Cotter, Paul D.

Fermented-food metagenomics reveals substrate-associated differences in taxonomy and health-associated and antibiotic resistance determinants

Leech, J., Cabrera-Rubio, R., Walsh, A. M., Macori, G., Walsh, C. J., Barton, W., Finnegan, L., Crispie, F., O’Sullivan, O., Claesson, M. J., et al. (2020) · mSystems

Probiotics and Fermented FoodsGut microbiota and health

Cited by 200

Metabolome-microbiome signatures in the fermented beverage, Kombucha

Villarreal-Soto, S. A., Bouajila, J., Pace, M., Leech, J., Cotter, P. D., Souchard, J.-P., Taillandier, P., & Beaufort, S. (2020) · International Journal of Food Microbiology

Probiotics and Fermented FoodsFermentation and Sensory Analysis

Cited by 196

The altered gut microbiota in adults with cystic fibrosis

Burke, D. G., Fouhy, F., Harrison, M. J., Rea, M. C., Cotter, P. D., O’Sullivan, O., Stanton, C., Hill, C., Shanahan, F., Plant, B. J., et al. (2017) · BMC Microbiology

Gut microbiota and healthCystic Fibrosis Research Advances

Cited by 179

Sequencing of the cheese microbiome and its relevance to industry

Yeluri Jonnala, B. R., McSweeney, P. L. H., Sheehan, J. J., & Cotter, P. D. (2018) · Frontiers in Microbiology

Probiotics and Fermented FoodsFermentation and Sensory Analysis

Cited by 160

Bacteriocin production: A relatively unharnessed probiotic trait?

Hegarty, J. W., Guinane, C. M., Ross, R. P., Hill, C., & Cotter, P. D. (2016) · F1000Research

Probiotics and Fermented FoodsAnimal Nutrition and Physiology

Cited by 141

Meta-analysis of cheese microbiomes highlights contributions to multiple aspects of quality

Walsh, A. M., Macori, G., Kilcawley, K. N., & Cotter, P. D. (2020) · Nature Food

Probiotics and Fermented FoodsBacteriophages and microbial interactions

Cited by 133

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

O’Donovan, C. M., Madigan, S. M., Garcia-Perez, I., Rankin, A., O’ Sullivan, O., & Cotter, P. D. (2020) · Journal of Science and Medicine in Sport

Gut microbiota and healthProbiotics and Fermented Foods

Cited by 133

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

Dunphy-Doherty, F., O'Mahony, S. M., Peterson, V. L., O'Sullivan, O., Crispie, F., Cotter, P. D., Wigmore, P., King, M. V., Cryan, J. F., & Fone, K. C. F. (2018) · Brain, Behavior, and Immunity

Gut microbiota and healthTryptophan and brain disorders

Cited by 124

Distinct actions of the fermented beverage kefir on host behaviour, immunity and microbiome gut-brain modules in the mouse

de Wouw, M. V., Walsh, A. M., Crispie, F., Leuven, L. V., Lyte, J. M., Boehme, M., Clarke, G., Dinan, T. G., Cotter, P. D., & Cryan, J. (2020) · Microbiome

Gut microbiota and healthProbiotics and Fermented Foods

Cited by 123

Distinct actions of the fermented beverage kefir on host behaviour, immunity and microbiome gut-brain modules in the mouse

van de Wouw, M., Walsh, A. M., Crispie, F., van Leuven, L., Lyte, J. M., Boehme, M., Clarke, G., Dinan, T. G., Cotter, P. D., & Cryan, J. F. (2020) · Microbiome

Gut microbiota and healthProbiotics and Fermented Foods

Cited by 123

The individual-specific and diverse nature of the preterm infant microbiota

Barrett, E., Kerr, C., Murphy, K., O'Sullivan, O., Ryan, C. A., Dempsey, E. M., Murphy, B. P., O'Toole, P. W., Cotter, P. D., Fitzgerald, G. F., et al. (2013) · Archives of Disease in Childhood - Fetal and Neonatal Edition

Gut microbiota and healthInfant Nutrition and Health

Cited by 120

Four men in a boat: Ultra-endurance exercise alters the gut microbiome

Keohane, D. M., Woods, T., O’Connor, P., Underwood, S., Cronin, O., Whiston, R., O'Sullivan, O., Cotter, P., Shanahan, F., & Molloy, M. G. M. (2019) · Journal of Science and Medicine in Sport

Gut microbiota and healthProbiotics and Fermented Foods

Cited by 113

The need for an integrated multi-OMICs approach in microbiome science in the food system

Ferrocino, I., Rantsiou, K., McClure, R., Kostic, T., de Souza, R. S. C., Lange, L., FitzGerald, J., Kriaa, A., Cotter, P., Maguin, E., et al. (2023) · Comprehensive Reviews in Food Science and Food Safety

Gut microbiota and healthProbiotics and Fermented Foods

Cited by 110

Protein Quality and the Protein to Carbohydrate Ratio within a High Fat Diet Influences Energy Balance and the Gut Microbiota In C57BL/6J Mice

McAllan, L., Skuse, P., Cotter, P. D., Connor, P. O., Cryan, J. F., Ross, R. P., Fitzgerald, G., Roche, H. M., & Nilaweera, K. N. (2014) · PLoS ONE

Gut microbiota and healthDiet, Metabolism, and Disease

Cited by 106

Enduring behavioral effects induced by birth by caesarean section in the mouse

Morais, L. H., Golubeva, A. V., Moloney, G. M., Moya-Pérez, A., Ventura-Silva, A. P., Arboleya, S., Bastiaanssen, T. F. S., O’Sullivan, O., Rea, K., Borre, Y., et al. (2020) · Current Biology

Gut microbiota and healthMaternal and Perinatal Health Interventions

Cited by 104

FoodMicrobionet: A Database for the Visualisation and Exploration of Food Bacterial Communities Based on Network Analysis

Parente, E., Cocolin, L., De Filippis, F., Zotta, T., Ferrocino, I., O'Sullivan, O., Neviani, E., De Angelis, M., Cotter, P. D., & Ercolini, D. (2016) · International Journal of Food Microbiology

Probiotics and Fermented FoodsGut microbiota and health

Cited by 82

Traditional kefir reduces weight gain and improves plasma and liver lipid profiles more successfully than a commercial equivalent in a mouse model of obesity

Bourrie, B. C. T., Cotter, P. D., & Willing, B. P. (2018) · Journal of Functional Foods

Probiotics and Fermented FoodsGut microbiota and health

Cited by 64

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

Cabrera-Rubio, R., Patterson, A. M., Cotter, P. D., & Beraza, N. (2019) · Scientific Reports

Gut microbiota and healthGastrointestinal motility and disorders

Cited by 61

‘Microbes in sport’ – The potential role of the gut microbiota in athlete health and performance

Rankin, A., O’Donavon, C., Madigan, S. M., O’Sullivan, O., & Cotter, P. D. (2017) · British Journal of Sports Medicine

Gut microbiota and healthProbiotics and Fermented Foods

Cited by 38

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

Nilaweera, K. N., Cabrera-Rubio, R., Speakman, J. R., O’Connor, P. M., McAuliffe, A., Guinane, C. M., Lawton, E. M., Crispie, F., Aguilera, M., Stanley, M., et al. (2017) · American Journal of Physiology-Endocrinology and Metabolism

Regulation of Appetite and ObesityAdipokines, Inflammation, and Metabolic Diseases

Cited by 32

Applications of Lactic Acid Bacteria‐Produced Bacteriocins

Collins, B., Cotter, P. D., Hill, C., & Ross, P. (2010) · Biotechnology of Lactic Acid Bacteria

Probiotics and Fermented FoodsBacteriophages and microbial interactions

Cited by 32

Strain-level variation among vaginal Lactobacillus crispatus and Lactobacillus iners as identified by comparative metagenomics

Nori, S. R. C., Walsh, C. J., McAuliffe, F. M., Moore, R. L., Van Sinderen, D., Feehily, C., & Cotter, P. D. (2025) · npj Biofilms and Microbiomes

Reproductive tract infections researchGut microbiota and health

Cited by 29

The detailed analysis of the microbiome and resistome of artisanal blue-veined cheeses provides evidence on sources and patterns of succession linked with quality and safety traits

Alexa, E. A., Cobo-Díaz, J. F., Renes, E., O´Callaghan, T. F., Kilcawley, K., Mannion, D., Skibinska, I., Ruiz, L., Margolles, A., Fernández-Gómez, P., et al. (2024) · Microbiome

Probiotics and Fermented FoodsAntibiotic Resistance in Bacteria

Cited by 28

Re: Gut microbiota depletion from early adolescence in mice: Implications for brain and behaviour

Desbonnet, L., Clarke, G., O’Sullivan, O., Cotter, P. D., Dinan, T. G., & Cryan, J. F. (2015) · Brain, Behavior, and Immunity

Gut microbiota and healthNeuroendocrine regulation and behavior

Cited by 24