• Comparative genomics of lactic acid bacteria reveals a niche-specific gene set

      O'Sullivan, Orla; O'Callaghan, John; Sangrador-Vegas, Amaia; McAuliffe, Olivia; Slattery, Lydia; Kaleta, Pawel; Callanan, Michael J.; Fitzgerald, Gerald F; Ross, R Paul; Beresford, Tom (Biomed Central, 2009-03-05)
      Background: The recently sequenced genome of Lactobacillus helveticus DPC4571 1 revealed a dairy organism with significant homology (75% of genes are homologous) to a probiotic bacteria Lb. acidophilus NCFM 2. This led us to hypothesise that a group of genes could be determined which could define an organism's niche. Results: Taking 11 fully sequenced lactic acid bacteria (LAB) as our target, (3 dairy LAB, 5 gut LAB and 3 multi-niche LAB), we demonstrated that the presence or absence of certain genes involved in sugar metabolism, the proteolytic system, and restriction modification enzymes were pivotal in suggesting the niche of a strain. We identified 9 niche specific genes, of which 6 are dairy specific and 3 are gut specific. The dairy specific genes identified in Lactobacillus helveticus DPC4571 were lhv_1161 and lhv_1171, encoding components of the proteolytic system, lhv_1031 lhv_1152, lhv_1978 and lhv_0028 encoding restriction endonuclease genes, while bile salt hydrolase genes lba_0892 and lba_1078, and the sugar metabolism gene lba_1689 from Lb. acidophilus NCFM were identified as gut specific genes. Conclusion: Comparative analysis revealed that if an organism had homologs to the dairy specific geneset, it probably came from a dairy environment, whilst if it had homologs to gut specific genes, it was highly likely to be of intestinal origin. We propose that this "barcode" of 9 genes will be a useful initial guide to researchers in the LAB field to indicate an organism's ability to occupy a specific niche.
    • Complete Genome Sequences of vB_LmoS_188 and vB_LmoS_293, Two Bacteriophages with Specificity for Listeria monocytogenes Strains of Serotypes 4b and 4e

      Casey, Aidan; Kieran, Jordan; Coffey, Aidan; McAuliffe, Olivia (American Society for Microbiology, 2015-04-09)
      Listeria monocytogenes is responsible for the rare disease listeriosis, which is associated with the consumption of contaminated food products. We report here the complete genome sequences of vB_LmoS_188 and vB_LmoS_293, phages isolated from environmental sources and that have host specificity for L. monocytogenes strains of the 4b and 4e serotypes.
    • Control of Cheese Microflora using Bacteriocins.

      Ross, R.Paul; Hill, Coln; O'Keeffe, T.; McAuliffe, Olivia; Ryan, M.; O'Connor, Paula M.; Freyne, T. (Teagasc, 2001-08-01)
      Bacteriocins are proteins, produced by some bacteria which are capable of inhibiting other bacteria. The overall aim of this project was the development and exploitation of bacteriocins such as Lacticin 3147 (produced by a food-grade microorganism), as biological tools to control the microflora of foods. Lacticin 3147-producing strains were evaluated for their ability to improve the microbial quality of a variety of dairy products and in particular, Cheddar cheese. The manipulation of cheese flora using bacteriocins should offer manufacturers greater control in the consistency and quality of the final product, in addition to improving its safety. In concert with these studies, Lacticin 3147 was studied in detail at the molecular level resulting in its biochemical and genetic analysis. These studies have demonstrated the complexity and uniqueness of this potent antimicrobial.
    • Draft Genome Sequences of Three Lactobacillus paracasei Strains, Members of the Nonstarter Microbiota of Mature Cheddar Cheese

      Stefanovic, Ewelina; Fitzgerald, Gerald; McAuliffe, Olivia (American Society for Microbiology, 2017-07-20)
      Lactobacillus paracasei strains are common members of the nonstarter microbiota present in various types of cheeses. The draft genome sequences of three strains isolated from mature cheddar cheeses are reported here.
    • Transcriptome analysis of Listeria monocytogenes exposed to biocide stress reveals a multi-system response involving cell wall synthesis, sugar uptake, and motility

      Casey, Aidan; Fox, Edward M.; Schmitz-Esser, Stephan; Coffey, Aidan; McAuliffe, Olivia; Jordan, Kieran (Frontiers Media SA, 2014-02-28)
      Listeria monocytogenes is a virulent food-borne pathogen most often associated with the consumption of “ready-to-eat” foods. The organism is a common contaminant of food processing plants where it may persist for extended periods of time. A commonly used approach for the control of Listeria monocytogenes in the processing environment is the application of biocides such as quaternary ammonium compounds. In this study, the transcriptomic response of a persistent strain of L. monocytogenes (strain 6179) on exposure to a sub-lethal concentration of the quaternary ammonium compound benzethonium chloride (BZT) was assessed. Using RNA-Seq, gene expression levels were quantified by sequencing the transcriptome of L. monocytogenes 6179 in the presence (4 ppm) and absence of BZT, and mapping each data set to the sequenced genome of strain 6179. Hundreds of differentially expressed genes were identified, and subsequent analysis suggested that many biological processes such as peptidoglycan biosynthesis, bacterial chemotaxis and motility, and carbohydrate uptake, were involved in the response of L. monocyotogenes to the presence of BZT. The information generated in this study further contributes to our understanding of the response of bacteria to environmental stress. In addition, this study demonstrates the importance of using the bacterium's own genome as a reference when analysing RNA-Seq data.
    • Use of Bacteriocins to Improve Cheese Quality and Safety

      Ross, R. Paul; Hill, Colin; Ryan, Maire; Cunniffe, Alan; McAuliffe, Olivia; Murray, Deirdre; O'Keefe, Triona; Rea, Mary (Teagasc, 1998-09-01)
      The objectives of this project were to generate, characterise and exploit a range of novel bacteriocin producing starter cultures to improve both the safety and the quality of fermented dairy foods. The main conclusions were as follows: Lacticin 3147 is a broad spectrum bacteriocin which inhibits a wide range of Gram-positive bacteria including lactobacilli, clostridia and Listeria. The bacteriocin has been purified by chromatographic procedures and has been shown to be composed of two peptides, both of which are required for biological activity. The mechanism of action of lacticin 3147 has been elucidated. The entire plasmid encoding lacticin 3147 has been sequenced and the bacteriocin in distinct from any previously characterised lactococcal bacteriocin. The Food Grade introduction of the bacteriocin genes into cheese starters was carried out. Lacticin 3147 producing starters have been used to control the pathogen Listeria monocytogenes on the surface of mould ripened cheese. Lacticin 3147 producing starters have been used to control the non-starter lactic acid bacteria complement in Cheddar cheese during the ripening process. A novel starter system using a bacteriocin (lactococcin)- producing adjunct has been designed which gives increased cell lysis during Cheddar cheese manufacture while ensuring that efficient acid production is not compromised. In summary these studies have found that naturally occurring antimicrobials such as bacteriocins have a wide range of applications in the food industry for improving both the quality and safety of fermented dairy products.