Now showing items 41-60 of 2799

    • 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.
    • Genomic prediction of starch content and chipping quality in tetraploid potato using genotyping-by-sequencing

      Sverrisdóttir, Elsa; Byrne, Stephen; Sundmark, Ea Høegh Riis; Johnsen, Heidi Øllegaard; Kirk, Hanne Grethe; Asp, Torben; Janss, Luc; Nielsen, Kåre L.; The Danish Council of Strategic Research; The Danish Council for Strategic Research; et al. (Springer Science and Business Media LLC, 2017-07-13)
      Genomic prediction models for starch content and chipping quality show promising results, suggesting that genomic selection is a feasible breeding strategy in tetraploid potato. Genomic selection uses genome-wide molecular markers to predict performance of individuals and allows selections in the absence of direct phenotyping. It is regarded as a useful tool to accelerate genetic gain in breeding programs, and is becoming increasingly viable for crops as genotyping costs continue to fall. In this study, we have generated genomic prediction models for starch content and chipping quality in tetraploid potato to facilitate varietal development. Chipping quality was evaluated as the colour of a potato chip after frying following cold induced sweetening. We used genotyping-by-sequencing to genotype 762 offspring, derived from a population generated from biparental crosses of 18 tetraploid parents. Additionally, 74 breeding clones were genotyped, representing a test panel for model validation. We generated genomic prediction models from 171,859 single-nucleotide polymorphisms to calculate genomic estimated breeding values. Cross-validated prediction correlations of 0.56 and 0.73 were obtained within the training population for starch content and chipping quality, respectively, while correlations were lower when predicting performance in the test panel, at 0.30-0.31 and 0.42-0.43, respectively. Predictions in the test panel were slightly improved when including representatives from the test panel in the training population but worsened when preceded by marker selection. Our results suggest that genomic prediction is feasible, however, the extremely high allelic diversity of tetraploid potato necessitates large training populations to efficiently capture the genetic diversity of elite potato germplasm and enable accurate prediction across the entire spectrum of elite potatoes. Nonetheless, our results demonstrate that GS is a promising breeding strategy for tetraploid potato.
    • 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.
    • Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome

      Rubino, Francesco; Carberry, Ciara; Waters, Sinéad M.; Kenny, David; McCabe, Matthew S; Creevey, Christopher J; European Community's Seventh Framework Programme; Teagasc and the Walsh Fellowships scheme; Science Foundation Ireland (SFI) Stokes lecturer scheme; Biotechnology and Biological Sciences Research Council (BBSRC); et al. (Springer Science and Business Media LLC, 2017-01-13)
      Many microbes in complex competitive environments share genes for acquiring and utilising nutrients, questioning whether niche specialisation exists and if so, how it is maintained. We investigated the genomic signatures of niche specialisation in the rumen microbiome, a highly competitive, anaerobic environment, with limited nutrient availability determined by the biomass consumed by the host. We generated individual metagenomic libraries from 14 cows fed an ad libitum diet of grass silage and calculated functional isoform diversity for each microbial gene identified. The animal replicates were used to calculate confidence intervals to test for differences in diversity of functional isoforms between microbes that may drive niche specialisation. We identified 153 genes with significant differences in functional isoform diversity between the two most abundant bacterial genera in the rumen (Prevotella and Clostridium). We found Prevotella possesses a more diverse range of isoforms capable of degrading hemicellulose, whereas Clostridium for cellulose. Furthermore, significant differences were observed in key metabolic processes indicating that isoform diversity plays an important role in maintaining their niche specialisation. The methods presented represent a novel approach for untangling complex interactions between microorganisms in natural environments and have resulted in an expanded catalogue of gene targets central to rumen cellulosic biomass degradation.
    • 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.
    • Effect of divergence in residual methane emissions on feed intake and efficiency, growth and carcass performance, and indices of rumen fermentation and methane emissions in finishing beef cattle

      Smith, Paul E; Waters, Sinead M; Kenny, David A; Kirwan, Stuart F; Conroy, Stephen; Kelly, Alan K; FACCE ERA-GAS; European Union; Teagasc Walsh Scholarship Programme; 16/RD/ERAGAS/1RUMENPREDICT-ROI2017; et al. (Oxford University Press, 2021-10-01)
      Residual expressions of enteric emissions favor a more equitable identification of an animal’s methanogenic potential compared with traditional measures of enteric emissions. The objective of this study was to investigate the effect of divergently ranking beef cattle for residual methane emissions (RME) on animal productivity, enteric emissions, and rumen fermentation. Dry matter intake (DMI), growth, feed efficiency, carcass output, and enteric emissions (GreenFeed emissions monitoring system) were recorded on 294 crossbred beef cattle (steers = 135 and heifers = 159; mean age 441 d (SD = 49); initial body weight (BW) of 476 kg (SD = 67)) at the Irish national beef cattle performance test center. Animals were offered a total mixed ration (77% concentrate and 23% forage; 12.6 MJ ME/kg of DM and 12% CP) ad libitum with emissions estimated for 21 d over a mean feed intake measurement period of 91 d. Animals had a mean daily methane emissions (DME) of 229.18 g/d (SD = 45.96), methane yield (MY) of 22.07 g/kg of DMI (SD = 4.06), methane intensity (MI) 0.70 g/kg of carcass weight (SD = 0.15), and RME 0.00 g/d (SD = 0.34). RME was computed as the residuals from a multiple regression model regressing DME on DMI and BW (R2 = 0.45). Animals were ranked into three groups namely high RME (>0.5 SD above the mean), medium RME (±0.5 SD above/below the mean), and low RME (>0.5 SD below the mean). Low RME animals produced 17.6% and 30.4% less (P < 0.05) DME compared with medium and high RME animals, respectively. A ~30% reduction in MY and MI was detected in low versus high RME animals. Positive correlations were apparent among all methane traits with RME most highly associated with (r = 0.86) DME. MY and MI were correlated (P < 0.05) with DMI, growth, feed efficiency, and carcass output. High RME had lower (P < 0.05) ruminal propionate compared with low RME animals and increased (P < 0.05) butyrate compared with medium and low RME animals. Propionate was negatively associated (P < 0.05) with all methane traits. Greater acetate:propionate ratio was associated with higher RME (r = 0.18; P < 0.05). Under the ad libitum feeding regime deployed here, RME was the best predictor of DME and only methane trait independent of animal productivity. Ranking animals on RME presents the opportunity to exploit interanimal variation in enteric emissions as well as providing a more equitable index of the methanogenic potential of an animal on which to investigate the underlying biological regulatory mechanisms.
    • Multiclonal human origin and global expansion of an endemic bacterial pathogen of livestock

      Yebra, Gonzalo; Harling-Lee, Joshua D.; Lycett, Samantha; Aarestrup, Frank M.; Larsen, Gunhild; Cavaco, Lina M.; Seo, Keun Seok; Abraham, Sam; Norris, Jacqueline M.; Schmidt, Tracy; et al. (Proceedings of the National Academy of Sciences, 2022-12-05)
      Most new pathogens of humans and animals arise via switching events from distinct host species. However, our understanding of the evolutionary and ecological drivers of successful host adaptation, expansion, and dissemination are limited. Staphylococcus aureus is a major bacterial pathogen of humans and a leading cause of mastitis in dairy cows worldwide. Here we trace the evolutionary history of bovine S. aureus using a global dataset of 10,254 S. aureus genomes including 1,896 bovine isolates from 32 countries in 6 continents. We identified 7 major contemporary endemic clones of S. aureus causing bovine mastitis around the world and traced them back to 4 independent host-jump events from humans that occurred up to 2,500 y ago. Individual clones emerged and underwent clonal expansion from the mid-19th to late 20th century coinciding with the commercialization and industrialization of dairy farming, and older lineages have become globally distributed via established cattle trade links. Importantly, we identified lineage-dependent differences in the frequency of host transmission events between humans and cows in both directions revealing high risk clones threatening veterinary and human health. Finally, pangenome network analysis revealed that some bovine S. aureus lineages contained distinct sets of bovine-associated genes, consistent with multiple trajectories to host adaptation via gene acquisition. Taken together, we have dissected the evolutionary history of a major endemic pathogen of livestock providing a comprehensive temporal, geographic, and gene-level perspective of its remarkable success.
    • 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.
    • Transcriptome characterization and differentially expressed genes under flooding and drought stress in the biomass grasses Phalaris arundinacea and Dactylis glomerata

      Klaas, Manfred; Haiminen, Niina; Grant, Jim; Cormican, Paul; Finnan, John; Arojju, Sai Krishna; Utro, Filippo; Vellani, Tia; Parida, Laxmi; Barth, Susanne; et al. (Oxford University Press (OUP), 2019-06-26)
      Background and Aims Perennial grasses are a global resource as forage, and for alternative uses in bioenergy and as raw materials for the processing industry. Marginal lands can be valuable for perennial biomass grass production, if perennial biomass grasses can cope with adverse abiotic environmental stresses such as drought and waterlogging. Methods In this study, two perennial grass species, reed canary grass (Phalaris arundinacea) and cocksfoot (Dactylis glomerata) were subjected to drought and waterlogging stress to study their responses for insights to improving environmental stress tolerance. Physiological responses were recorded, reference transcriptomes established and differential gene expression investigated between control and stress conditions. We applied a robust non-parametric method, RoDEO, based on rank ordering of transcripts to investigate differential gene expression. Furthermore, we extended and validated vRoDEO for comparing samples with varying sequencing depths. Key Results This allowed us to identify expressed genes under drought and waterlogging whilst using only a limited number of RNA sequencing experiments. Validating the methodology, several differentially expressed candidate genes involved in the stage 3 step-wise scheme in detoxification and degradation of xenobiotics were recovered, while several novel stress-related genes classified as of unknown function were discovered. Conclusions Reed canary grass is a species coping particularly well with flooding conditions, but this study adds novel information on how its transcriptome reacts under drought stress. We built extensive transcriptomes for the two investigated C3 species cocksfoot and reed canary grass under both extremes of water stress to provide a clear comparison amongst the two species to broaden our horizon for comparative studies, but further confirmation of the data would be ideal to obtain a more detailed picture.
    • Deficiency of essential dietary n-3 PUFA disrupts the caecal microbiome and metabolome in mice

      Robertson, Ruairi C.; Seira Oriach, Clara; Murphy, Kiera; Moloney, Gerard M.; Cryan, John F.; Dinan, Timothy G.; Ross, R. P.; Stanton, Catherine; Science Foundation Ireland; Health Research Board of Ireland; et al. (Cambridge University Press (CUP), 2017-11-27)
      n-3 PUFA are lipids that play crucial roles in immune-regulation, cardio-protection and neurodevelopment. However, little is known about the role that these essential dietary fats play in modulating caecal microbiota composition and the subsequent production of functional metabolites. To investigate this, female C57BL/6 mice were assigned to one of three diets (control (CON), n-3 supplemented (n3+) or n-3 deficient (n3−)) during gestation, following which their male offspring were continued on the same diets for 12 weeks. Caecal content of mothers and offspring were collected for 16S sequencing and metabolic phenotyping. n3− male offspring displayed significantly less % fat mass than n3+ and CON. n-3 Status also induced a number of changes to gut microbiota composition such that n3− offspring had greater abundance of Tenericutes, Anaeroplasma and Coriobacteriaceae. Metabolomics analysis revealed an increase in caecal metabolites involved in energy metabolism in n3+ including α-ketoglutaric acid, malic acid and fumaric acid. n3− animals displayed significantly reduced acetate, butyrate and total caecal SCFA production. These results demonstrate that dietary n-3 PUFA regulate gut microbiota homoeostasis whereby n-3 deficiency may induce a state of disturbance. Further studies are warranted to examine whether these microbial and metabolic disturbances are causally related to changes in metabolic health outcomes.
    • An investigation of the effect of rapid slurry chilling on blown pack spoilage of vacuum-packaged beef primals

      Reid, R.; Fanning, S.; Whyte, P.; Kerry, J.; Bolton, D.; Department of Agriculture, Fisheries and Food, Ireland (Wiley, 2017-01-12)
      The aim of this study was to investigate if rapid slurry chilling would retard or prevent blown pack spoilage (BPS) of vacuum-packaged beef primals. Beef primals were inoculated with Clostridium estertheticum subspp. estertheticum (DSMZ 8809), C. estertheticum subspp. laramenise (DSMZ 14864) and C. gasigenes (DSMZ 12272), and vacuum-packaged with and without heat shrinkage (90°C for 3 s). These packs were then subjected to immediate chilling in an ice slurry or using conventional blast chilling systems and stored at 2°C for up to 100 days. The onset and progress of BPS was monitored using the following scale; 0‑no gas bubbles in drip; 1‑gas bubbles in drip; 2‑loss of vacuum; 3‑‘blown’; 4‑presence of sufficient gas inside the packs to produce pack distension and 5‑tightly stretched, ‘overblown’ packs/packs leaking. Rapid slurry chilling (as compared to conventional chilling) did not significantly affect (P > 0.05) the time to the onset or progress of BPS. It was therefore concluded that rapid chilling of vacuum-packaged beef primals, using an ice slurry system, may not be used as a control intervention to prevent or retard blown pack spoilage.
    • Real-time PCR methods for the detection of blown pack spoilage causing Clostridium species; C. estertheticum, C. gasigenes and C. ruminantium

      Reid, Rachael; Burgess, Catherine M.; McCabe, Evonne; Fanning, Séamus; Whyte, Paul; Kerry, Joe; Bolton, Declan; Department of Agriculture, Food and the Marine (Ireland); Teagasc core funding (Elsevier, 2017-11)
      A set of real-time PCR methods for the detection of C. estertheticum, C. gasigenes and C. ruminantium, the causative agents of blown pack spoilage (BPS) in vacuum packaged beef, was developed. Robust validation of the sensitivity and specificity was carried out in the three matrices (beef meat drip, wet environmental swabs and dry environmental swabs) as encountered in our testing laboratory and against Clostridium strains (n = 76) and non-Clostridium strains (n = 36). It was possible to detect 4–5 spores per ml for C. estertheticum, 2 spores per ml for C. gasigenes and 8 spores per ml for C. ruminantium, without the need for enrichment of the samples. This high sensitivity is particularly important for the beef sector, not just for testing spoiled product but also in the early detection of contaminated beef and in validation of sporicidal cleaning procedures for critical pieces of equipment such as the vacuum packaging machine, which have the potential to contaminate large volumes of product.
    • Bifidobacterium breve with α-linolenic acid alters the composition, distribution and transcription factor activity associated with metabolism and absorption of fat

      Patterson, Elaine; Wall, Rebecca; Lisai, Sara; Ross, R. Paul; Dinan, Timothy G.; Cryan, John F.; Fitzgerald, Gerald F.; Banni, Sebastiano; Quigley, Eamonn M.; Shanahan, Fergus; et al. (Springer Science and Business Media LLC, 2017-03-07)
      This study focused on the mechanisms that fatty acid conjugating strains - Bifidobacterium breve NCIMB 702258 and Bifidobacterium breve DPC 6330 - influence lipid metabolism when ingested with α-linolenic acid (ALA) enriched diet. Four groups of BALB/c mice received ALA enriched diet (3% (w/w)) either alone or in combination with B. breve NCIMB 702258 or B. breve DPC 6330 (109 CFU/day) or unsupplemented control diet for six weeks. The overall n-3 PUFA score was increased in all groups receiving the ALA enriched diet. Hepatic peroxisomal beta oxidation increased following supplementation of the ALA enriched diet with B. breve (P < 0.05) and so the ability of the strains to produce c9t11 conjugated linoleic acid (CLA) was identified in adipose tissue. Furthermore, a strain specific effect of B. breve NCIMB 702258 was found on the endocannabinoid system (ECS). Liver triglycerides (TAG) were reduced following ALA supplementation, compared with unsupplemented controls (P < 0.01) while intervention with B. breve further reduced liver TAG (P < 0.01), compared with the ALA enriched control. These data indicate that the interactions of the gut microbiota with fatty acid metabolism directly affect host health by modulating n-3 PUFA score and the ECS.
    • Draft Genome Sequences of 25 Listeria monocytogenes Isolates Associated with Human Clinical Listeriosis in Ireland

      O’Callaghan, Amy; Hilliard, Amber; Morgan, Ciara A.; Culligan, Eamonn P.; Leong, Dara; DeLappe, Niall; Hill, Colin; Jordan, Kieran; Cormican, Martin; Gahan, Cormac G. M.; et al. (American Society for Microbiology, 2017-05-11)
      Listeria monocytogenes is a Gram-positive opportunistic pathogen that is the causative agent of listeriosis. Here, we report the draft genome sequences of 25 L. monocytogenes strains isolated from patients with clinical listeriosis in the Republic of Ireland between 2013 and 2015.
    • Impact of intrapartum antimicrobial prophylaxis upon the intestinal microbiota and the prevalence of antibiotic resistance genes in vaginally delivered full-term neonates

      Nogacka, Alicja; Salazar, Nuria; Suárez, Marta; Milani, Christian; Arboleya, Silvia; Solís, Gonzalo; Fernández, Nuria; Alaez, Lidia; Hernández-Barranco, Ana M.; de los Reyes-Gavilán, Clara G.; et al. (Springer Science and Business Media LLC, 2017-08-08)
      Background: Disturbances in the early establishment of the intestinal microbiota may produce important implications for the infant’s health and for the risk of disease later on. Different perinatal conditions may be affecting the development of the gut microbiota. Some of them, such as delivery mode or feeding habits, have been extensively assessed whereas others remain to be studied, being critical to identify their impact on the microbiota and, if any, to minimize it. Antibiotics are among the drugs most frequently used in early life, the use of intrapartum antimicrobial prophylaxis (IAP), present in over 30% of deliveries, being the most frequent source of exposure. However, our knowledge on the effects of IAP on the microbiota establishment is still limited. The aim of the present work was to evaluate the impact of IAP investigating a cohort of 40 full-term vaginally delivered infants born after an uncomplicated pregnancy, 18 of which were born from mothers receiving IAP. Results: Fecal samples were collected at 2, 10, 30, and 90 days of age. We analyzed the composition of the fecal microbiota during the first 3 months of life by 16S rRNA gene sequencing and quantified fecal short chain fatty acids by gas chromatography. The presence of genes for resistance to antibiotics was determined by PCR in the samples from 1-month-old infants. Our results showed an altered pattern of intestinal microbiota establishment in IAP infants during the first weeks of life, with lower relative proportions of Actinobacteria and Bacteroidetes and increased of Preoteobacteria and Firmicutes. A delay in the increase on the levels of acetate was observed in IAP infants. The analyses of specific antibiotic resistance genes showed a higher occurrence of some β-lactamase coding genes in infants whose mothers received IAP. Conclusions: Our results indicate an effect of IAP on the establishing early microbiota during the first months of life, which represent a key moment for the development of the microbiota-induced host homeostasis. Understanding the impact of IAP in the gut microbiota development is essential for developing treatments to minimize it, favoring a proper gut microbiota development in IAP-exposed neonates.
    • Pathogens, patterns of pneumonia, and epidemiologic risk factors associated with respiratory disease in recently weaned cattle in Ireland

      Murray, Gerard M.; More, Simon J.; Sammin, Dónal; Casey, Mìcheàl J.; McElroy, Máire C.; O’Neill, Rónan G.; Byrne, William J.; Earley, Bernadette; Clegg, Tracy A.; Ball, Hywel; et al. (SAGE, 2017-01-11)
      We examined the pathogens, morphologic patterns, and risk factors associated with bovine respiratory disease (BRD) in 136 recently weaned cattle (“weanlings”), 6–12 mo of age, that were submitted for postmortem examination to regional veterinary laboratories in Ireland. A standardized sampling protocol included routine microbiologic investigations as well as polymerase chain reaction and immunohistochemistry. Lungs with histologic lesions were categorized into 1 of 5 morphologic patterns of pneumonia. Fibrinosuppurative bronchopneumonia (49%) and interstitial pneumonia (48%) were the morphologic patterns recorded most frequently. The various morphologic patterns of pulmonary lesions suggest the involvement of variable combinations of initiating and compounding infectious agents that hindered any simple classification of the etiopathogenesis of the pneumonias. Dual infections were detected in 58% of lungs, with Mannheimia haemolytica and Histophilus somni most frequently recorded in concert. M. haemolytica (43%) was the most frequently detected respiratory pathogen; H. somni was also shown to be frequently implicated in pneumonia in this age group of cattle. Bovine parainfluenza virus 3 (BPIV-3) and Bovine respiratory syncytial virus (16% each) were the viral agents detected most frequently. Potential respiratory pathogens (particularly Pasteurella multocida, BPIV-3, and H. somni) were frequently detected (64%) in lungs that had neither gross nor histologic pulmonary lesions, raising questions regarding their role in the pathogenesis of BRD. The breadth of respiratory pathogens detected in bovine lungs by various detection methods highlights the diagnostic value of parallel analyses in respiratory disease postmortem investigation.