Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome von Pasolli, Edoardo, De Filippis, Francesca, Mauriello, Italia E., Cumbo, Fabio, Walsh, Aaron M., Leech, John, Cotter, Paul D., Segata, Nicola, Ercolini, Danilo

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Microbiome definition re-visited: old concepts and new challenges von Berg, Gabriele, Rybakova, Daria, Fischer, Doreen, Cernava, Tomislav, Vergès, Marie-Christine Champomier, Charles, Trevor, Chen, Xiaoyulong, Cocolin, Luca, Eversole, Kellye, Corral, Gema Herrero, Kazou, Maria, Kinkel, Linda, Lange, Lene, Lima, Nelson, Loy, Alexander, Macklin, James A, Maguin, Emmanuelle, Mauchline, Tim, McClure, Ryan, Mitter, Birgit, Ryan, Matthew, Sarand, Inga, Smidt, Hauke, Schelkle, Bettina, Roume, Hugo, Kiran, G Seghal, Selvin, Joseph, Souza, Rafael Soares Correa de, van Overbeek, Leo, Singh, Brajesh K, Wagner, Michael, Walsh, Aaron, Sessitsch, Angela, Schloter, Michael

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Fermented-Food Metagenomics Reveals Substrate-Associated Differences in Taxonomy and Health-Associated and Antibiotic Resistance Determinants von Leech, John, Cabrera-Rubio, Raul, Walsh, Aaron M, Macori, Guerrino, Walsh, Calum J, Barton, Wiley, Finnegan, Laura, Crispie, Fiona, O'Sullivan, Orla, Claesson, Marcus J, Cotter, Paul D

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Strain-Level Metagenomic Analysis of the Fermented Dairy Beverage Nunu Highlights Potential Food Safety Risks von Walsh, Aaron M, Crispie, Fiona, Daari, Kareem, O'Sullivan, Orla, Martin, Jennifer C, Arthur, Cornelius T, Claesson, Marcus J, Scott, Karen P, Cotter, Paul D

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Integrated molecular approaches for fermented food microbiome research von Walsh, Aaron M, Leech, John, Huttenhower, Curtis, Delhomme-Nguyen, Hue, Crispie, Fiona, Chervaux, Christian, Cotter, Paul D

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Meta-analysis of cheese microbiomes highlights contributions to multiple aspects of quality von Walsh, Aaron M, Macori, Guerrino, Kilcawley, Kieran N, Cotter, Paul D

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Mechanistic Insights of a Concerted Metalation–Deprotonation Reaction with [CpRhCl2]2 von Walsh, Aaron P, Jones, William D

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Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir von Walsh, Aaron M, Crispie, Fiona, Kilcawley, Kieran, O'Sullivan, Orla, O'Sullivan, Maurice G, Claesson, Marcus J, Cotter, Paul D

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Translating Omics to Food Microbiology von Walsh, Aaron M, Crispie, Fiona, Claesson, Marcus J, Cotter, Paul D

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Kefir ameliorates specific microbiota-gut-brain axis impairments in a mouse model relevant to autism spectrum disorder von van de Wouw, Marcel, Walsh, Calum J., Vigano, Giulia M.D., Lyte, Joshua M., Boehme, Marcus, Gual-Grau, Andreu, Crispie, Fiona, Walsh, Aaron M., Clarke, Gerard, Dinan, Timothy G., Cotter, Paul D., Cryan, John F.

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

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Species classifier choice is a key consideration when analysing low-complexity food microbiome data von Walsh, Aaron M, Crispie, Fiona, O'Sullivan, Orla, Finnegan, Laura, Claesson, Marcus J, Cotter, Paul D

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Using Surface Amide Couplings to Assemble Photocathodes for Solar Fuel Production Applications von Materna, Kelly L, Lalaoui, Noémie, Laureanti, Joseph A, Walsh, Aaron P, Rimgard, Belinda Pettersson, Lomoth, Reiner, Thapper, Anders, Ott, Sascha, Shaw, Wendy J, Tian, Haining, Hammarström, Leif

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Insights into the Adolescent Cystic Fibrosis Airway Microbiome Using Shotgun Metagenomics von McDermott, Gillian, Walsh, Aaron, Crispie, Fiona, Frost, Susanna, Greally, Peter, Cotter, Paul D, O'Sullivan, Orla, Renwick, Julie

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Analysis of the milk kefir pan-metagenome reveals four community types, core species, and associated metabolic pathways von Walsh, Liam H., Coakley, Mairéad, Walsh, Aaron M., Crispie, Fiona, O’Toole, Paul W., Cotter, Paul D.

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Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods von Branck, Tobyn, Hu, Zhiji, Nickols, William A, Walsh, Aaron M, Bhosle, Amrisha, Short, Meghan I, Nearing, Jacob T, Asnicar, Francesco, McIver, Lauren J, Maharjan, Sagun, Rahnavard, Ali, Louyakis, Artemis S, Badri, Dayakar V, Brockel, Christoph, Thompson, Kelsey N, Huttenhower, Curtis

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Differences in Faecal Microbiome Taxonomy, Diversity and Functional Potential in a Bovine Cohort Experimentally Challenged with Mycobacterium avium subsp. paratuberculosis (MAP) von Matthews, Chloe, Walsh, Aaron M, Gordon, Stephen V, Markey, Bryan, Cotter, Paul D, O' Mahony, Jim

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The Lung Microbiome in Young Children with Cystic Fibrosis: A Prospective Cohort Study von Linnane, Barry, Walsh, Aaron M, Walsh, Calum J, Crispie, Fiona, O'Sullivan, Orla, Cotter, Paul D, McDermott, Michael, Renwick, Julie, McNally, Paul

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Comparison of the relative impacts of acute consumption of an inulin-enriched diet, milk kefir or a commercial probiotic product on the human gut microbiome and metabolome von Walsh, Liam H., Walsh, Aaron M., Garcia-Perez, Isabel, Crispie, Fiona, Costabile, Adele, Ellis, Richard, Finlayson, Jim, Finnegan, Laura A., Claesson, Marcus J., Holmes, Elaine, Cotter, Paul D.

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Proficiency Testing of Metagenomics-Based Detection of Food-Borne Pathogens Using a Complex Artificial Sequencing Dataset von Höper, Dirk, Grützke, Josephine, Brinkmann, Annika, Mossong, Joël, Matamoros, Sébastien, Ellis, Richard J, Deneke, Carlus, Tausch, Simon H, Cuesta, Isabel, Monzón, Sara, Juliá, Miguel, Petersen, Thomas Nordahl, Hendriksen, Rene S, Pamp, Sünje J, Leijon, Mikael, Hakhverdyan, Mikhayil, Walsh, Aaron M, Cotter, Paul D, Chandrasekaran, Lakshmi, Tay, Moon Y F, Schlundt, Joergen, Sala, Claudia, De Cesare, Alessandra, Nitsche, Andreas, Beer, Martin, Wylezich, Claudia

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