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Identification and characterisation of capidermicin, a novel bacteriocin produced by Staphylococcus capitis.

Lynch D, O'Connor PM, Cotter PD, Hill C, Field D, Begley M.

PLoS One. 2019 Oct 16;14(10):e0223541. doi: 10.1371/journal.pone.0223541. eCollection 2019.


Distinct microbiome composition and metabolome exists across subgroups of elite Irish athletes.

O'Donovan CM, Madigan SM, Garcia-Perez I, Rankin A, O' Sullivan O, Cotter PD.

J Sci Med Sport. 2020 Jan;23(1):63-68. doi: 10.1016/j.jsams.2019.08.290. Epub 2019 Sep 18.


The Potential Impact of Probiotics on the Gut Microbiome of Athletes.

Wosinska L, Cotter PD, O'Sullivan O, Guinane C.

Nutrients. 2019 Sep 21;11(10). pii: E2270. doi: 10.3390/nu11102270. Review.


Improvement of Feed Efficiency in Pigs through Microbial Modulation via Fecal Microbiota Transplantation in Sows and Dietary Supplementation of Inulin in Offspring.

McCormack UM, Curião T, Metzler-Zebeli BU, Wilkinson T, Reyer H, Crispie F, Cotter PD, Creevey CJ, Gardiner GE, Lawlor PG.

Appl Environ Microbiol. 2019 Oct 30;85(22). pii: e01255-19. doi: 10.1128/AEM.01255-19. Print 2019 Nov 15.


Cholestasis induced by bile duct ligation promotes changes in the intestinal microbiome in mice.

Cabrera-Rubio R, Patterson AM, Cotter PD, Beraza N.

Sci Rep. 2019 Aug 23;9(1):12324. doi: 10.1038/s41598-019-48784-z.


Porcine Feed Efficiency-Associated Intestinal Microbiota and Physiological Traits: Finding Consistent Cross-Locational Biomarkers for Residual Feed Intake.

McCormack UM, Curião T, Metzler-Zebeli BU, Magowan E, Berry DP, Reyer H, Prieto ML, Buzoianu SG, Harrison M, Rebeiz N, Crispie F, Cotter PD, O'Sullivan O, Gardiner GE, Lawlor PG.

mSystems. 2019 Jun 18;4(4). pii: e00324-18. doi: 10.1128/mSystems.00324-18.


Analysis of Health Benefits Conferred by Lactobacillus Species from Kefir.

Slattery C, Cotter PD, O'Toole PW.

Nutrients. 2019 Jun 1;11(6). pii: E1252. doi: 10.3390/nu11061252. Review.


Potential for enriching next-generation health-promoting gut bacteria through prebiotics and other dietary components.

Lordan C, Thapa D, Ross RP, Cotter PD.

Gut Microbes. 2019 May 22:1-20. doi: 10.1080/19490976.2019.1613124. [Epub ahead of print]


Brevibacillus laterosporus strains BGSP7, BGSP9 and BGSP11 isolated from silage produce broad spectrum multi-antimicrobials.

Miljkovic M, Jovanovic S, O'Connor PM, Mirkovic N, Jovcic B, Filipic B, Dinic M, Studholme DJ, Fira D, Cotter PD, Kojic M.

PLoS One. 2019 May 10;14(5):e0216773. doi: 10.1371/journal.pone.0216773. eCollection 2019.


Diversity and composition of the gut microbiota of Atlantic salmon (Salmo salar) farmed in Irish waters.

Fogarty C, Burgess CM, Cotter PD, Cabrera-Rubio R, Whyte P, Smyth C, Bolton DJ.

J Appl Microbiol. 2019 Sep;127(3):648-657. doi: 10.1111/jam.14291. Epub 2019 Jun 28.


Influence of the Intestinal Microbiota on Colonization Resistance to Salmonella and the Shedding Pattern of Naturally Exposed Pigs.

Argüello H, Estellé J, Leonard FC, Crispie F, Cotter PD, O'Sullivan O, Lynch H, Walia K, Duffy G, Lawlor PG, Gardiner GE.

mSystems. 2019 Apr 23;4(2). pii: e00021-19. doi: 10.1128/mSystems.00021-19. eCollection 2019 Mar-Apr.


The dynamics of the antibiotic resistome in the feces of freshly weaned pigs following therapeutic administration of oxytetracycline.

Ghanbari M, Klose V, Crispie F, Cotter PD.

Sci Rep. 2019 Mar 11;9(1):4062. doi: 10.1038/s41598-019-40496-8.


Lactobacillus gasseri APC 678 Reduces Shedding of the Pathogen Clostridium difficile in a Murine Model.

Quigley L, Coakley M, Alemayehu D, Rea MC, Casey PG, O'Sullivan Ó, Murphy E, Kiely B, Cotter PD, Hill C, Ross RP.

Front Microbiol. 2019 Feb 20;10:273. doi: 10.3389/fmicb.2019.00273. eCollection 2019.


Dietary α-lactalbumin alters energy balance, gut microbiota composition and intestinal nutrient transporter expression in high-fat diet-fed mice.

Boscaini S, Cabrera-Rubio R, Speakman JR, Cotter PD, Cryan JF, Nilaweera KN.

Br J Nutr. 2019 May;121(10):1097-1107. doi: 10.1017/S0007114519000461. Epub 2019 Mar 5.


Moderate-intensity aerobic and resistance exercise is safe and favorably influences body composition in patients with quiescent Inflammatory Bowel Disease: a randomized controlled cross-over trial.

Cronin O, Barton W, Moran C, Sheehan D, Whiston R, Nugent H, McCarthy Y, Molloy CB, O'Sullivan O, Cotter PD, Molloy MG, Shanahan F.

BMC Gastroenterol. 2019 Feb 12;19(1):29. doi: 10.1186/s12876-019-0952-x.


Multiparametric liquid biopsy analysis in metastatic prostate cancer.

Hodara E, Morrison G, Cunha A, Zainfeld D, Xu T, Xu Y, Dempsey PW, Pagano PC, Bischoff F, Khurana A, Koo S, Ting M, Cotter PD, Moore MW, Gunn S, Usher J, Rabizadeh S, Danenberg P, Danenberg K, Carpten J, Dorff T, Quinn D, Goldkorn A.

JCI Insight. 2019 Mar 7;4(5). pii: 125529. doi: 10.1172/jci.insight.125529. eCollection 2019 Mar 7.


Short-term consumption of a high-fat diet increases host susceptibility to Listeria monocytogenes infection.

Las Heras V, Clooney AG, Ryan FJ, Cabrera-Rubio R, Casey PG, Hueston CM, Pinheiro J, Rudkin JK, Melgar S, Cotter PD, Hill C, Gahan CGM.

Microbiome. 2019 Jan 18;7(1):7. doi: 10.1186/s40168-019-0621-x.


Biofilms in Food Processing Environments: Challenges and Opportunities.

Alvarez-Ordóñez A, Coughlan LM, Briandet R, Cotter PD.

Annu Rev Food Sci Technol. 2019 Mar 25;10:173-195. doi: 10.1146/annurev-food-032818-121805. Epub 2019 Jan 17.


Bioengineering nisin to overcome the nisin resistance protein.

Field D, Blake T, Mathur H, O' Connor PM, Cotter PD, Paul Ross R, Hill C.

Mol Microbiol. 2019 Mar;111(3):717-731. doi: 10.1111/mmi.14183. Epub 2019 Feb 12.


Functional Characterization of the Lactolisterin BU Gene Cluster of Lactococcus lactis subsp. lactis BGBU1-4.

Miljkovic M, Lozo J, Mirkovic N, O'Connor PM, Malesevic M, Jovcic B, Cotter PD, Kojic M.

Front Microbiol. 2018 Nov 15;9:2774. doi: 10.3389/fmicb.2018.02774. eCollection 2018.


In silico Prediction and Exploration of Potential Bacteriocin Gene Clusters Within the Bacterial Genus Geobacillus.

Egan K, Field D, Ross RP, Cotter PD, Hill C.

Front Microbiol. 2018 Sep 20;9:2116. doi: 10.3389/fmicb.2018.02116. eCollection 2018.


The Human Mesenteric Lymph Node Microbiome Differentiates Between Crohn's Disease and Ulcerative Colitis.

Kiernan MG, Coffey JC, McDermott K, Cotter PD, Cabrera-Rubio R, Kiely PA, Dunne CP.

J Crohns Colitis. 2019 Jan 1;13(1):58-66. doi: 10.1093/ecco-jcc/jjy136.


The rumen microbiome: a crucial consideration when optimising milk and meat production and nitrogen utilisation efficiency.

Matthews C, Crispie F, Lewis E, Reid M, O'Toole PW, Cotter PD.

Gut Microbes. 2019;10(2):115-132. doi: 10.1080/19490976.2018.1505176. Epub 2018 Sep 12. Review.


Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX.

Milani C, Casey E, Lugli GA, Moore R, Kaczorowska J, Feehily C, Mangifesta M, Mancabelli L, Duranti S, Turroni F, Bottacini F, Mahony J, Cotter PD, McAuliffe FM, van Sinderen D, Ventura M.

Microbiome. 2018 Aug 20;6(1):145. doi: 10.1186/s40168-018-0527-z.


Heterologous Expression of Biopreservative Bacteriocins With a View to Low Cost Production.

Mesa-Pereira B, Rea MC, Cotter PD, Hill C, Ross RP.

Front Microbiol. 2018 Jul 26;9:1654. doi: 10.3389/fmicb.2018.01654. eCollection 2018. Review.


Mesophilic Sporeformers Identified in Whey Powder by Using Shotgun Metagenomic Sequencing.

McHugh AJ, Feehily C, Tobin JT, Fenelon MA, Hill C, Cotter PD.

Appl Environ Microbiol. 2018 Oct 1;84(20). pii: e01305-18. doi: 10.1128/AEM.01305-18. Print 2018 Oct 15.


Genomic Characterization of Sulphite Reducing Bacteria Isolated From the Dairy Production Chain.

Doyle CJ, O'Toole PW, Cotter PD.

Front Microbiol. 2018 Jul 5;9:1507. doi: 10.3389/fmicb.2018.01507. eCollection 2018.


Oral Delivery of Nisin in Resistant Starch Based Matrices Alters the Gut Microbiota in Mice.

Gough R, Cabrera Rubio R, O'Connor PM, Crispie F, Brodkorb A, Miao S, Hill C, Ross RP, Cotter PD, Nilaweera KN, Rea MC.

Front Microbiol. 2018 Jun 15;9:1186. doi: 10.3389/fmicb.2018.01186. eCollection 2018.


Sequencing of the Cheese Microbiome and Its Relevance to Industry.

Yeluri Jonnala BR, McSweeney PLH, Sheehan JJ, Cotter PD.

Front Microbiol. 2018 May 23;9:1020. doi: 10.3389/fmicb.2018.01020. eCollection 2018. Review.


Build the Read: A Hands-On Activity for Introducing Microbiology Students to Next-Generation DNA Sequencing and Bioinformatics.

Macori G, Romano A, Decastelli L, Cotter PD.

J Microbiol Biol Educ. 2017 Dec 1;18(3). pii: 18.3.62. doi: 10.1128/jmbe.v18i3.1363. eCollection 2017. No abstract available.


Early Salmonella Typhimurium infection in pigs disrupts Microbiome composition and functionality principally at the ileum mucosa.

Argüello H, Estellé J, Zaldívar-López S, Jiménez-Marín Á, Carvajal A, López-Bascón MA, Crispie F, O'Sullivan O, Cotter PD, Priego-Capote F, Morera L, Garrido JJ.

Sci Rep. 2018 May 17;8(1):7788. doi: 10.1038/s41598-018-26083-3.


A Prospective Metagenomic and Metabolomic Analysis of the Impact of Exercise and/or Whey Protein Supplementation on the Gut Microbiome of Sedentary Adults.

Cronin O, Barton W, Skuse P, Penney NC, Garcia-Perez I, Murphy EF, Woods T, Nugent H, Fanning A, Melgar S, Falvey EC, Holmes E, Cotter PD, O'Sullivan O, Molloy MG, Shanahan F.

mSystems. 2018 Apr 24;3(3). pii: e00044-18. doi: 10.1128/mSystems.00044-18. eCollection 2018 May-Jun.


Fighting biofilms with lantibiotics and other groups of bacteriocins.

Mathur H, Field D, Rea MC, Cotter PD, Hill C, Ross RP.

NPJ Biofilms Microbiomes. 2018 Apr 19;4:9. doi: 10.1038/s41522-018-0053-6. eCollection 2018. Review.


Loss of MicroRNA-21 Influences the Gut Microbiota, Causing Reduced Susceptibility in a Murine Model of Colitis.

Johnston DGW, Williams MA, Thaiss CA, Cabrera-Rubio R, Raverdeau M, McEntee C, Cotter PD, Elinav E, O'Neill LAJ, Corr SC.

J Crohns Colitis. 2018 Jun 28;12(7):835-848. doi: 10.1093/ecco-jcc/jjy038.


Gut microbiota as a source of novel antimicrobials.

Garcia-Gutierrez E, Mayer MJ, Cotter PD, Narbad A.

Gut Microbes. 2019;10(1):1-21. doi: 10.1080/19490976.2018.1455790. Epub 2018 May 22. Review.


Fecal Microbiota Transplantation in Gestating Sows and Neonatal Offspring Alters Lifetime Intestinal Microbiota and Growth in Offspring.

McCormack UM, Curião T, Wilkinson T, Metzler-Zebeli BU, Reyer H, Ryan T, Calderon-Diaz JA, Crispie F, Cotter PD, Creevey CJ, Gardiner GE, Lawlor PG.

mSystems. 2018 Mar 13;3(3). pii: e00134-17. doi: 10.1128/mSystems.00134-17. eCollection 2018 May-Jun.


Species classifier choice is a key consideration when analysing low-complexity food microbiome data.

Walsh AM, Crispie F, O'Sullivan O, Finnegan L, Claesson MJ, Cotter PD.

Microbiome. 2018 Mar 20;6(1):50. doi: 10.1186/s40168-018-0437-0.


Effect of milk centrifugation and incorporation of high heat-treated centrifugate on the microbial composition and levels of volatile organic compounds of Maasdam cheese.

Lamichhane P, Pietrzyk A, Feehily C, Cotter PD, Mannion DT, Kilcawley KN, Kelly AL, Sheehan JJ.

J Dairy Sci. 2018 Jul;101(7):5738-5750. doi: 10.3168/jds.2017-14180. Epub 2018 Mar 15.


Reference Size Matching, Whole-Genome Amplification, and Fluorescent Labeling as a Method for Chromosomal Microarray Analysis of Clinically Actionable Copy Number Alterations in Formalin-Fixed, Paraffin-Embedded Tumor Tissue.

Gunn SR, Govender S, Sims CL, Khurana A, Koo S, Scoggin J, Moore MW, Cotter PD.

J Mol Diagn. 2018 May;20(3):279-288. doi: 10.1016/j.jmoldx.2018.01.004. Epub 2018 Feb 19.


Omics-Based Insights into Flavor Development and Microbial Succession within Surface-Ripened Cheese.

Bertuzzi AS, Walsh AM, Sheehan JJ, Cotter PD, Crispie F, McSweeney PLH, Kilcawley KN, Rea MC.

mSystems. 2018 Jan 30;3(1). pii: e00211-17. doi: 10.1128/mSystems.00211-17. eCollection 2018 Jan-Feb.


The intestinal protist Blastocystis is not a common member of the healthy infant gut microbiota in a Westernized country (Ireland).

Scanlan PD, Hill CJ, Ross RP, Ryan CA, Stanton C, Cotter PD.

Parasitology. 2018 Sep;145(10):1274-1278. doi: 10.1017/S0031182018000033. Epub 2018 Feb 5.


Mosaicism for structural non-centromeric autosomal rearrangement in prenatal diagnoses: evidence for sex-specific selection against chromosomal abnormalities.

Kovaleva NV, Cotter PD.

Mol Cytogenet. 2017 Dec 11;10:45. doi: 10.1186/s13039-017-0346-0. eCollection 2017. Review.


Post-weaning social isolation of rats leads to long-term disruption of the gut microbiota-immune-brain axis.

Dunphy-Doherty F, O'Mahony SM, Peterson VL, O'Sullivan O, Crispie F, Cotter PD, Wigmore P, King MV, Cryan JF, Fone KCF.

Brain Behav Immun. 2018 Feb;68:261-273. doi: 10.1016/j.bbi.2017.10.024. Epub 2017 Nov 6.


Genome Sequence of Geobacillus stearothermophilus DSM 458, an Antimicrobial-Producing Thermophilic Bacterium, Isolated from a Sugar Beet Factory.

Egan K, Kelleher P, Field D, Rea MC, Ross RP, Cotter PD, Hill C.

Genome Announc. 2017 Oct 26;5(43). pii: e01172-17. doi: 10.1128/genomeA.01172-17.


Plantaricyclin A, a Novel Circular Bacteriocin Produced by Lactobacillus plantarum NI326: Purification, Characterization, and Heterologous Production.

Borrero J, Kelly E, O'Connor PM, Kelleher P, Scully C, Cotter PD, Mahony J, van Sinderen D.

Appl Environ Microbiol. 2017 Dec 15;84(1). pii: e01801-17. doi: 10.1128/AEM.01801-17. Print 2018 Jan 1.


Novel insights into the microbiology of fermented dairy foods.

Macori G, Cotter PD.

Curr Opin Biotechnol. 2018 Feb;49:172-178. doi: 10.1016/j.copbio.2017.09.002. Epub 2017 Sep 29. Review.


Lack of Heterogeneity in Bacteriocin Production Across a Selection of Commercial Probiotic Products.

Hegarty JW, Guinane CM, Ross RP, Hill C, Cotter PD.

Probiotics Antimicrob Proteins. 2017 Dec;9(4):459-465. doi: 10.1007/s12602-017-9326-2.


Crop Establishment Practices Are a Driver of the Plant Microbiota in Winter Oilseed Rape (Brassica napus).

Rathore R, Dowling DN, Forristal PD, Spink J, Cotter PD, Bulgarelli D, Germaine KJ.

Front Microbiol. 2017 Aug 9;8:1489. doi: 10.3389/fmicb.2017.01489. eCollection 2017.


Lactolisterin BU, a Novel Class II Broad-Spectrum Bacteriocin from Lactococcus lactis subsp. lactis bv. diacetylactis BGBU1-4.

Lozo J, Mirkovic N, O'Connor PM, Malesevic M, Miljkovic M, Polovic N, Jovcic B, Cotter PD, Kojic M.

Appl Environ Microbiol. 2017 Oct 17;83(21). pii: e01519-17. doi: 10.1128/AEM.01519-17. Print 2017 Nov 1.

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