Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples 由 Aoife J. McHugh, Min Yap, Fiona Crispie, Conor Feehily, Colin Hill, Paul D. Cotter

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Tracking the Dairy Microbiota from Farm Bulk Tank to Skimmed Milk Powder 由 Aoife J. McHugh, Conor Feehily, Mark A. Fenelon, David Gleeson, Colin Hill, Paul D. Cotter

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Divergent evolution of the activity and regulation of the glutamate decarboxylase systems in Listeria monocytogenes EGD-e and 10403S: roles in virulence and acid tolerance. 由 Conor Feehily, Aiden Finnerty, Pat G Casey, Colin Hill, Cormac G M Gahan, Conor P O'Byrne, Kimon-Andreas G Karatzas

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Deep learning and single-cell phenotyping for rapid antimicrobial susceptibility detection in Escherichia coli 由 Alexander Zagajewski, Piers Turner, Conor Feehily, Hafez El Sayyed, Monique Andersson, Lucinda Barrett, Sarah Oakley, Mathew Stracy, Derrick Crook, Christoffer Nellåker, Nicole Stoesser, Achillefs N. Kapanidis

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Maternal breastfeeding is associated with offspring microbiome diversity; a secondary analysis of the MicrobeMom randomized control trial 由 Cara A. Yelverton, Sarah Louise Killeen, Conor Feehily, Conor Feehily, Rebecca L. Moore, Shauna L. Callaghan, Aisling A. Geraghty, Aisling A. Geraghty, David F. Byrne, Calum J. Walsh, Calum J. Walsh, Elaine M. Lawton, Elaine M. Lawton, Eileen F. Murphy, Douwe Van Sinderen, Douwe Van Sinderen, Paul D. Cotter, Paul D. Cotter, Fionnuala M. McAuliffe

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Ribosome phenotypes for rapid classification of antibiotic-susceptible and resistant strains of Escherichia coli 由 Alison Farrar, Piers Turner, Hafez El Sayyed, Conor Feehily, Stelios Chatzimichail, Sammi Ta, Derrick Crook, Monique Andersson, Sarah Oakley, Lucinda Barrett, Christoffer Nellåker, Nicole Stoesser, Achillefs Kapanidis

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Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome 由 Min Yap, Conor Feehily, Calum J. Walsh, Mark Fenelon, Eileen F. Murphy, Fionnuala M. McAuliffe, Douwe van Sinderen, Paul W. O’Toole, Orla O’Sullivan, Paul D. Cotter

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Infection Inspection: using the power of citizen science for image-based prediction of antibiotic resistance in Escherichia coli treated with ciprofloxacin 由 Alison Farrar, Conor Feehily, Piers Turner, Alexander Zagajewski, Stelios Chatzimichail, Derrick Crook, Monique Andersson, Sarah Oakley, Lucinda Barrett, Hafez El Sayyed, Philip W. Fowler, Christoffer Nellåker, Achillefs N. Kapanidis, Nicole Stoesser

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Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX 由 Christian Milani, Eoghan Casey, Gabriele Andrea Lugli, Rebecca Moore, Joanna Kaczorowska, Conor Feehily, Marta Mangifesta, Leonardo Mancabelli, Sabrina Duranti, Francesca Turroni, Francesca Bottacini, Jennifer Mahony, Paul D. Cotter, Fionnuala M. McAuliffe, Douwe van Sinderen, Marco Ventura

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Dietary amino acids, macronutrients, vaginal birth, and breastfeeding are associated with the vaginal microbiome in early pregnancy 由 Gillian A. Corbett, Rebecca Moore, Conor Feehily, Sarah Louise Killeen, Eileen O'Brien, Douwe Van Sinderen, Elizabeth Matthews, Roisin O'Flaherty, Pauline M. Rudd, Radka Saldova, Calum J. Walsh, Elaine M. Lawton, David A. MacIntyre, Siobhan Corcoran, Paul D. Cotter, Fionnuala M. McAuliffe

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Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach 由 Conor Feehily, Ian J. O’Neill, Calum J. Walsh, Rebecca L. Moore, Sarah Louise Killeen, Aisling A. Geraghty, Elaine M. Lawton, David Byrne, Rocio Sanchez-Gallardo, Sai Ravi Chandra Nori, Ida Busch Nielsen, Esther Wortmann, Elizabeth Matthews, Roisin O’Flaherty, Pauline M. Rudd, David Groeger, Fergus Shanahan, Radka Saldova, Fionnuala M. McAuliffe, Douwe Van Sinderen, Paul D. Cotter

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