Stanton, Catherine; Cryan, John F.; Science Foundation Ireland; Health Research Board of Ireland; European Union; SFI/12/RC/2273; HRA_POR/2011/23; HRA_POR/2012/32 (Elsevier BV, 2015-04)
      The human gut harbors a dynamic and complex microbial ecosystem, consisting of approximately 1 kg of bacteria in the average adult, approximately the weight of the human brain. The evolutionary formation of a complex gut microbiota in mammals has played an important role in enabling brain development and perhaps sophisticated social interaction. Genes within the human gut microbiota, termed the microbiome, significantly outnumber human genes in the body, and are capable of producing a myriad of neuroactive compounds. Gut microbes are part of the unconscious system regulating behavior. Recent investigations indicate that these microbes majorly impact on cognitive function and fundamental behavior patterns, such as social interaction and stress management. In the absence of microbes, underlying neurochemistry is profoundly altered. Studies of gut microbes may play an important role in advancing understanding of disorders of cognitive functioning and social interaction, such as autism.
    • Collective unconscious: How gut microbes shape human behavior

      Dinan, Timothy G.; Stilling, Roman M.; Stanton, Catherine; Cryan, John F.; Science Foundation Ireland; Health Research Board of Ireland; European Community's Seventh Framework Programme; SFI/12/RC/2273; HRA_POR/2011/23; HRA_POR/2012/32; et al. (Elsevier, 2015-03-03)
      The human gut harbors a dynamic and complex microbial ecosystem, consisting of approximately 1 kg of bacteria in the average adult, approximately the weight of the human brain. The evolutionary formation of a complex gut microbiota in mammals has played an important role in enabling brain development and perhaps sophisticated social interaction. Genes within the human gut microbiota, termed the microbiome, significantly outnumber human genes in the body, and are capable of producing a myriad of neuroactive compounds. Gut microbes are part of the unconscious system regulating behavior. Recent investigations indicate that these microbes majorly impact on cognitive function and fundamental behavior patterns, such as social interaction and stress management. In the absence of microbes, underlying neurochemistry is profoundly altered. Studies of gut microbes may play an important role in advancing understanding of disorders of cognitive functioning and social interaction, such as autism.
    • Commercial systems for ultra-rapid chilling of lamb

      Redmond, Grainne; McGeehin, Brian; Henchion, Maeve; Sheridan, James J.; Troy, Declan J.; Cowan, Cathal; Butler, Francis (Teagasc, 2001-08)
      The overall objective was to devise a rapid chilling system for the Irish lamb processing industry. The objective of the first trial was to assess the effect of ultra-rapid chilling in air at - 4ºC, -10ºC and -20ºC and subsequent ageing on the appearance and tenderness of lamb carcasses. The objective of the next trial was to investigate the effect of carcass splitting, which produces faster chilling rates and reduces skeletal constraint of muscles, on the tenderness of rapidly and conventionally chilled lamb. The next task was to compare the effects of immersion chilling and conventional air chilling on meat tenderness and evaporative weight loss in lamb carcasses. The next task was to assess the level of interest in industry. This required costings of the process and a survey of several lamb processors focusing on their perceptions of rapid chilling in general, its advantages and disadvantages, and the implications of adopting the new system. The final objective was to introduce the ultra-rapid chilling process to industry via a factory trial. Lambs were ultra-rapidly chilled and then exported to France for assessment.
    • Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine

      Claesson, Marcus J.; O'Sullivan, Orla; Wang, Qiong; Nikkila, Janne; Marchesi, Julian R.; Smidt, Hauka; de Vos, Willem M.; Ross, R Paul; O'Toole, Paul W.; Department of Agriculture, Food and the Marine, Ireland; et al. (PLOS, 20/08/2009)
      Background: Variations in the composition of the human intestinal microbiota are linked to diverse health conditions. Highthroughput molecular technologies have recently elucidated microbial community structure at much higher resolution than was previously possible. Here we compare two such methods, pyrosequencing and a phylogenetic array, and evaluate classifications based on two variable 16S rRNA gene regions. Methods and Findings: Over 1.75 million amplicon sequences were generated from the V4 and V6 regions of 16S rRNA genes in bacterial DNA extracted from four fecal samples of elderly individuals. The phylotype richness, for individual samples, was 1,400–1,800 for V4 reads and 12,500 for V6 reads, and 5,200 unique phylotypes when combining V4 reads from all samples. The RDP-classifier was more efficient for the V4 than for the far less conserved and shorter V6 region, but differences in community structure also affected efficiency. Even when analyzing only 20% of the reads, the majority of the microbial diversity was captured in two samples tested. DNA from the four samples was hybridized against the Human Intestinal Tract (HIT) Chip, a phylogenetic microarray for community profiling. Comparison of clustering of genus counts from pyrosequencing and HITChip data revealed highly similar profiles. Furthermore, correlations of sequence abundance and hybridization signal intensities were very high for lower-order ranks, but lower at family-level, which was probably due to ambiguous taxonomic groupings. Conclusions: The RDP-classifier consistently assigned most V4 sequences from human intestinal samples down to genuslevel with good accuracy and speed. This is the deepest sequencing of single gastrointestinal samples reported to date, but microbial richness levels have still not leveled out. A majority of these diversities can also be captured with five times lower sampling-depth. HITChip hybridizations and resulting community profiles correlate well with pyrosequencing-based compositions, especially for lower-order ranks, indicating high robustness of both approaches. However, incompatible grouping schemes make exact comparison difficult.
    • Comparative analysis of Salmonella susceptibility and tolerance to the biocide chlorhexidine identifies a complex cellular defense network

      Condell, Orla; Power, Karen A.; Handler, Kristian; Finn, Sarah; Sheridan, Aine; Sergeant, Kjell; Renaut, Jenny; Burgess, Catherine; Hinton, Jay C.D.; Nally, Jarlath E.; et al. (Frontiers Media SA, 2014-08-01)
      Chlorhexidine is one of the most widely used biocides in health and agricultural settings as well as in the modern food industry. It is a cationic biocide of the biguanide class. Details of its mechanism of action are largely unknown. The frequent use of chlorhexidine has been questioned recently, amidst concerns that an overuse of this compound may select for bacteria displaying an altered susceptibility to antimicrobials, including clinically important anti-bacterial agents. We generated a Salmonella enterica serovar Typhimurium isolate (ST24CHX) that exhibited a high-level tolerant phenotype to chlorhexidine, following several rounds of in vitro selection, using sub-lethal concentrations of the biocide. This mutant showed altered suceptibility to a panel of clinically important antimicrobial compounds. Here we describe a genomic, transcriptomic, proteomic, and phenotypic analysis of the chlorhexidine tolerant S. Typhimurium compared with its isogenic sensitive progenitor. Results from this study describe a chlorhexidine defense network that functions in both the reference chlorhexidine sensitive isolate and the tolerant mutant. The defense network involved multiple cell targets including those associated with the synthesis and modification of the cell wall, the SOS response, virulence, and a shift in cellular metabolism toward anoxic pathways, some of which were regulated by CreB and Fur. In addition, results indicated that chlorhexidine tolerance was associated with more extensive modifications of the same cellular processes involved in this proposed network, as well as a divergent defense response involving the up-regulation of additional targets such as the flagellar apparatus and an altered cellular phosphate metabolism. These data show that sub-lethal concentrations of chlorhexidine induce distinct changes in exposed Salmonella, and our findings provide insights into the mechanisms of action and tolerance to this biocidal agent.