Publications by authors named "Paul D Cotter"

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Fermented foods: Harnessing their potential to modulate the microbiota-gut-brain axis for mental health.
Ramya Balasubramanian, Elizabeth Schneider, Eoin Gunnigle, Paul D Cotter, John F Cryan

Neurosci Biobehav Rev· March 2024

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Distinct actions of the fermented beverage kefir on host behaviour, immunity and microbiome gut-brain modules in the mouse.
Marcel van de Wouw, Aaron M Walsh, Fiona Crispie, Lucas van Leuven, Joshua M Lyte, Marcus Boehme, Gerard Clarke, Timothy G Dinan, Paul D Cotter, John F Cryan

Microbiome· May 2020

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Health benefits of fermented foods: microbiota and beyond.
Maria L Marco, Dustin Heeney, Sylvie Binda, Christopher J Cifelli, Paul D Cotter, Benoit Foligné, Michael Gänzle, Remco Kort, Gonca Pasin, Anne Pihlanto

April 2017

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The Microbiota and Health Promoting Characteristics of the Fermented Beverage Kefir.
Benjamin C T Bourrie, Benjamin P Willing, Paul D Cotter

May 2016

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Breastfeeding and the milk resistome shape the establishment and transmission of antibiotic resistance genes in the infant gut microbiome.
Zhe Pan, Calum J Walsh, Conor Feehily, Sai Ravi Chandra Nori, Fionnuala M McAuliffe, Paul D Cotter

Gut Microbes· December 2025

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Effects of a combined energy restriction and vigorous-intensity exercise intervention on the human gut microbiome: A randomised controlled trial.
Russell G Davies, Laura A Wood, Aaron Hengist, Ciara O'Donovan, Wiley Barton, Paul D Cotter

J Physiol· December 2025

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Water kefir multi-omics reveals functional redundancies despite taxonomic differences and the underappreciated contribution of yeast.
Samuel Breselge, Luiza de Paula Dias Moreira, Iwona Skibinska, Xiaofei Yin, Lorraine Brennan, Paul D Cotter

NPJ Sci Food· December 2025

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Cottage cheese, a relatively underexplored cultured dairy product with potential health benefits?
Dominic N Farsi, Harsh Mathur, Tom Beresford, Paul D Cotter

Crit Rev Food Sci Nutr· November 2025

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Effects of kefir on symptoms, sleep, and gut microbiota in children with ADHD: a randomised controlled trial.
Kate Lawrence, Philippa Fibert, Miguel Toribio-Mateas, Alice M Gregory, Jemima Hobbs, Paul D Cotter

BMC Psychiatry· November 2025

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Maternal immune activation and antibiotics affect offspring neurodevelopment, behaviour, and microbiome.
Clara Deady, Jamie FitzGerald, Nirit Kara, Martina Mazzocchi, Adam O'Mahony, Paul D Cotter

Brain Behav Immun Health· October 2025

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Stress and depression risk in pregnancy associates with altered immune function.
Grace Mealy, Sofia Hempelmann Perez, Kiva Brennan, Sophie Callanan, Radka Saldova, Paul D Cotter

World J Biol Psychiatry· October 2025

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Health benefits of ethnic fermented foods.
Dushica Santa, Melanie Huch, Dominic A Stoll, Hülya Cunedioglu, Reimo Priidik, Paul D Cotter

Front Nutr· October 2025

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Genomic characterisation of recurrent Mycobacterium avium isolates from chronically infected patients reveals patterns of within-host evolution.
Aaron M Walsh, Emma Roycroft, Kate Hinchion, Sharee A Basdeo, Frederick J Sheedy, Paul D Cotter

Genome Med· October 2025

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Impact of fermented foods consumption on gastrointestinal wellbeing in healthy adults: a systematic review and meta-analysis.
Arghya Mukherjee, Dominic N Farsi, Enriqueta Garcia-Gutierrez, Ecem Akan, Jose Angel Salas Millan, Paul D Cotter

Front Nutr· October 2025

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Effects of feeding a simulated waste milk on growth, health, fecal microbiota, and antibiotic resistance in dairy heifer calves.
Anna Flynn, Wiley Barton, Catherine McAloon, Marie McFadden, Fiona Crispie, Paul D Cotter

J Dairy Sci· August 2025

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The food-associated resistome is shaped by processing and production environments.
Narciso M Quijada, José F Cobo-Díaz, Vincenzo Valentino, Coral Barcenilla, Francesca De Filippis, Paul D Cotter

Nat Microbiol· August 2025

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Exploring the Functional Potential of the Broiler Gut Microbiome Using Shotgun Metagenomics.
Nuria Peña, Irene Lafuente, Ester Sevillano, Javier Feito, Gastón Allendez, Paul D Cotter

Genes (Basel)· August 2025

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Faecal microbiota and serum metabolome association with equine metabolic syndrome in connemara ponies.
Ahmed Saleh Al-Ansari, Vivienne Duggan, Grace Mulcahy, Xiaofei Yin, Lorraine Brennan, Paul D Cotter

BMC Vet Res· July 2025

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Development of a bio-functional fermented soy beverage supplemented with microbial exopolysaccharides and its effect on the human gut microbiome .
Giulia Bisson, Clara Comuzzi, Jamie A FitzGerald, Arghya Mukherjee, Niccolò Renoldi, Paul D Cotter

Food Funct· July 2025

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Vitamin biosynthesis in the gut: interplay between mammalian host and its resident microbiota.
Chiara Tarracchini, Cathy Lordan, Christian Milani, Luiza P D Moreira, Qusai M Alabedallat, Paul D Cotter

Microbiol Mol Biol Rev· June 2025

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The effects of offering adequate-quality or high-quality colostrum on the passive immunity, health, growth, and fecal microbiome development of dairy heifer calves.
Anna Flynn, John Leech, Marie McFadden, Catherine McAloon, John Paul Murphy, Paul D Cotter

J Dairy Sci· June 2025

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OPTIMATRIX v2.0: Optimised protocol to mitigate microbial blooms in the micro-Matrix bioreactor platform used as an human distal colon model.
Arghya Mukherjee, Nicola Ferremi Leali, Elisa Salvetti, Sandra Torriani, Paul D Cotter

MethodsX· June 2025

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Gene-trait matching among strains reveals various glycan metabolism loci including a strain-specific fucosyllactose utilization cluster.
Ortensia Catalano Gonzaga, Stephen McKenna, Ian O'Neill, Paul D Cotter, Fionnuala M McAuliffe

Front Microbiol· May 2025

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A genomics-based investigation of acetic acid bacteria across a global fermented food metagenomics dataset.
Erkang Zhang, Samuel Breselge, Niccolò Carlino, Nicola Segata, Marcus J Claesson, Paul D Cotter

iScience· April 2025

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The core microbiomes and associated metabolic potential of water kefir as revealed by pan multi-omics.
Samuel Breselge, Iwona Skibinska, Xiaofei Yin, Lorraine Brennan, Kieran Kilcawley, Paul D Cotter

Commun Biol· March 2025

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Strain-level variation among vaginal Lactobacillus crispatus and Lactobacillus iners as identified by comparative metagenomics.
Sai Ravi Chandra Nori, Calum J Walsh, Fionnuala M McAuliffe, Rebecca L Moore, Douwe Van Sinderen, Paul D Cotter

NPJ Biofilms Microbiomes· March 2025

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Temporal stability and lack of variance in microbiome composition and functionality in fit recreational athletes.
Ciara M O' Donovan, Sai Ravi Chandra Nori, Fergus Shanahan, Gerardina Celentano, Thomas Brendan Murphy, Paul D Cotter

Sci Rep· February 2025

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Bactofencin A Displays a Delayed Killing Effect on a Clinical Strain of Which Is Greatly Accelerated in the Presence of Nisin.
Paula M O'Connor, Paul D Cotter, Colin Hill, R Paul Ross

Antibiotics (Basel)· February 2025

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Evaluating the efficiency of 16S-ITS-23S operon sequencing for species level resolution in microbial communities.
Meghana Srinivas, Calum J Walsh, Fiona Crispie, Orla O'Sullivan, Paul D Cotter

Sci Rep· January 2025

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