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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 Feb 19. pii: S1525-1578(17)30253-2. doi: 10.1016/j.jmoldx.2018.01.004. [Epub ahead of print]


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 Feb 5:1-5. doi: 10.1017/S0031182018000033. [Epub ahead of print]


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.


The Fungal Frontier: A Comparative Analysis of Methods Used in the Study of the Human Gut Mycobiome.

Huseyin CE, Rubio RC, O'Sullivan O, Cotter PD, Scanlan PD.

Front Microbiol. 2017 Jul 31;8:1432. doi: 10.3389/fmicb.2017.01432. eCollection 2017.


Metagenome-based surveillance and diagnostic approaches to studying the microbial ecology of food production and processing environments.

Doyle CJ, O'Toole PW, Cotter PD.

Environ Microbiol. 2017 Nov;19(11):4382-4391. doi: 10.1111/1462-2920.13859. Epub 2017 Sep 14. Review.


Bacteriocin-Antimicrobial Synergy: A Medical and Food Perspective.

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

Front Microbiol. 2017 Jun 29;8:1205. doi: 10.3389/fmicb.2017.01205. eCollection 2017. Review.


Whole-Genome Shotgun Sequence of Salmonella bongori, First Isolated in Northwestern Italy.

Romano A, Bellio A, Macori G, Cotter PD, Bianchi DM, Gallina S, Decastelli L.

Genome Announc. 2017 Jul 6;5(27). pii: e00560-17. doi: 10.1128/genomeA.00560-17.


Strain-Level Metagenomic Analysis of the Fermented Dairy Beverage Nunu Highlights Potential Food Safety Risks.

Walsh AM, Crispie F, Daari K, O'Sullivan O, Martin JC, Arthur CT, Claesson MJ, Scott KP, Cotter PD.

Appl Environ Microbiol. 2017 Aug 1;83(16). pii: e01144-17. doi: 10.1128/AEM.01144-17. Print 2017 Aug 15.


Controlled functional expression of the bacteriocins pediocin PA-1 and bactofencin A in Escherichia coli.

Mesa-Pereira B, O'Connor PM, Rea MC, Cotter PD, Hill C, Ross RP.

Sci Rep. 2017 Jun 8;7(1):3069. doi: 10.1038/s41598-017-02868-w.


High-throughput metataxonomic characterization of the raw milk microbiota identifies changes reflecting lactation stage and storage conditions.

Doyle CJ, Gleeson D, O'Toole PW, Cotter PD.

Int J Food Microbiol. 2017 Aug 16;255:1-6. doi: 10.1016/j.ijfoodmicro.2017.05.019. Epub 2017 May 22.


Exploring a Possible Link between the Intestinal Microbiota and Feed Efficiency in Pigs.

McCormack UM, Curião T, Buzoianu SG, Prieto ML, Ryan T, Varley P, Crispie F, Magowan E, Metzler-Zebeli BU, Berry D, O'Sullivan O, Cotter PD, Gardiner GE, Lawlor PG.

Appl Environ Microbiol. 2017 Jul 17;83(15). pii: e00380-17. doi: 10.1128/AEM.00380-17. Print 2017 Aug 1.


Insights into the Mode of Action of the Sactibiotic Thuricin CD.

Mathur H, Fallico V, O'Connor PM, Rea MC, Cotter PD, Hill C, Ross RP.

Front Microbiol. 2017 Apr 20;8:696. doi: 10.3389/fmicb.2017.00696. eCollection 2017.


A Profile Hidden Markov Model to investigate the distribution and frequency of LanB-encoding lantibiotic modification genes in the human oral and gut microbiome.

Walsh CJ, Guinane CM, O' Toole PW, Cotter PD.

PeerJ. 2017 Apr 27;5:e3254. doi: 10.7717/peerj.3254. eCollection 2017.


Erratum to: The altered gut microbiota in adults with cystic fibrosis.

Burke DG, Fouhy F, Harrison MJ, Rea MC, Cotter PD, O'Sullivan O, Stanton C, Hill C, Shanahan F, Plant BJ, Ross RP.

BMC Microbiol. 2017 Apr 27;17(1):102. doi: 10.1186/s12866-017-1006-6. No abstract available.


'Microbes in sport' -The potential role of the gut microbiota in athlete health and performance.

Rankin A, O'Donavon C, Madigan SM, O'Sullivan O, Cotter PD.

Br J Sports Med. 2017 May;51(9):698-699. doi: 10.1136/bjsports-2016-097227. Epub 2017 Jan 25. No abstract available.


Forgotten fungi-the gut mycobiome in human health and disease.

Huseyin CE, O'Toole PW, Cotter PD, Scanlan PD.

FEMS Microbiol Rev. 2017 Jul 1;41(4):479-511. doi: 10.1093/femsre/fuw047. Review.


Use of enhanced nisin derivatives in combination with food-grade oils or citric acid to control Cronobacter sakazakii and Escherichia coli O157:H7.

Campion A, Morrissey R, Field D, Cotter PD, Hill C, Ross RP.

Food Microbiol. 2017 Aug;65:254-263. doi: 10.1016/ Epub 2017 Feb 7.


The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level.

Barton W, Penney NC, Cronin O, Garcia-Perez I, Molloy MG, Holmes E, Shanahan F, Cotter PD, O'Sullivan O.

Gut. 2018 Apr;67(4):625-633. doi: 10.1136/gutjnl-2016-313627. Epub 2017 Mar 30.


Whey protein effects on energy balance link the intestinal mechanisms of energy absorption with adiposity and hypothalamic neuropeptide gene expression.

Nilaweera KN, Cabrera-Rubio R, Speakman JR, O'Connor PM, McAuliffe A, Guinane CM, Lawton EM, Crispie F, Aguilera M, Stanley M, Boscaini S, Joyce S, Melgar S, Cryan JF, Cotter PD.

Am J Physiol Endocrinol Metab. 2017 Jul 1;313(1):E1-E11. doi: 10.1152/ajpendo.00356.2016. Epub 2017 Mar 21.


The altered gut microbiota in adults with cystic fibrosis.

Burke DG, Fouhy F, Harrison MJ, Rea MC, Cotter PD, O'Sullivan O, Stanton C, Hill C, Shanahan F, Plant BJ, Ross RP.

BMC Microbiol. 2017 Mar 9;17(1):58. doi: 10.1186/s12866-017-0968-8. Erratum in: BMC Microbiol. 2017 Apr 27;17 (1):102.


Correction for Walsh et al., Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir.

Walsh AM, Crispie F, Kilcawley K, O'Sullivan O, O'Sullivan MG, Claesson MJ, Cotter PD.

mSystems. 2017 Feb 21;2(1). pii: e00003-17. doi: 10.1128/mSystems.00003-17. eCollection 2017 Jan-Feb.


Unravelling the metabolic impact of SBS-associated microbial dysbiosis: Insights from the piglet short bowel syndrome model.

Pereira-Fantini PM, Byars SG, Pitt J, Lapthorne S, Fouhy F, Cotter PD, Bines JE.

Sci Rep. 2017 Feb 23;7:43326. doi: 10.1038/srep43326.


The influence of rosuvastatin on the gastrointestinal microbiota and host gene expression profiles.

Nolan JA, Skuse P, Govindarajan K, Patterson E, Konstantinidou N, Casey PG, MacSharry J, Shanahan F, Stanton C, Hill C, Cotter PD, Joyce SA, Gahan CGM.

Am J Physiol Gastrointest Liver Physiol. 2017 May 1;312(5):G488-G497. doi: 10.1152/ajpgi.00149.2016. Epub 2017 Feb 16.


Detection and Enumeration of Spore-Forming Bacteria in Powdered Dairy Products.

McHugh AJ, Feehily C, Hill C, Cotter PD.

Front Microbiol. 2017 Jan 31;8:109. doi: 10.3389/fmicb.2017.00109. eCollection 2017. Review.


Drunk bugs: Chronic vapour alcohol exposure induces marked changes in the gut microbiome in mice.

Peterson VL, Jury NJ, Cabrera-Rubio R, Draper LA, Crispie F, Cotter PD, Dinan TG, Holmes A, Cryan JF.

Behav Brain Res. 2017 Apr 14;323:172-176. doi: 10.1016/j.bbr.2017.01.049. Epub 2017 Feb 1.


Translating Omics to Food Microbiology.

Walsh AM, Crispie F, Claesson MJ, Cotter PD.

Annu Rev Food Sci Technol. 2017 Feb 28;8:113-134. doi: 10.1146/annurev-food-030216-025729. Epub 2017 Jan 11.


Gut microbiota: implications for sports and exercise medicine.

Cronin O, O'Sullivan O, Barton W, Cotter PD, Molloy MG, Shanahan F.

Br J Sports Med. 2017 May;51(9):700-701. doi: 10.1136/bjsports-2016-097225. Epub 2017 Jan 11. No abstract available.


Health benefits of fermented foods: microbiota and beyond.

Marco ML, Heeney D, Binda S, Cifelli CJ, Cotter PD, Foligné B, Gänzle M, Kort R, Pasin G, Pihlanto A, Smid EJ, Hutkins R.

Curr Opin Biotechnol. 2017 Apr;44:94-102. doi: 10.1016/j.copbio.2016.11.010. Epub 2016 Dec 18. Review.


A Bioengineered Nisin Derivative, M21A, in Combination with Food Grade Additives Eradicates Biofilms of Listeria monocytogenes.

Smith MK, Draper LA, Hazelhoff PJ, Cotter PD, Ross RP, Hill C.

Front Microbiol. 2016 Nov 30;7:1939. eCollection 2016.


Bacteriocin production: a relatively unharnessed probiotic trait?

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

F1000Res. 2016 Oct 27;5:2587. eCollection 2016. Review.


Synergistic Nisin-Polymyxin Combinations for the Control of Pseudomonas Biofilm Formation.

Field D, Seisling N, Cotter PD, Ross RP, Hill C.

Front Microbiol. 2016 Oct 26;7:1713. eCollection 2016.


Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir.

Walsh AM, Crispie F, Kilcawley K, O'Sullivan O, O'Sullivan MG, Claesson MJ, Cotter PD.

mSystems. 2016 Oct 4;1(5). pii: e00052-16. eCollection 2016 Sep-Oct. Erratum in: mSystems. 2017 Feb 21;2(1):.


Thermus and the Pink Discoloration Defect in Cheese.

Quigley L, O'Sullivan DJ, Daly D, O'Sullivan O, Burdikova Z, Vana R, Beresford TP, Ross RP, Fitzgerald GF, McSweeney PL, Giblin L, Sheehan JJ, Cotter PD.

mSystems. 2016 Jun 14;1(3). pii: e00023-16. eCollection 2016 May-Jun.


Impacts of Seasonal Housing and Teat Preparation on Raw Milk Microbiota: a High-Throughput Sequencing Study.

Doyle CJ, Gleeson D, O'Toole PW, Cotter PD.

Appl Environ Microbiol. 2016 Dec 30;83(2). pii: e02694-16. doi: 10.1128/AEM.02694-16. Print 2017 Jan 15.


New Weapons to Fight Old Enemies: Novel Strategies for the (Bio)control of Bacterial Biofilms in the Food Industry.

Coughlan LM, Cotter PD, Hill C, Alvarez-Ordóñez A.

Front Microbiol. 2016 Oct 18;7:1641. eCollection 2016. Review.


Prevalence and genetic diversity of Blastocystis in family units living in the United States.

Scanlan PD, Knight R, Song SJ, Ackermann G, Cotter PD.

Infect Genet Evol. 2016 Nov;45:95-97. doi: 10.1016/j.meegid.2016.08.018. Epub 2016 Aug 18.


16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform.

Fouhy F, Clooney AG, Stanton C, Claesson MJ, Cotter PD.

BMC Microbiol. 2016 Jun 24;16(1):123. doi: 10.1186/s12866-016-0738-z.


The Microbiota and Health Promoting Characteristics of the Fermented Beverage Kefir.

Bourrie BC, Willing BP, Cotter PD.

Front Microbiol. 2016 May 4;7:647. doi: 10.3389/fmicb.2016.00647. eCollection 2016. Review.


The bacteriocin bactofencin A subtly modulates gut microbial populations.

Guinane CM, Lawton EM, O'Connor PM, O'Sullivan Ó, Hill C, Ross RP, Cotter PD.

Anaerobe. 2016 Aug;40:41-9. doi: 10.1016/j.anaerobe.2016.05.001. Epub 2016 May 3.


In Vitro Activities of Nisin and Nisin Derivatives Alone and In Combination with Antibiotics against Staphylococcus Biofilms.

Field D, O' Connor R, Cotter PD, Ross RP, Hill C.

Front Microbiol. 2016 Apr 18;7:508. doi: 10.3389/fmicb.2016.00508. eCollection 2016.

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