Now showing items 1-20 of 1529

    • Blood parameters as biomarkers in a Salmonella spp. disease model of weaning piglets

      Barba-Vidal, Emili; Buttow Roll, Victor Fernando; Garcia Manzanilla, Edgar; Torrente, Carlos; Moreno Muñoz, Jose Antonio; PeÂrez, Jose Francisco; Martin-Orue, Susana Maria; Spanish Ministry of Education and Science; Laboratorios Ordesa S.L.; CNPQ Brazil; AGL 2012-31924 (PLOS, 2017-10-26)
      Background The weaning pig is used as an experimental model to assess the impact of diet on intestinal health. Blood parameters (BP) are considered a useful tool in humans, but there is very scarce information of such indicators in the weaning pig. The objective of the present study is to evaluate the use of different BP as indicators in an experimental model of salmonellosis. Methodology Seventy-two 28-day-old piglets were divided into four groups in a 2x2 factorial arrangement, with animals receiving or not a probiotic combination based on B. infantis IM1® and B. lactis BPL6 (109 colony forming units (cfu)/d) and orally challenged or not a week later with Salmonella Typhimurium (5x108 cfu). Blood samples of one animal per pen (N = 24) were taken four days post-inoculation for the evaluation of different BP using an I-stat® System and of plasmatic concentrations of zinc, iron and copper. Principal findings Results reported marginal deficiencies of zinc in piglets at weaning. Moreover, plasmatic zinc, copper and iron presented good correlations with weight gain (r 0.57, r -0.67, r 0.54 respectively; P < 0.01). Blood electrolytes (Na+, Cl- and K+) decreased (P < 0.01) only when the performance of the animals was seriously compromised and clinical symptoms were more apparent. Acid-base balance parameters such as HCO3-, TCO2 and BEecf significantly correlated with weight gain, but only in the challenged animals (r -0.54, r -0.55, and r -0.51, respectively; P < 0.05), suggesting metabolic acidosis depending on Salmonella infection. Glucose was affected by the challenge (P = 0.040), while Htc and Hgb increased with the challenge and decreased with the probiotic (P < 0.05). Furthermore, correlations of Glu, Htc and Hgb with weight gain were observed (P < 0.05). Overall, BP could be regarded as simple, useful indexes to assess performance and health of weaning piglets.
    • Crop Establishment Practices Are a Driver of the Plant Microbiota in Winter Oilseed Rape (Brassica napus)

      Rathore, Ridhdhi; Dowling, David N.; Forristal, Patrick D.; Spink, John; Cotter, Paul D.; Bulgarelli, Davide; Germaine, Kieran J.; Teagasc Walsh Fellowship Programme; Royal Society of Edinburgh/Scottish Government Personal Research Fellowship (Frontiers, 2017-08-09)
      Gaining a greater understanding of the plant microbiota and its interactions with its host plant heralds a new era of scientific discovery in agriculture. Different agricultural management practices influence soil microbial populations by changing a soil’s physical, chemical and biological properties. However, the impact of these practices on the microbiota associated with economically important crops such as oilseed rape, are still understudied. In this work we investigated the impact of two contrasting crop establishment practices, conventional (plow based) and conservation (strip–tillage) systems, on the microbiota inhabiting different plant microhabitats, namely rhizosphere, root and shoot, of winter oilseed rape under Irish agronomic conditions. Illumina 16S rRNA gene sequence profiling showed that the plant associated microhabitats (root and shoot), are dominated by members of the bacterial phyla Proteobacteria, Actinobacteria and Bacteroidetes. The root and shoot associated bacterial communities displayed markedly distinct profiles as a result of tillage practices. We observed a very limited ‘rhizosphere effect’ in the root zone of WOSR, i.e., there was little or no increase in bacterial community richness and abundance in the WOSR rhizosphere compared to the bulk soil. The two tillage systems investigated did not appear to lead to any major long term differences on the bulk soil or rhizosphere bacterial communities. Our data suggests that the WOSR root and shoot microbiota can be impacted by management practices and is an important mechanism that could allow us to understand how plants respond to different management practices and environments.
    • Genetic variability in the humoral immune response to bovine herpesvirus-1 infection in dairy cattle and genetic correlations with performance traits

      Ring, S. C.; Graham, D. A.; Sayers, Riona; Byrne, N.; Kelleher, M. M.; Doherty, M. L.; Berry, Donagh P.; Department of Agriculture, Food and the Marine (Elsevier for American Dairy Science Association, 2018-04-26)
      Bovine herpesvirus-1 (BoHV-1) is a viral pathogen of global significance that is known to instigate several diseases in cattle, the most notable of which include infectious bovine rhinotracheitis and bovine respiratory disease. The genetic variability in the humoral immune response to BoHV-1 has, to our knowledge, not ever been quantified. Therefore, the objectives of the present study were to estimate the genetic parameters for the humoral immune response to BoHV-1 in Irish female dairy cattle, as well as to investigate the genetic relationship between the humoral immune response to BoHV-1 with milk production performance, fertility performance, and animal mortality. Information on antibody response to BoHV-1 was available to the present study from 2 BoHV-1 sero-prevalence research studies conducted between the years 2010 to 2015, inclusive; after edits, BoHV-1 antibody test results were available on a total of 7,501 female cattle from 58 dairy herds. National records of milk production (i.e., 305-d milk yield, fat yield, protein yield, and somatic cell score; n = 1,211,905 milk-recorded cows), fertility performance (i.e., calving performance, pregnancy diagnosis, and insemination data; n = 2,365,657 cows) together with animal mortality data (i.e., birth, farm movement, death, slaughter, and export events; n = 12,853,257 animals) were also available. Animal linear mixed models were used to quantify variance components for BoHV-1 as well as to estimate genetic correlations among traits. The estimated genetic parameters for the humoral immune response to BoHV-1 in the present study (i.e., heritability range: 0.09 to 0.16) were similar to estimates previously reported for clinical signs of bovine respiratory disease in dairy and beef cattle (i.e., heritability range: 0.05 to 0.11). Results from the present study suggest that breeding for resistance to BoHV-1 infection could reduce the incidence of respiratory disease in cattle while having little or no effect on genetic selection for milk yield or milk constituents (i.e., genetic correlations ranged from −0.13 to 0.17). Moreover, even though standard errors were large, results also suggest that breeding for resistance to BoHV-1 infection may indirectly improve fertility performance while also reducing the incidence of mortality in older animals (i.e., animals >182 d of age). Results can be used to inform breeding programs of potential genetic gains achievable for resistance to BoHV-1 infection in cattle.
    • A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies

      Cao, Yu; Fanning, Séamus; Proos, Sinéad; Jordan, Kieran; Srikumar, Shabarinath; Department of Agriculture, Food and Marine; Enterprise Ireland; 13/F/423; IP 2015 0380 (Frontiers, 2017-09-21)
      The development of next generation sequencing (NGS) techniques has enabled researchers to study and understand the world of microorganisms from broader and deeper perspectives. The contemporary advances in DNA sequencing technologies have not only enabled finer characterization of bacterial genomes but also provided deeper taxonomic identification of complex microbiomes which in its genomic essence is the combined genetic material of the microorganisms inhabiting an environment, whether the environment be a particular body econiche (e.g., human intestinal contents) or a food manufacturing facility econiche (e.g., floor drain). To date, 16S rDNA sequencing, metagenomics and metatranscriptomics are the three basic sequencing strategies used in the taxonomic identification and characterization of food-related microbiomes. These sequencing strategies have used different NGS platforms for DNA and RNA sequence identification. Traditionally, 16S rDNA sequencing has played a key role in understanding the taxonomic composition of a food-related microbiome. Recently, metagenomic approaches have resulted in improved understanding of a microbiome by providing a species-level/strain-level characterization. Further, metatranscriptomic approaches have contributed to the functional characterization of the complex interactions between different microbial communities within a single microbiome. Many studies have highlighted the use of NGS techniques in investigating the microbiome of fermented foods. However, the utilization of NGS techniques in studying the microbiome of non-fermented foods are limited. This review provides a brief overview of the advances in DNA sequencing chemistries as the technology progressed from first, next and third generations and highlights how NGS provided a deeper understanding of food-related microbiomes with special focus on non-fermented foods.
    • Editorial: Microbial Food Safety along the Dairy Chain

      Fox, Edward M.; Fanning, Seamus; Corsetti, Aldo; Jordan, Kieran (Frontiers, 2017-08-23)
      Milk is susceptible to contamination with pathogenic and spoilage organisms and, therefore, Microbial food safety along the dairy chain is an important topic, from public health and industry perspectives. The dairy chain is an integral part of global food supply, with dairy food products a staple component of recommended healthy diets. The dairy food chain from production through to the consumer is complex, with various opportunities for microbial contamination of ingredients or food products, and as such interventions are key to preventing or controlling such contamination. Dairy foods often include a microbial control step in their production such as pasteurization, but in some cases may not, as with raw milk products. Microbial contamination may lead to a deterioration in food quality due to spoilage organisms, or may become a health risk to consumers should the contaminant be a pathogenic microorganism. As such food safety and food production are intrinsically linked.
    • Novel “gel demineralizing” method for protein recovery from fat rendering waste stream based on its gelling properties

      Álvarez, Carlos; Drummond, Liana; Mullen, Anne Maria (Elsevier, 2018-11)
      Fat rendering is a common process in the meat industry, whereby fatty or oily materials are melted away or cooked from the solid portion of the animal tissue. Once the fat, and more solid protein in the form of greaves, has been removed a co-product called glue water or stick water is produced which in generally considered a waste product. This study was established to investigate ways to revalorise this product and reduce the economic and environmental impact of this waste material. Proximate characterisation shows it contains 1.1–1.3% w/w of protein along with similar concentration of ashes (1.3% w/w). While low in protein this is a key pollutant if the product is disposed of, and could also represent an interesting protein source for downstream applications. In order to recover these proteins the salt has to be removed. Therefore, after the techno-functional properties of the raw material and of the recovered proteins were evaluated, especially those related to gelling formation, a new demineralizing method based on the excellent gelling properties of these proteins was developed and results compared with those obtained from three different ultrafiltration membranes (10, 3 and 1 kDa MWCO). Protein recovery was greater for the new method (79–90%) (50–77%); however, the amount of salt removed was higher when ultrafiltration was employed (90% compared to 81%).
    • Effect of human chorionic gonadotrophin administration 2 days after insemination on progesterone concentration and pregnancy per artificial insemination in lactating dairy cows

      Sánchez, J. M.; Randi, F.; Passaro, C.; Mathew, D. J.; Butler, S. T.; Lonergan, P.; Department of Agriculture, Food and the Marine; 13S528 (Elsevier for American Dairy Science Association, 2018-03-28)
      The aim of this study was to examine the effect of a single administration of human chorionic gonadotrophin (hCG) during the establishment of the corpus luteum (CL) on progesterone (P4) concentration and pregnancy per artificial insemination (P/AI) in lactating dairy cows. Postpartum spring-calving lactating dairy cows (n = 800; mean ± SD days in milk and parity were 78.5 ± 16.7 and 2.3 ± 0.8, respectively) on 3 farms were enrolled on the study. All cows underwent the same fixed-time AI (FTAI) protocol involving a 7-d progesterone-releasing intravaginal device with gonadotrophin-releasing hormone (GnRH) administration at device insertion, prostaglandin at device removal followed by GnRH 56 h later, and AI 16 h after the second GnRH injection. Cows were blocked on days postpartum, body condition score, and parity and randomly assigned to receive either 3,000 IU of hCG 2 d after FTAI or no further treatment (control). Blood samples were collected on d 7 and 14 postestrus by coccygeal venipuncture on a subset of 204 cows to measure serum P4 concentration, and pregnancy was diagnosed by ultrasonography approximately 30 and 70 d after FTAI. Administration of hCG caused an increase in circulating P4 concentrations compared with the control treatment on d 7 (+22.2%) and d 14 (+25.7%). The P/AI at 30 d after FTAI was affected by treatment, farm, body condition score, and calving to service interval. Overall, administration of hCG decreased P/AI (46.3% vs. 55.1% for the control). Among cows that did not become pregnant following AI, a greater proportion of control cows exhibited a short repeat interval (≤17 d) compared with cows treated with hCG (8.6% vs. 2.8%, respectively). In addition, the percentages of cows pregnant at d 21 (59.6% vs. 52.0%) and d 42 (78.3% vs. 71.9%) were greater in control than in hCG-treated cows. The overall incidence of embryo loss was 10.7% and was not affected by treatment. There was a tendency for an interaction between treatment and CL status at synchronization protocol initiation for both P4 concentration and P/AI. In conclusion, administration of hCG 2 d after FTAI increased circulating P4 concentrations. Unexpectedly, cows treated with hCG had lower fertility; however, this negative effect on fertility was manifested primarily in cows lacking a CL at the onset of the synchronization protocol.
    • Sustainability indicators for improved assessment of the effects of agricultural policy across the EU: Is FADN the answer?

      Kelly, Edel; Latruffe, Laure; Desjeux, Yann; Ryan, Mary; Uthes, Sandra; Diazabakanab, Ambre; Dillon, Emma; Finn, John; European Union; 613800 (Elsevier, 2018-06)
      Policy reform of the CAP and society’s expectations of agriculture have resulted in a growing need for improved information on the effectiveness of policy in achieving high-level objectives for more sustainable practice in agriculture. This is a high priority given its importance for consumers, public policy and private industry. Data collection programmes will need to adapt their scope if their information is to adequately address new information needs about high-level objectives. Assessment of sustainability at the farm level is hindered by the lack of data with which to derive appropriate, meaningful, and relevant indicators. This is particularly problematic for assessment of agricultural sustainability across the European Union (EU). Various databases exist at the EU scale regarding agricultural data sources and we identify one of these, the EU Farm Accountancy Data Network (FADN), as having considerable potential to assess farm-level sustainability at EU level. We critique several examples of published work that has attempted to assess agricultural sustainability using: FADN data alone; FADN data in combination with data from supplementary surveys, and; FADN data in combination with data from other EU databases. We conclude that the FADN would need to broaden its scope of data collection if it is to address the new information needs of policy, and we discuss the challenges in expanding FADN with a view towards wider farm-level assessment of sustainability. These include careful selection of indicators based on various criteria, the representativeness of the FADN, and the need to include new themes to address environmental, social, and animal welfare effects of policy.
    • Perinatal immuno/inflammatory responses in the presence or absence of bovine fetal infection

      Jawor, Paulina; Mee, John F; Stefaniak, Tadeusz; The National Centre for Research and Development; PBS2/A8/20/2013 (Biomed Central, 2018-11-01)
      Background It is known that the bovine fetus can mount an immune and inflammatory reaction to infection, but it is not known whether there is a contemporaneous maternal response. Nor is it known whether the response of calves which die perinatally, with or without infection, differs from that of live perinates. Hence, the objective of this study was to determine if acute phase reactant and immunoglobulin concentrations differed between calves (and their dams) in three groups: live calves (CC; n = 21) and dead calves with (PM INF+; n = 22) or without (PM INF-; n = 89) in utero infection. In calf plasma, serum amyloid A, haptoglobin, immunoglobulins M, G1 and G2 and interleukin-6 were measured. In dam serum, SAA and Hp was measured and in amniotic and abomasal fluid, IL-6 was measured. Results Live calves had higher plasma concentrations of SAA and IL-6 than dead calves with (PM INF+) or without (PM INF-) in utero infection. Calves in the PM INF-, but not PM INF+ group, had higher Hp concentrations than calves in the CC group. Calves in the PM INF+ group had higher IgG1 concentrations than calves in the PM INF- and CC groups. Except for higher IgG1 and IgG2 concentrations, biomarker values did not differ significantly between dead calves with or without in utero infection. Live calves had higher IL-6 concentrations in abomasal fluid compared to PM INF- calves. There were no significant differences in blood biomarker concentrations between dams of the three groups of calves. Amniotic fluid IL-6 concentrations were higher from the dams of control calves than the dams of uninfected calves. Conclusions Differences in biomarkers (higher Hp and IgG1; lower SAA and IL-6) between perinatal mortalities and live perinates probably reflect differences between these two groups in age at sampling (SAA and IL-6) and in utero infection (IgG1). Out of the six analytes measured in calves, only IgG1 and IgG2 were biomarkers of (chronic) in utero infection.
    • Correction to: Residual feed intake phenotype and gender affect the expression of key genes of the lipogenesis pathway in subcutaneous adipose tissue of beef cattle

      McKenna, Clare; Porter, Richard K; Keogh, Kate A; Waters, Sinead M; McGee, Mark; Kenny, David A; Teagasc Walsh Fellowship Programme (Biomed Central, 2018-11-07)
      In the original publication of this article [1], some errors in Table 4 need to be corrected as below:
    • Fertilizer Use Survey 1995

      Murphy, W. E.; Culleton, N.; Roche, M.; Power, D. (Teagasc, 1997)
      The farm management data for 1994 and 1995 were used as the basis for a fertilizer use survey. The samples were drawn up by the Central Statistics Office on the basis of farm size and farming system. The survey was carried out on 1226 farms.
    • RNA-seq of muscle from pigs divergent in feed efficiency and product quality identifies differences in immune response, growth, and macronutrient and connective tissue metabolism

      Horodyska, Justyna; Wimmers, Klaus; Reyer, Henry; Trakooljul, Nares; Mullen, Anne Maria; Lawlor, Peadar G; Hamill, Ruth M; European Union; 311794 (Biomed Central, 2018-11-01)
      Background Feed efficiency (FE) is an indicator of efficiency in converting energy and nutrients from feed into a tissue that is of major environmental and economic significance. The molecular mechanisms contributing to differences in FE are not fully elucidated, therefore the objective of this study was to profile the porcine Longissimus thoracis et lumborum (LTL) muscle transcriptome, examine the product quality from pigs divergent in FE and investigate the functional networks underpinning the potential relationship between product quality and FE. Results RNA-Seq (n = 16) and product quality (n = 40) analysis were carried out in the LTL of pigs differing in FE status. A total of 272 annotated genes were differentially expressed with a P < 0.01. Functional annotation revealed a number of biological events related to immune response, growth, carbohydrate & lipid metabolism and connective tissue indicating that these might be the key mechanisms governing differences in FE. Five most significant bio-functions altered in FE groups were ‘haematological system development & function’, ‘lymphoid tissue structure & development’, ‘tissue morphology’, ‘cellular movement’ and ‘immune cell trafficking’. Top significant canonical pathways represented among the differentially expressed genes included ‘IL-8 signalling’, ‘leukocyte extravasation signalling, ‘sphingosine-1-phosphate signalling’, ‘PKCθ signalling in T lymphocytes’ and ‘fMLP signalling in neutrophils’. A minor impairment in the quality of meat, in relation to texture and water-holding capacity, produced by high-FE pigs was observed. High-FE pigs also had reduced intramuscular fat content and improved nutritional profile in terms of fatty acid composition. Conclusions Ontology analysis revealed enhanced activity of adaptive immunity and phagocytes in high-FE pigs suggesting more efficient conserving of resources, which can be utilised for other important biological processes. Shifts in carbohydrate conversion into glucose in FE-divergent muscle may underpin the divergent evolution of pH profile in meat from the FE-groups. Moreover, altered amino acid metabolism and increased mobilisation & flux of calcium may influence growth in FE-divergent muscle. Furthermore, decreased degradation of fibroblasts in FE-divergent muscle could impact on collagen turnover and alter tenderness of meat, whilst enhanced lipid degradation in high-FE pigs may potentially underlie a more efficient fat metabolism in these animals.
    • Complete Genome Sequence of Clostridium estertheticum DSM 8809, a Microbe Identified in Spoiled Vacuum Packed Beef

      Yu, Zhongyi; Gunn, Lynda; Brennan, Evan; Reid, Rachael; Wall, Patrick G.; Gaora, Peadar O.; Hurley, Daniel; Bolton, Declan; Fanning, Séamus; Department of Agriculture, Food and the Marine (Ireland) (Frontiers, 2016-11-11)
      Blown pack spoilage (BPS) is a major issue for the beef industry. Etiological agents of BPS involve members of a group of Clostridium species, including Clostridium estertheticum which has the ability to produce gas, mostly carbon dioxide, under anaerobic psychotrophic growth conditions. This spore-forming bacterium grows slowly under laboratory conditions, and it can take up to 3 months to produce a workable culture. These characteristics have limited the study of this commercially challenging bacterium. Consequently information on this bacterium is limited and no effective controls are currently available to confidently detect and manage this production risk. In this study the complete genome of C. estertheticum DSM 8809 was determined by SMRT® sequencing. The genome consists of a circular chromosome of 4.7 Mbp along with a single plasmid carrying a potential tellurite resistance gene tehB and a Tn3-like resolvase-encoding gene tnpR. The genome sequence was searched for central metabolic pathways that would support its biochemical profile and several enzymes contributing to this phenotype were identified. Several putative antibiotic/biocide/metal resistance-encoding genes and virulence factors were also identified in the genome, a feature that requires further research. The availability of the genome sequence will provide a basic blueprint from which to develop valuable biomarkers that could support and improve the detection and control of this bacterium along the beef production chain.
    • The Proportion of Fermented Milk in Dehydrated Fermented Milk–Parboiled Wheat Composites Significantly Affects Their Composition, Pasting Behaviour, and Flow Properties on Reconstitution

      Shevade, Ashwini V.; O’Callaghan, Yvonne C.; O’Brien, Nora M.; O’Connor, Tom P.; Guinee, Timothy P.; Department of Agriculture, Food and the Marine; 14/F/805 (MDPI, 2018-07-14)
      Dairy and cereal are frequently combined to create composite foods with enhanced nutritional benefits. Dehydrated fermented milk–wheat composites (FMWC) were prepared by blending fermented milk (FM) and parboiled wheat (W), incubating at 35 °C for 24 h, drying at 46 °C for 48 h, and milling to 1 mm. Increasing the weight ratio of FM to W from 1.5 to 4.0 resulted in reductions in total solids (from 96 to 92%) and starch (from 52 to 39%), and increases in protein (15.2–18.9%), fat (3.7–5.9%), lactose (6.4–11.4%), and lactic acid (2.7–4.2%). FMWC need to be reconstituted prior to consumption. The water-holding capacity, pasting viscosity, and setback viscosity of the reconstituted FMWC (16.7% total solids) decreased with the ratio of FM to W. The reconstituted FMWC exhibited pseudoplastic flow behaviour on shearing from 18 to 120 s−1. Increasing the FM:W ratio coincided with a lower yield stress, consistency index, and viscosity at 120 s−1. The results demonstrate the critical impact of the FM:W ratio on the composition, pasting behavior, and consistency of the reconstituted FMWC. The difference in consistency associated with varying the FM:W ratio is likely to impact on satiety and nutrient value of the FMWCs.
    • Intestinal microbiota profiles associated with low and high residual feed intake in chickens across two geographical locations

      Siegerstetter, Sina-Catherine; Schmitz-Esser, Stephan; Magowan, Elizabeth; Wetzels, Stefanie Urimare; Zebeli, Qendrim; Lawlor, Peadar G; O'Connell, Niamh E.; Metzler-Zebeli, Barbara U.; European Union; 311794 (PLOS, 2017-11-15)
      Intestinal microbe-host interactions can affect the feed efficiency (FE) of chickens. As inconsistent findings for FE-associated bacterial taxa were reported across studies, the present objective was to identify whether bacterial profiles and predicted metabolic functions that were associated with residual feed intake (RFI) and performance traits in female and male chickens were consistent across two different geographical locations. At six weeks of life, the microbiota in ileal, cecal and fecal samples of low (n = 34) and high (n = 35) RFI chickens were investigated by sequencing the V3-5 region of the 16S rRNA gene. Location-associated differences in α-diversity and relative abundances of several phyla and genera were detected. RFI-associated bacterial abundances were found at the phylum and genus level, but differed among the three intestinal sites and between males and females. Correlation analysis confirmed that, of the taxonomically classifiable bacteria, Lactobacillus (5% relative abundance) and two Lactobacillus crispatus-OTUs in feces were indicative for high RFI in females (P < 0.05). In males, Ruminococcus in cecal digesta (3.1% relative abundance) and Dorea in feces (<0.1% relative abundance) were best indicative for low RFI, whereas Acinetobacter in feces (<1.5% relative abundance) related to high RFI (P < 0.05). Predicted metabolic functions in feces of males confirmed compositional relationships as functions related to amino acid, fatty acid and vitamin metabolism correlated with low RFI, whereas an increasing abundance of bacterial signaling and interaction (i.e. cellular antigens) genes correlated with high RFI (P < 0.05). In conclusion, RFI-associated bacterial profiles could be identified across different geographical locations. Results indicated that consortia of low- abundance taxa in the ileum, ceca and feces may play a role for FE in chickens, whereby only bacterial FE-associations found in ileal and cecal digesta may serve as useful targets for dietary strategies.
    • Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir

      Walsh, Aaron M.; Crispie, Fiona; Kilcawley, Kieran N.; O’Sullivan, Orla; O’Sullivan, Maurice G.; Claesson, Marcus J.; Cottera, Paul D.; Science Foundation Ireland; SFI/12/RC/2273; SFI/11/PI/1137; SFI/13/SIRG/2160 (2018-11-05)
      Kefir is a putatively health-promoting dairy beverage that is produced when a kefir grain, consisting of a consortium of microorganisms, is added to milk to initiate a natural fermentation. Here, a detailed analysis was carried out to determine how the microbial population, gene content, and flavor of three kefirs from distinct geographic locations change over the course of 24-h fermentations. Metagenomic sequencing revealed that Lactobacillus kefiranofaciens was the dominant bacterial species in kefir during early stages of fermentations but that Leuconostoc mesenteroides became more prevalent in later stages. This pattern is consistent with an observation that genes involved in aromatic amino acid biosynthesis were absent from L. kefiranofaciens but were present in L. mesenteroides. Additionally, these shifts in the microbial community structure, and associated pathways, corresponded to changes in the levels of volatile compounds. Specifically, Acetobacter spp. correlated with acetic acid; Lactobacillus spp. correlated with carboxylic acids, esters and ketones; Leuconostoc spp. correlated with acetic acid and 2,3-butanedione; and Saccharomyces spp. correlated with esters. The correlation data suggest a causal relationship between microbial taxa and flavor that is supported by observations that addition of L. kefiranofaciens NCFB 2797 increased the levels of esters and ketones whereas addition of L. mesenteroides 213M0 increased the levels of acetic acid and 2,3-butanedione. Finally, we detected genes associated with probiotic functionalities in the kefir microbiome. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein and can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods. IMPORTANCE Traditional fermented foods represent relatively low-complexity microbial environments that can be used as model microbial communities to understand how microbes interact in natural environments. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein. In the process, the link between individual species, and associated pathways, with flavor compounds is revealed and several genes that could be responsible for the purported gut health-associated benefits of consuming kefir are identified. Ultimately, in addition to providing an important fundamental insight into microbial interactions, this information can be applied to optimize the fermentation processes, flavors, and health-related attributes of this and other fermented foods.
    • Genome Sequence of Geobacillus stearothermophilus DSM 458, an Antimicrobial-Producing Thermophyllic Bacterium, Isolated from a Sugar Beet Factory

      Egan, Kevin; Kelleher, Philip; Field, Des; Rea, Mary C.; Ross, R. Paul; Cotter, Paul D.; Hill, Colin; Department of Agriculture, Food and the Marine; Science Foundation Ireland; DAFM 13/F/462; SFI/12/RC/2273; SFI/11/PI/1137; SFI/10/IN.1/B3027 (American Society for Microbiology, 2017-10-26)
      This paper reports the full genome sequence of the antimicrobial-producing bacterium Geobacillus stearothermophilus DSM 458, isolated in a sugar beet factory in Austria. In silico analysis reveals the presence of a number of novel bacteriocin biosynthetic genes.
    • Improved emulsion stability and modified nutrient release by structuring O/W emulsions using konjac glucomannan

      Lu, Wei; Zheng, Baodong; Miao, Song; National Natural Science Foundation of China; China Scholarship Council; 31628016; 201508300001 (Elsevier, 2018-02-22)
      Functional konjac glucomannan (KGM) was used to structure the water phase of O/W emulsions containing a lipophilic bioactive compound (β-carotene). KGM greatly increased the viscosity of the water phase and thus the viscosity of final emulsions. Results of Fourier-transform infrared spectroscopy (FT-IR) showed that there is no significant non-covalent interaction between KGM and whey proteins in the water phase. KGM significantly improved the creaming and pH stability of whey-protein-stabilized emulsions (p < 0.05), and significantly decreased the oiling-off of emulsions during freeze-thaw test. Emulsions with or without KGM all had good thermal stability at 80 °C. Microscopy observations indicated obvious aggregation of free proteins and oil droplets in gastric phase and an enzymatic-induced break-down of droplets, mainly in the intestinal phase of the simulated gastrointestinal tract (GIT) digestion. Emulsions with KGM-structured water phase showed a lower final release rate of encapsulated β-carotene than emulsion without KGM (p < 0.05), and the release rate decreased with the increasing KGM content. The findings of this study contribute to a better understanding of the influence of the water phase on the release of encapsulated compounds from emulsions, and make it possible to achieve controlled release of encapsulated compounds, and/or to deliver multiple health-beneficial nutrients at once by structuring emulsion-based carriers with functional natural biopolymers.
    • Sequencing of the Cheese Microbiome and Its Relevance to Industry

      Yeluri Jonnala, Bhagya. R.; McSweeney, Paul L. H.; Sheehan, Jeremiah J.; Cotter, Paul D.; Teagasc Walsh Fellowship Programme (Frontiers, 2018-05-23)
      The microbiota of cheese plays a key role in determining its organoleptic and other physico-chemical properties. It is essential to understand the various contributions, positive or negative, of these microbial components in order to promote the growth of desirable taxa and, thus, characteristics. The recent application of high throughput DNA sequencing (HTS) facilitates an even more accurate identification of these microbes, and their functional properties, and has the potential to reveal those microbes, and associated pathways, responsible for favorable or unfavorable characteristics. This technology also facilitates a detailed analysis of the composition and functional potential of the microbiota of milk, curd, whey, mixed starters, processing environments, and how these contribute to the final cheese microbiota, and associated characteristics. Ultimately, this information can be harnessed by producers to optimize the quality, safety, and commercial value of their products. In this review we highlight a number of key studies in which HTS was employed to study the cheese microbiota, and pay particular attention to those of greatest relevance to industry.
    • CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software

      Wilkinson, Toby J.; Huws, Sharon A.; Edwards, Joan E.; Kingston-Smith, Alison H.; Siu-Ting, Karen; Hughes, Martin; Rubino, Francesco; Friedersdorff, Maximillian; Creevey, Christopher J.; Biotechnology and Biological Sciences Research Council; BBSRC Institute Strategic Programme; Irish Research Council; BBS/OS/GC/000011B; BB/E/W/10964A01; ELEVATEPD/2014/69 (Frontiers, 2018-05-25)
      Metataxonomic 16S rDNA based studies are a commonplace and useful tool in the research of the microbiome, but they do not provide the full investigative power of metagenomics and metatranscriptomics for revealing the functional potential of microbial communities. However, the use of metagenomic and metatranscriptomic technologies is hindered by high costs and skills barrier necessary to generate and interpret the data. To address this, a tool for Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was developed for inferring the functional potential of an observed microbiome profile, based on 16S data. This allows functional inferences to be made from metataxonomic 16S rDNA studies with little extra work or cost, but its accuracy relies on the availability of completely sequenced genomes of representative organisms from the community being investigated. The rumen microbiome is an example of a community traditionally underrepresented in genome and sequence databases, but recent efforts by projects such as the Global Rumen Census and Hungate 1000 have resulted in a wide sampling of 16S rDNA profiles and almost 500 fully sequenced microbial genomes from this environment. Using this information, we have developed “CowPI,” a focused version of the PICRUSt tool provided for use by the wider scientific community in the study of the rumen microbiome. We evaluated the accuracy of CowPI and PICRUSt using two 16S datasets from the rumen microbiome: one generated from rDNA and the other from rRNA where corresponding metagenomic and metatranscriptomic data was also available. We show that the functional profiles predicted by CowPI better match estimates for both the meta-genomic and transcriptomic datasets than PICRUSt, and capture the higher degree of genetic variation and larger pangenomes of rumen organisms. Nonetheless, whilst being closer in terms of predictive power for the rumen microbiome, there were differences when compared to both the metagenomic and metatranscriptome data and so we recommend, where possible, functional inferences from 16S data should not replace metagenomic and metatranscriptomic approaches. The tool can be accessed at http://www.cowpi.org and is provided to the wider scientific community for use in the study of the rumen microbiome.