• HACCP for Irish beef, pork and lamb slaughter

      Bolton, Declan J.; Sheridan, James J.; US-Ireland Co-operation Programme in Agriculture Science and Technology; Department of Agriculture, Food and the Marine, Ireland (Teagasc, 2002-02)
      It is generally accepted that HACCP principles should be incorporated into the food safety control systems in meat processing plants to better assure food safety. The objective of this project was to publish detailed HACCP slaughter documents for the Irish beef, pork and lamb processing industries. These would provide the necessary information and detail to facilitate the implementation of HACCP on the slaughter floor (from lairage to chilling) in Irish meat plants. To this end `HACCP for Irish Beef Slaughter' was published in October 2000, `HACCP for Irish Pork Slaughter' in December 2001 and `HACCP for Irish Lamb Slaughter' will be available early in 2002. These are non-generic, detailed documents which provide the scientific basis for establishing critical control points (CCP), critical limits, monitoring and corrective action procedures.
    • Hazard analysis and critical control point (HACCP) and hygiene control auditing in Irish beef abattoirs

      Bolton, Declan J.; Pearce, Rachel; Tergney, Anabel; Howlett, Brendan (Teagasc, 2007-06)
      This project validated two innovative technologies for use in improving the safety of Irish beef. Online monitoring was developed and successfully tested as a tool for controlling faecal contamination on beef carcasses with the resultant reduction in microbial counts. A novel anti-microbial, LactiSAL®, was also tested and validated for use in the beef industry. Sponge swabbing using a polyurethane sponge was developed and validated for use in carcass testing as required in European Commission Decision 2001/471/EC. The costs of developing and implementing a HACCP system in Irish beef slaughter plants were assessed. Furthermore, a guide to relevant food safety legislation, including the development and auditing of HACCP and prerequisites for beef slaughter (in compliance with 2001/471/EC and the European Commission Hygiene Regulations), was developed and published.
    • Heat-induced Maillard reaction of the tripeptide IPP and ribose: Structural characterization and implication on bioactivity

      Jiang, Zhanmei; Rai, Dilip K; O'Connor, Paula M.; Brodkorb, Andre; National Natural Science Foundation of China; Innovative Research Team of Higher Education of Heilongjiang Province (Elsevier, 28/09/2012)
      Maillard reaction products (MRPs) were prepared from aqueous model mixtures containing 60 g L− 1 ribose and 30 g L− 1 of the bioactive tripeptide IPP (Ile-Pro-Pro), heated at 98 °C. MRP and associated reactions with changes in IPP were observed within one hour of heat-treatment. The pH of MRPs decreased significantly during the heat treatment of IPP–ribose mixtures from 9.0 to 7.6 after one hour. The amino group content, IPP and ribose concentration decreased significantly during heat treatment. The fluorescence intensity of the IPP–ribose MRPs reached the maximum within 2 h. Modification of the UV/vis spectra for IPP–ribose MRPs was mainly due to a condensation reaction of IPP with ribose. Compounds with molecular weight between 300 and 650 Da were dominant while compounds smaller than 250 Da were also produced during the reactions, as characterized by size exclusion chromatography. Mass spectrometry revealed that IPP was conjugated to ribose at the N-terminal (m/z of 458.3) upon heat-treatment. The presence of ribose also promoted peptide degradation to dehydrated IP (m/z of 211.1). IPP–ribose MRPs lost the known angiotensin-I-converting enzyme (ACE) inhibitory activity of IPP; however, strong antioxidant properties were detected.
    • High conjugated linoleic acid enriched ghee (clarified butter) increases the antioxidant and antiatherogenic potency in female Wistar rats

      Chinnadurai, Kathirvelan; Kanwal, Harpreet K; Tyagi, Amrish K; Stanton, Catherine; Ross, R Paul; Department of Biotechnology/Department of Science and Technology, Government of India (Biomed Central, 07/08/2013)
      Background: Hypercholesterolemia and oxidative stress are the main stimulating factors responsible for coronary artery disease and progression of atherosclerosis. Dairy food products are rich in conjugated linoleic acid (CLA) which is considered as an important component due to its potential health benefits such as anticarcinogenic, antiatherogenic, antidiabetic and antiadipogenic properties. In the present study, the effect of CLA enriched ghee on the antioxidant enzyme system and antiatherogenic properties in Wistar rats has been studied. Methods: Female Wistar rats of 21 days were taken for the study and fed with soybean diet (Control diet), low CLA diet and high CLA ghee diet (treatments) for thirty five days for studying antioxidative enzymes and sixteen weeks in case of antiatherogenic studies. Results: Feeding of high CLA enhanced ghee during pubescent period in rats lead to an increase in catalase (CAT) and superoxide dismutase (SOD) enzyme activities in blood and increased CAT, SOD and glutathione transferase (GST) enzymes activities in liver by 27, 130 and 168 percent, respectively. Plasma nitrate concentration and Haemoglobin levels remained the same in all the treatments. Feeding of high CLA ghee resulted in lower (P < 0.01) plasma cholesterol & triglyceride level (52.17 and 30.27%), and higher high density lipoproteins (33.26%) than feeding of soybean oil (control group) and thus manifested in decreased (P < 0.05) atherogenic index (from 0.472 to 0.244). Lesser cholesterol and triglyceride levels were observed in the liver and aorta of high CLA fed rats than in those of the other groups. Histopathological studies of liver showed normal hepatic cords with portal triad in the high CLA ghee fed rats whereas fatty degeneration of hepatocytes containing fat vacuoles was observed in the liver of the other groups. Conclusion: This paper is the first report of the antioxidant and antiatherogenic properties of the high CLA enriched ghee suggesting that high CLA ghee can be used as a potential food for decreasing the risk of cardiovascular diseases, particularly in India, where, ghee is widely used for culinary and medicinal purposes.
    • High conjugated linoleic acid enriched ghee (clarified butter) increases the antioxidant and antiatherogenic potency in female Wistar rats

      Chinnadurai, Kathirvelan; Kanwal, Harpreet K; Tyagi, Amrish K; Stanton, Catherine; Ross, R Paul; Department of Biotechnology/Department of Science and Technology, Government of India (Biomed Central, 07/08/2013)
      Background Hypercholesterolemia and oxidative stress are the main stimulating factors responsible for coronary artery disease and progression of atherosclerosis. Dairy food products are rich in conjugated linoleic acid (CLA) which is considered as an important component due to its potential health benefits such as anticarcinogenic, antiatherogenic, antidiabetic and antiadipogenic properties. In the present study, the effect of CLA enriched ghee on the antioxidant enzyme system and antiatherogenic properties in Wistar rats has been studied. Methods Female Wistar rats of 21 days were taken for the study and fed with soybean diet (Control diet), low CLA diet and high CLA ghee diet (treatments) for thirty five days for studying antioxidative enzymes and sixteen weeks in case of antiatherogenic studies. Results Feeding of high CLA enhanced ghee during pubescent period in rats lead to an increase in catalase (CAT) and superoxide dismutase (SOD) enzyme activities in blood and increased CAT, SOD and glutathione transferase (GST) enzymes activities in liver by 27, 130 and 168 percent, respectively. Plasma nitrate concentration and Haemoglobin levels remained the same in all the treatments. Feeding of high CLA ghee resulted in lower (P < 0.01) plasma cholesterol & triglyceride level (52.17 and 30.27%), and higher high density lipoproteins (33.26%) than feeding of soybean oil (control group) and thus manifested in decreased (P < 0.05) atherogenic index (from 0.472 to 0.244). Lesser cholesterol and triglyceride levels were observed in the liver and aorta of high CLA fed rats than in those of the other groups. Histopathological studies of liver showed normal hepatic cords with portal triad in the high CLA ghee fed rats whereas fatty degeneration of hepatocytes containing fat vacuoles was observed in the liver of the other groups. Conclusion This paper is the first report of the antioxidant and antiatherogenic properties of the high CLA enriched ghee suggesting that high CLA ghee can be used as a potential food for decreasing the risk of cardiovascular diseases, particularly in India, where, ghee is widely used for culinary and medicinal purposes.
    • High pressure technology in the manufacture of minimally-processed meat products

      Troy, Declan J.; Crehan, Clodagh; Mullen, Anne Maria; Desmond, Eoin (Teagasc, 2001-07)
      High hydrostatic pressure processing was applied to raw minced meat prior to product formulation and the results indicate that with 50 MPa pressure it was possible to reduce the salt in frankfurters from 2.5% to 1.5% without compromising the safety and overall quality. Similarly the phosphate content of frankfurters could be reduced from 0.5% to 0.25% after pressure treatment. Cook loss from the treated frankfurters was significantly reduced indicating a higher yield of product due to the high pressure.
    • High-throughput DNA sequencing to survey bacterial histidine and tyrosine decarboxylases in raw milk cheeses

      O'Sullivan, Daniel J.; Fallico, Vincenzo; O’Sullivan, Orla; McSweeney, Paul L H; Sheehan, Jeremiah J; Cotter, Paul D.; Giblin, Linda; Teagasc Walsh Fellowship Programme; Department of Agriculture, Food and the Marine; 2012205 (Biomed Central, 17/11/2015)
      Background: The aim of this study was to employ high-throughput DNA sequencing to assess the incidence of bacteria with biogenic amine (BA; histamine and tyramine) producing potential from among 10 different cheeses varieties. To facilitate this, a diagnostic approach using degenerate PCR primer pairs that were previously designed to amplify segments of the histidine (hdc) and tyrosine (tdc) decarboxylase gene clusters were employed. In contrast to previous studies in which the decarboxylase genes of specific isolates were studied, in this instance amplifications were performed using total metagenomic DNA extracts. Results: Amplicons were initially cloned to facilitate Sanger sequencing of individual gene fragments to ensure that a variety of hdc and tdc genes were present. Once this was established, high throughput DNA sequencing of these amplicons was performed to provide a more in-depth analysis of the histamine- and tyramine-producing bacteria present in the cheeses. High-throughput sequencing resulted in generation of a total of 1,563,764 sequencing reads and revealed that Lactobacillus curvatus, Enterococcus faecium and E. faecalis were the dominant species with tyramine producing potential, while Lb. buchneri was found to be the dominant species harbouring histaminogenic potential. Commonly used cheese starter bacteria, including Streptococcus thermophilus and Lb. delbreueckii, were also identified as having biogenic amine producing potential in the cheese studied. Molecular analysis of bacterial communities was then further complemented with HPLC quantification of histamine and tyramine in the sampled cheeses. Conclusions: In this study, high-throughput DNA sequencing successfully identified populations capable of amine production in a variety of cheeses. This approach also gave an insight into the broader hdc and tdc complement within the various cheeses. This approach can be used to detect amine producing communities not only in food matrices but also in the production environment itself.
    • High-throughput DNA sequencing to survey bacterial histidine and tyrosine decarboxylases in raw milk cheeses

      O'Sullivan, Daniel J.; Fallico, Vincenzo; O’Sullivan, Orla; McSweeney, Paul L H; Sheehan, Jeremiah J; Cotter, Paul D.; Giblin, Linda (Biomed Central, 17/11/2015)
      Background The aim of this study was to employ high-throughput DNA sequencing to assess the incidence of bacteria with biogenic amine (BA; histamine and tyramine) producing potential from among 10 different cheeses varieties. To facilitate this, a diagnostic approach using degenerate PCR primer pairs that were previously designed to amplify segments of the histidine (hdc) and tyrosine (tdc) decarboxylase gene clusters were employed. In contrast to previous studies in which the decarboxylase genes of specific isolates were studied, in this instance amplifications were performed using total metagenomic DNA extracts. Results Amplicons were initially cloned to facilitate Sanger sequencing of individual gene fragments to ensure that a variety of hdc and tdc genes were present. Once this was established, high throughput DNA sequencing of these amplicons was performed to provide a more in-depth analysis of the histamine- and tyramine-producing bacteria present in the cheeses. High-throughput sequencing resulted in generation of a total of 1,563,764 sequencing reads and revealed that Lactobacillus curvatus, Enterococcus faecium and E. faecalis were the dominant species with tyramine producing potential, while Lb. buchneri was found to be the dominant species harbouring histaminogenic potential. Commonly used cheese starter bacteria, including Streptococcus thermophilus and Lb. delbreueckii, were also identified as having biogenic amine producing potential in the cheese studied. Molecular analysis of bacterial communities was then further complemented with HPLC quantification of histamine and tyramine in the sampled cheeses. Conclusions In this study, high-throughput DNA sequencing successfully identified populations capable of amine production in a variety of cheeses. This approach also gave an insight into the broader hdc and tdc complement within the various cheeses. This approach can be used to detect amine producing communities not only in food matrices but also in the production environment itself.
    • High-Throughput Sequencing Reveals the Incomplete, Short-Term Recovery of Infant Gut Microbiota following Parenteral Antibiotic Treatment with Ampicillin and Gentamicin

      Fouhy, Fiona; Guinane, Caitriona M.; Hussey, Seamus; Wall, Rebecca; Ryan, C. Anthony; Dempsey, Eugene M.; Murphy, Brendan; Ross, R Paul; Fitzgerald, Gerald F; Stanton, Catherine; Cotter, Paul D.; Irish Research Council for Science, Engineering and Technology; Teagasc Walsh Fellowship Programme; Science Foundation Ireland; SFI/11/PI/1137 (American Society for Microbiology, 04/09/2012)
      The infant gut microbiota undergoes dramatic changes during the first 2 years of life. The acquisition and development of this population can be influenced by numerous factors, and antibiotic treatment has been suggested as one of the most significant. Despite this, however, there have been relatively few studies which have investigated the short-term recovery of the infant gut microbiota following antibiotic treatment. The aim of this study was to use high-throughput sequencing (employing both 16S rRNA and rpoB-specific primers) and quantitative PCR to compare the gut microbiota of nine infants who underwent parenteral antibiotic treatment with ampicillin and gentamicin (within 48 h of birth), 4 and 8 weeks after the conclusion of treatment, relative to that of nine matched healthy controls. The investigation revealed that the gut microbiota of the antibiotic-treated infants had significantly higher proportions of Proteobacteria (P = 0.0049) and significantly lower proportions of Actinobacteria (P = 0.00001) (and the associated genus Bifidobacterium [P = 0.0132]) as well as the genus Lactobacillus (P = 0.0182) than the untreated controls 4 weeks after the cessation of treatment. By week 8, the Proteobacteria levels remained significantly higher in the treated infants (P = 0.0049), but the Actinobacteria, Bifidobacterium, and Lactobacillus levels had recovered and were similar to those in the control samples. Despite this recovery of total Bifidobacterium numbers, rpoB-targeted pyrosequencing revealed that the number of different Bifidobacterium species present in the antibiotic-treated infants was reduced. It is thus apparent that the combined use of ampicillin and gentamicin in early life can have significant effects on the evolution of the infant gut microbiota, the long-term health implications of which remain unknown.
    • Host Specific Diversity in Lactobacillus johnsonii as Evidenced by a Major Chromosomal Inversion and Phage Resistance Mechanisms

      Guinane, Caitriona M.; Kent, Robert M.; Norberg, Sarah; Hill, Colin; Fitzgerald, Gerald F.; Stanton, Catherine; Ross, R Paul; Enterprise Ireland; CFTD/07/116 (PLOS, 20/04/2011)
      Genetic diversity and genomic rearrangements are a driving force in bacterial evolution and niche adaptation. We sequenced and annotated the genome of Lactobacillus johnsonii DPC6026, a strain isolated from the porcine intestinal tract. Although the genome of DPC6026 is similar in size (1.97mbp) and GC content (34.8%) to the sequenced human isolate L. johnsonii NCC 533, a large symmetrical inversion of approximately 750 kb differentiated the two strains. Comparative analysis among 12 other strains of L. johnsonii including 8 porcine, 3 human and 1 poultry isolate indicated that the genome architecture found in DPC6026 is more common within the species than that of NCC 533. Furthermore a number of unique features were annotated in DPC6026, some of which are likely to have been acquired by horizontal gene transfer (HGT) and contribute to protection against phage infection. A putative type III restriction-modification system was identified, as were novel Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) elements. Interestingly, these particular elements are not widely distributed among L. johnsonii strains. Taken together these data suggest intra-species genomic rearrangements and significant genetic diversity within the L. johnsonii species and indicate towards a host-specific divergence of L. johnsonii strains with respect to genome inversion and phage exposure.
    • Hygiene and safety of Irish beef carcasses.

      Kerr, Marie; Sheridan, James J. (Teagasc, 2002-10)
      Investigations were carried out in a number of beef abattoirs in Ireland. Information was obtained on the hygienic status of the carcasses being produced and also on their safety, using the presence of Salmonella as an indicator. The data showed that, in general, the hygiene of the carcasses being produced was of a satisfactory quality and that faecal contamination was low, as indicated by the coliform and E. coli counts. The safety of the carcasses as indicated by the presence of Salmonella was considered to be a cause for concern. The level of contamination by this pathogen of 7.6% was considered to be high and requires investigation. The majority of the Salmonella present on carcasses was S. typhimurium DT104, which is resistant to a range of antibodies. The work was part of an EU project and some results are presented from other partners.
    • Identification of existing and emerging chemical residue contamination concerns in milk

      Danaher, Martin; Jordan, Kieran; Department of Agriculture, Food and the Marine, Ireland (Teagasc (Agriculture and Food Development Authority), Ireland, 2013)
      In order to maintain the quality of Irish milk and meet increasingly demanding specifications, it is necessary to focus on chemical residues in milk, in addition to other quality issues. The objective of the work was to assess the current status of chemical contaminant analysis and to identify technological and knowledge needs. This was achieved through a review of literature with respect to chemical contaminants. Quaternary ammonium compounds (QACs) have been identified as an area of concern for the dairy industry because of the recent reports of QAC residues in dairy products internationally. Analytical support to analyse QAC residues in milk and dairy products on an ongoing basis is required. Furthermore, the source of QAC residues along the milk production chain needs to be identified. Similarly, analytical support and research is needed in the area of phthalates, to support the development of intervention strategies to reduce contamination, if present. Cephalosporin antibiotics have been a concern for the dairy industry because of the lack of suitable chemical tests to measure these substances.
    • Identification of short peptide sequences in the nanofiltration permeate of a bioactive whey protein hydrolysate

      Le Maux, Solene; Nongoniermaa, Alice B.; Murray, Brian; Kelly, Philip M.; Fitzgerald, Richard J.; Enterprise Ireland; TC2013-0001 (Elsevier, 16/09/2015)
      Short peptides in food protein hydrolysates are of significant interest as they may be highly bioactive whilst also being bioavailable. A dipeptidyl peptidase IV (DPP-IV) inhibitory whey protein hydrolysate (WPH) was fractionated using nanofiltration (NF) with a 200 Da MWCO membrane. The DPP-IV half maximal inhibitory concentration of the NF permeate (IC50 = 0.66 ± 0.08 mg protein equivalent mL− 1) was significantly more potent (P > 0.05) than that of the starting WPH (IC50 = 0.94 ± 0.24 mg protein equivalent mL− 1) and associated retentate (IC50 = 0.82 ± 0.13 mg protein equivalent mL− 1). This confirmed the contribution of short peptides within the NF permeate to the overall DPP-IV inhibitory activity. An hydrophilic interaction liquid chromatography (HILIC-) and reverse-phase (RP-) liquid chromatography tandem mass spectrometry (LC–MS/MS) strategy, based on two retention time models, allowed detection of eight free amino acids and eight di- to tetrapeptides in the NF permeate. The potential sequences of the peptides within the NF permeate were then ranked on the basis of their highest probability of occurrence. A confirmatory study with synthetic peptides showed that valine–alanine (VA), valine–leucine (VL), tryptophan–leucine (WL) and tryptophan–isoleucine (WI) displayed DPP-IV IC50 values < 170 μM. The NF and LC–MS strategies employed herein represent a new approach for the targeted identification of short peptides within bioactive food protein hydrolysates.
    • Image Processing of Outer-Product matrices - a new way to classify samples: Examples using visible/NIR/MIR spectral data.

      Jaillais, B.; Morrin, V.; Downey, Gerard (Elsevier, 2007)
      A chemometric analysis has been developed to emphasise the discrimination power of spectroscopic techniques such as near infrared, mid-infrared and visible spectroscopy. The combination of two spectral domains using outer product analysis (OPA) leads to the calculation of an outer product (OP) matrix. The representation of this matrix is called the "analytical fingerprint" of the samples and their classification is performed in the following steps. First, two different techniques are tested by subtracting the images one-by-one and the sum of all the elements of the resulting difference matrix gives a scalar, characteristic of the distance between the two images. Combining chemical analysis with image processing techniques provides an original approach to study butters and margarines in relation to their fat content. Best results were obtained with the OP matrix built from NIR and visible signals following the use of city block distance and average linkage. Samples were arranged in four groups: 100 %, 82-75 %, 70-59 % and 38-25 % w/w fat. The cophenetic correlation coefficient (validity of the cluster information generated by the linkage function) associated with these spectral data has a value of 0.973. Similar results were obtained using Ward's algorithm which generated four groups and a cophenetic correlation coefficient equal to 0.959.
    • Impact of Environmental Factors on Bacteriocin Promoter Activity in Gut-Derived Lactobacillus salivarius

      Guinane, Caitriona M.; Piper, Clare; Draper, Lorraine A.; O'Connor, Paula M.; Hill, Colin; Ross, R Paul; Cotter, Paul D.; Science Foundation Ireland; SFI/11/PI/1137 (American Society for Microbiology, 04/09/2015)
      Bacteriocin production is regarded as a desirable probiotic trait that aids in colonization and persistence in the gastrointestinal tract (GIT). Strains of Lactobacillus salivarius, a species associated with the GIT, are regarded as promising probiotic candidates and have a number of associated bacteriocins documented to date. These include multiple class IIb bacteriocins (salivaricin T, salivaricin P, and ABP-118) and the class IId bacteriocin bactofencin A, which show activity against medically important pathogens. However, the production of a bacteriocin in laboratory media does not ensure production under stressful environmental conditions, such as those encountered within the GIT. To allow this issue to be addressed, the promoter regions located upstream of the structural genes encoding the L. salivarius bacteriocins mentioned above were fused to a number of reporter proteins (green fluorescent protein [GFP], red fluorescent protein [RFP], and luciferase [Lux]). Of these, only transcriptional fusions to GFP generated signals of sufficient strength to enable the study of promoter activity in L. salivarius. While analysis of the class IIb bacteriocin promoter regions indicated relatively weak GFP expression, assessment of the promoter of the antistaphylococcal bacteriocin bactofencin A revealed a strong promoter that is most active in the absence of the antimicrobial peptide and is positively induced in the presence of mild environmental stresses, including simulated gastric fluid. Taken together, these data provide information on factors that influence bacteriocin production, which will assist in the development of strategies to optimize in vivo and in vitro production of these antimicrobials.
    • 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.
    • Improving the quality of gluten-free products

      Gallagher, Eimear; McCarthy, Denise; Gormley, Ronan T.; Arendt, Elke (Teagasc, 2004-03)
      The incidence of coeliac disease or other allergic reactions/intolerances to gluten is increasing, largely due to improved diagnostic procedures and changes in eating habits. The worldwide number of sufferers of coeliac disease has been predicted to increase by a factor of ten over the next number of years, resulting in a growing market for gluten-free cereal-based products. Market research has shown that many of the products currently on sale are of inferior quality. The replacement of gluten presents a major technological challenge, as it is an essential structure-building protein which is necessary for formulating high quality cereal-based goods. Therefore, the production of high quality gluten-free bread is difficult.
    • In silico analysis highlights the frequency and diversity of type 1 lantibiotic gene clusters in genome sequenced bacteria

      Marsh, Alan J.; O'Sullivan, Orla; Ross, R Paul; Cotter, Paul D.; Hill, Colin; Science Foundation Ireland (Biomed Central, 30/11/2010)
      Background: Lantibiotics are lanthionine-containing, post-translationally modified antimicrobial peptides. These peptides have significant, but largely untapped, potential as preservatives and chemotherapeutic agents. Type 1 lantibiotics are those in which lanthionine residues are introduced into the structural peptide (LanA) through the activity of separate lanthionine dehydratase (LanB) and lanthionine synthetase (LanC) enzymes. Here we take advantage of the conserved nature of LanC enzymes to devise an in silico approach to identify potential lantibiotic-encoding gene clusters in genome sequenced bacteria. Results: In total 49 novel type 1 lantibiotic clusters were identified which unexpectedly were associated with species, genera and even phyla of bacteria which have not previously been associated with lantibiotic production. Conclusions: Multiple type 1 lantibiotic gene clusters were identified at a frequency that suggests that these antimicrobials are much more widespread than previously thought. These clusters represent a rich repository which can yield a large number of valuable novel antimicrobials and biosynthetic enzymes.
    • In Silico Assigned Resistance Genes Confer Bifidobacterium with Partial Resistance to Aminoglycosides but Not to Β-Lactams

      Fouhy, Fiona; O’Connell Motherway, Mary; Fitzgerald, Gerald F.; Ross, R Paul; Stanton, Catherine; van Sinderen, Douwe; Cotter, Paul D.; Irish Research Council for Science, Engineering and Technology; Science Foundation Ireland; Health Research Board; Teagasc Walsh Fellowship Programme; SFI/11/PI/1137; SFI/02/CE/B124; SFI/07/CE/B1368; PDTM/20011/9) (PLoS, 06/12/2013)
      Bifidobacteria have received significant attention due to their contribution to human gut health and the use of specific strains as probiotics. It is thus not surprising that there has also been significant interest with respect to their antibiotic resistance profile. Numerous culture-based studies have demonstrated that bifidobacteria are resistant to the majority of aminoglycosides, but are sensitive to β-lactams. However, limited research exists with respect to the genetic basis for the resistance of bifidobacteria to aminoglycosides. Here we performed an in-depth in silico analysis of putative Bifidobacterium-encoded aminoglycoside resistance proteins and β-lactamases and assess the contribution of these proteins to antibiotic resistance. The in silico-based screen detected putative aminoglycoside and β-lactam resistance proteins across the Bifidobacterium genus. Laboratory-based investigations of a number of representative bifidobacteria strains confirmed that despite containing putative β-lactamases, these strains were sensitive to β-lactams. In contrast, all strains were resistant to the aminoglycosides tested. To assess the contribution of genes encoding putative aminoglycoside resistance proteins in Bifidobacterium sp. two genes, namely Bbr_0651 and Bbr_1586, were targeted for insertional inactivation in B. breve UCC2003. As compared to the wild-type, the UCC2003 insertion mutant strains exhibited decreased resistance to gentamycin, kanamycin and streptomycin. This study highlights the associated risks of relying on the in silico assignment of gene function. Although several putative β-lactam resistance proteins are located in bifidobacteria, their presence does not coincide with resistance to these antibiotics. In contrast however, this approach has resulted in the identification of two loci that contribute to the aminoglycoside resistance of B. breve UCC2003 and, potentially, many other bifidobacteria.
    • In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project’s reference genome database

      Walsh, Calum J.; Guinane, Caitriona M.; Hill, Colin; Ross, R Paul; O’Toole, Paul W.; Cotter, Paul D.; Science Foundation Ireland; SFI/11/PI/1137 (Biomed Central, 16/09/2015)
      Background The human gut microbiota comprises approximately 100 trillion microbial cells which significantly impact many aspects of human physiology - including metabolism, nutrient absorption and immune function. Disturbances in this population have been implicated in many conditions and diseases, including obesity, type-2 diabetes and inflammatory bowel disease. This suggests that targeted manipulation or shaping of the gut microbiota, by bacteriocins and other antimicrobials, has potential as a therapeutic tool for the prevention or treatment of these conditions. With this in mind, several studies have used traditional culture-dependent approaches to successfully identify bacteriocin-producers from the mammalian gut. In silico-based approaches to identify novel gene clusters are now also being utilised to take advantage of the vast amount of data currently being generated by next generation sequencing technologies. In this study, we employed an in silico screening approach to mine potential bacteriocin clusters in genome-sequenced isolates from the gastrointestinal tract (GIT). More specifically, the bacteriocin genome-mining tool BAGEL3 was used to identify potential bacteriocin producers in the genomes of the GIT subset of the Human Microbiome Project’s reference genome database. Each of the identified gene clusters were manually annotated and potential bacteriocin-associated genes were evaluated. Results We identified 74 clusters of note from 59 unique members of the Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria and Synergistetes. The most commonly identified class of bacteriocin was the >10 kDa class, formerly known as bacteriolysins, followed by lantibiotics and sactipeptides. Conclusions Multiple bacteriocin gene clusters were identified in a dataset representative of the human gut microbiota. Interestingly, many of these were associated with species and genera which are not typically associated with bacteriocin production.