PUBLICATIONS
Papers published by CMRF users, using CMRF resources:
Updated as of July 17, 2023
2023
Ryan A. Groves, Carly C. Chan, Spencer D. Wildman, Daniel B. Gregson, Thomas Rydzak, Ian A. Lewis. 2023. Rapid LC-MS assay for targeted metabolite quantification by serial injection into isocratic gradients. Anal. Bioanal. Chem. https://doi.org/10.1007/s00216-022-04384-x
Regula Burkhard, Mia Koegler, Kirsty Brown, Kirsten Wilson, Lukas F. Mager, Amanda Z. Zucoloto, Carolyn Thomson, Nanjundappa Roopa Hebbandi, Isla Skalosky, Shokouh Ahmadi, Braedon McDonald, Markus B. Geuking. 2023. Intestinal colonization regulates systemic anti-commensal immune sensitivity and hyperreactivity. Frontiers in Immunology https://doi.org/10.3389/fimmu.2023.1030395
Marcel van de Wouw, Laura Rojas, Elnaz Vaghef-Mehrabani, Yanan Wang, Chloe Fichter, Matthew L. Workentine, Deborah Dewey, Marie-Claire Arrieta, Raylene A. Reimer, Lianne Tomfohr-Madsen, Gerald F. Giesbrecht. 2023. Exploring associations between the gut microbiota and full-scale intelligence in preschool children. Neuroscience Letters https://doi.org/10.1016/j.neulet.2023.137357
Kirsty Brown, Carolyn A. Thomson, Soren Wacker, Marija Drikic, Ryan Groves, Vina Fan, Ian A. Lewis and Kathy D. McCoy. 2023. Microbiota alters the metabolome in an age- and sex- dependent manner in mice. Nature Communications https://doi.org/10.1038/s41467-023-37055-1
Ali Pormohammad, Andrea Firrinciel, Daniel A. Salazar-Alemán, Mehdi Mohammadi, Dave Hansen, Martina Cappelletti, Davide Zannoni, Mohammad Zarei, Raymond J. Turner. 2023. Insights into the Synergistic Antibacterial Activity of Silver Nitrate with Potassium Tellurite against Pseudomonas aeruginosa. Antimicrobial Chemotherapy. https://doi.org/10.1128/spectrum.00628-23
Tosca A. van Gelderen, Claudia Ladisa, Marcela Salazar-Moscoso, Carla Folgado, Hamid R. Habibi, Laia Ribas. 2023. Metabolomic and transcriptomic profiles after immune stimulation in the zebrafish testes. Genomics. https://doi.org/10.1016/j.ygeno.2023.110581
2022
Mehdi Mohammadi, Stephanie L. Bishop, Raied Aburashed, Saad Luqman, Ryan A. Groves, Dominique G. Bihan, Thomas Rydzak, Ian A. Lewis. 2022. Microbial containment device: A platform for comprehensive analysis of microbial metabolism without sample preparation. Frontiers in Microbiology https://doi.org/10.3389/fmicb.2022.958785
Maryam Mapar, Thomas Rydzak, Ryan A. Groves, Ian A. Lewis. 2022. Biomarker enrichment medium: A defined medium for metabolomic analysis of microbial pathogens. Frontiers in Microbiology https://doi.org/10.3389/fmicb.2022.957158
Ryan A. Groves, Maryam Mapar, Raied Aburashed, Luis F. Ponce, Stephanie L. Bishop, Thomas Rydzak, Marija Drikic, Dominique G. Bihan, Hallgrimur Benediktsson, Fiona Clement, Daniel B. Gregson, Ian A. Lewis. 2022. Methods for Quantifying the Metabolic Boundary Fluxes of Cell Cultures in Large Cohorts by High-Resolution Hydrophilic Liquid Chromatography Mass Spectrometry. Analytical Chemistry https://doi.org/10.1021/acs.analchem.2c00078
Tania Wong Fok Lung, Daniel Charytonowicz, Kristin G. Beaumont, Shivang S. Shah, Shwetha H. Sridhar, Claire L. Gorrie, Andre Mu, Casey E. Hofstaedter, David Varisco, Thomas H. McConville, Marija Drikic, Brandon Fowler, Andreacarola Urso, Wei Shi, Dario Fucich, Medini K. Annavajhala, Ibrahim N. Khan, Irina Oussenko, Nancy Francoeur, Melissa L. Smith, Brent R. Stockwell, Ian A. Lewis. Abderrahman Hachani, Swikrity Upadhyay Baskota, Anne-Catrin Uhlemann, Danielle Ahn, Robert K. Ernst, Benjamin P. Howden, Robert Sebra, Alice Prince. 2022. Klebsiella pneumoniae induces host metabolic stress that promotes tolerance to pulmonary infection. Cell Metabolism https://doi.org/10.1016/j.cmet.2022.03.009
Fernando A. Vicentini, Jake C. Szamosi, Laura Rossi, Lateece Griffin, Kristoff Nieves, Dominique Bihan, Ian A. Lewis, Quentin J. Pittman, Mark G. Swain, Michael G. Surette, Simon A. Hirota, Keith A. Sharkey. 2022. Colitis-associated microbiota drives changes in behaviour in male mice in the absence of inflammation. Brain Behavior and Immunity https://doi.org/10.1016/j.bbi.2022.03.001
Thomas Rydzak, Ryan A. Groves, Ruichan Zhang, Raied Aburashed, Rajnigandha Pushpker, Maryam Mapar, Ian A. Lewis. 2022. Metabolic preference assay for rapid diagnosis of bloodstream infections. Nature Communications https://doi.org/10.1038/s41467-022-30048-6
Dominique G. Bihan, Thomas Rydzak, Madeleine Wyss, Keir Pittman, Kathy D. McCoy, Ian A. Lewis. 2022. Method for absolute quantification of short chain fatty acids via reverse phase chromatography mass spectrometry. PLoS One https://doi.org/10.1371/journal.pone.0267093
Rosica Valcheva, Heather Armstrong, Ognjen Kovic, Michael Bording-Jorgensen, Simona Veniamin, María Elisa Pérez-Muñoz, Natasha Haskey, Melissa Silva, Farhad Peerani, Karen Wong, Dina H. Kao, Sander Veldhuyzen Van Zanten, Karen I. Kroeker, Deanna L. Gibson, Eytan Wine, Michael Gänzle, Jens Walter, Levinus A. Dieleman. 2022. Double blind placebo-controlled trial for the prevention of ulcerative colitis relapses by β-fructan prebiotics: efficacy and metabolomic analysis. MedRxiv https://doi.org/10.1101/2022.01.16.22269376
Yanan Wang, Marcel van de Wouw, Lauren Drogos, Elnaz Vaghef-Mehrabani, Raylene A Reimer, Lianne Tomfohr-Madsen, Gerald F Giesbrecht. 2022. Sleep and the gut microbiota in preschool aged children. Sleep: zsac020. https://doi.org/10.1093/sleep/zsac020
Christian Giommi, Claudia Ladisa, Oliana Carnevali, Francesca Maradonna, Hamid R Habibi. 2022. Metabolomic and Transcript Analysis Revealed a Sex-Specific Effect of Glyphosate in Zebrafish Liver. Int J Mol Sci https://doi.org/10.3390/ijms23052724
Arthur Lau, Jennifer J. Rahn, Mona Chappellaz, Hyunjae Chung, Hallgrimur Benediktsson, Dominique Bihan, Anne von Massenhausen, Andreas Linkermann, Craig N. Jenne, Stephen M. Robbins, Donna L. Senger, Ian A. Lewis, Justin Chun, Daniel A. Muruve. 2022. Dipeptidase-1 governs renal inflammation during ischemia reperfusion injury. Sciences Advances https://doi.org/10.1126/sciadv.abm0142
Moonhyuk Kwon, Joseph C. Utomo, Keunwan Park, Cameron A. Pascoe, Sorina Chiorean, Iris Ngo, Kyle A. Pelot, Cheol-Ho Pan, Seon-Won Kim, Philipp Zerbe, John C. Vederas, and Dae-Kyun Ro. 2022. Cytochrome P450-Catalyzed Biosynthesis of a Dihydrofuran Neoclerodane in Magic Mint (Salvia divinorum). ACS Catal. https://doi.org/10.1021/acscatal.1c03691
Jumana Samara, Shirin Moossavi, Belal Alshaikh, Van A. Ortega, Veronika Kuchařová Pettersen, Tahsin Ferdous, Suzie L. Hoops, Amuchou Soraisham, Joseph Vayalumkal, Deonne Dersch-Mills, Jeffrey S. Gerber, Sagori Mukhopadhyay, Karen Puopolo, Thomas A. Tompkins, Dan Knights, Jens Walter, Harish Amin, Marie-Claire Arrieta. 2022. Supplementation with a probiotic mixture accelerates gut microbiome maturation and reduces intestinal inflammation in extremely preterm infants. Cell Host & Microbe 30(5): P696-711. https://doi.org/10.1016/j.chom.2022.04.005
Claudia Ladisa, Yifei Ma, Hamid R. Habibi. 2022. Metabolic Changes During Growth and Reproductive Phases in the Liver of Female Goldfish (Carassius auratus). Front Cell Dev Biol https://doi.org/10.3389/fcell.2022.834688
Luiz Gustavo N. de Almeida, Daniel Young , Lorraine Chow, Joshua Nicholas, Adrienne Lee, Man-Chiu Poon, Antoine Dufour, Ejaife O. Agbani. 2022. Proteomics and Metabolomics Profiling of Platelets and Plasma Mediators of Thrombo-Inflammation in Gestational Hypertension and Preeclampsia. Cells https://doi.org/10.3390/cells11081256
Anirban Chakraborty, Jayne E. Rattray, Sienna S. Drake, Stuart Matthews, Carmen Li, Bo Barker Jørgensen, Casey R. J. Hubert. 2022. Metabolic responses of thermophilic endospores to sudden heat-induced perturbation in marine sediment samples. Frontiers in Microbiology https://doi.org/10.3389/fmicb.2022.958417
Heather K Armstrong, Michael Bording-Jorgensen, Deanna M Santer, Zhengxiao Zhang, Rosica Valcheva, Aja M Rieger, Justin Sung-Ho Kim, Stephanie I Dijk, Ramsha Mahmood, Olamide Ogungbola, Juan Jovel, France Moreau, Hayley Gorman, Robyn Dickner, Jeremy Jerasi, Inderdeep K Mander, Dawson Lafleur, Christopher Cheng, Alexandra Petrova, Terri-Lyn Jeanson, Andrew Mason, Consolato M Sergi, Arie Levine, Kris Chadee, David Armstrong, Sarah Rauscher, Charles N Bernstein, Matthew W Carroll, Hien Q Huynh, Jens Walter, Karen L Madsen, Levinus A Dieleman, Eytan Wine. 2022. Unfermented b-fructan Fibers Fuel Inflammation in Select Inflammatory Bowel Disease Patients. Gastroenterology https://doi.org/10.1053/j.gastro.2022.09.034
2021
Greta Baggio, Ryan A. Groves, Roberto Chignola, Elena Piacenza, Alessandro Presentato, Ian A. Lewis, Silvia Lampis, Giovanni Vallini, Raymond J. Turner. 2021. Untargeted Metabolomics Investigation on Selenite Reduction to Elemental Selenium by Bacillus mycoides SeITE01. Frontiers in Microbiology https://doi.org/10.3389/fmicb.2021.711000
Adam Shute, Blanca E. Callejas, ShuHua Li, Arthur Wang, Timothy S. Jayme, Christina Ohland, Ian A. Lewis, Brian T. Layden, Andre G. Buret, Derek M. McKay. 2021. Cooperation between host immunity and the gut bacteria is essential for helminth-evoked suppression of colitis. Microbiome https://doi.org/10.1186/s40168-021-01146-2
Anna Laura Voigt, Douglas Andrew Kondro, Diana Powell, Hanna Valli-Pulaski, Mark Ungrin, Jan-Bernd Stukenborg, Claudia Klein, Ian A. Lewis, Kyle E. Orwig, Ina Dobrinkski. 2021. Unique metabolic phenotype and its transition during maturation of juvenile male germ cells. FASEB Journal https://doi.org/10.1096/fj.202002799R
Henrik Almblad, Trevor E. Randall, Fanny Liu, Katherine Leblanc, Ryan A. Groves, Weerayuth Kittichotirat, Geoffrey L. Winsor, Nicolas Fournier, Emily Au, Julie Groizeleau, Jacquelyn D. Rich, Yuefei Lou, Elise Granton, Laura K. Jennings, Larissa A. Singletary, Tara M. L. Winstone, Nathan M. Good, Roger E. Bumgarner, Michael F. Hynes, Manu Singh, Maria Silvina Stietz, Fiona S. L. Brinkman, Ayush Kumar, Ann Karen Cornelia Brassinga, Matthew R. Parsek, Boo Shan Tseng, Ian A. Lewis, Bryan G. Yipp, Justin L. MacCallum, Joe Jonathan Harrison. 2021. Bacterial cyclic diguanylate signaling networks sense temperatures. Nature Communications https://doi.org/10.1038/s41467-021-22176-2
Aubrey N. Michi, Bryan G. Yipp, Antoine Dufour, Fernando Lopes & David Proud. 2021. PGC-1α mediates a metabolic host defense response in human airway epithelium during rhinovirus infections. Nature Communications https://doi.org/10.1038/s41467-021-23925-z
Kira L. Tomlinson, Tania Wong Fok Lung, Felix Dach, Medini K. Annavajhala, Stanislaw J. Gabryszewski, Ryan A. Groves, Marija Drikic, Nancy J. Francoeur, Shwetha H. Sridhar, Melissa L. Smith, Sara Khanal, Clemente J. Britto, Robert Sebra, Ian Lewis, Anne-Catrin Uhlemann, Barbara C. Kahl, Alice S. Prince, Sebastian A. Riquelme . 2021. Staphylococcus aureus induces an itaconate-dominated immunometabolic response that drives biofilm formation. Nature Communications https://doi.org/10.1038/s41467-021-21718-y
2020
Erik van Tilburg Bernardes, Veronika Kuchařová Pettersen, Mackenzie W. Gutierrez, Isabelle Laforest-Lapointe, Nicholas G. Jendzjowsky, Jean-Baptiste Cavin, Fernando A. Vicentini, Catherine M. Keenan, Hena R. Ramay, Jumana Samara, Wallace K. MacNaughton, Richard J. A. Wilson, Margaret M. Kelly, Kathy D. McCoy, Keith A. Sharkey, & Marie-Claire Arrieta. 2020. Intestinal fungi are causally implicated in microbiome assembly and immune development in mice. Nature Communications https://doi.org/10.1038/s41467-020-16431-1
Nadia K Monych, Raymond J Turner. 2020. Multiple Compounds Secreted by Pseudomonas aeruginosa Increase the Tolerance of Staphylococcus aureus to the Antimicrobial Metals Copper and Silver. mSystems https://doi.org/10.1128/mSystems.00746-20
Sebastián A Riquelme, Kalle Liimatta, Tania Wong Fok Lung, Blanche Fields, Danielle Ahn, David Chen, Carmen Lozano, Yolanda Sáenz, Anne-Catrin Uhlemann, Barbara C Kahl, Clemente J Britto, Emily DiMango, Alice Prince. 2020. Pseudomonas aeruginosa utilizes host-derived itaconate to redirect its metabolism to promote biofilm formation. Cell Metab https://doi.org/10.1016/j.cmet.2020.04.017
Lukas F. Mager, Regula Burkhard, Nicola Pett, Noah C. A. Cooke, Kirsty Brown, Hena Ramay, Seungil Paik, John Stagg, Ryan A. Groves, Marco Gallo, Ian A. Lewis, Markus B. Geuking, Kathy D. McCoy. 2020. Microbiome-derived inosine modulates response to checkpoint inhibitor immunotherapy. Science https://doi.org/10.1126/science.abc3421
Xiyang Dong, Jayne E. Rattray, Calvin D. Campbell, Jamie Webb, Anirban Chakraborty, Oyeboade Adebayo, Stuart Matthews, Carmen Li, Martin Fowler, Natasha M. Morrison, Adam MacDonald, Ryan A. Groves, Ian A. Lewis, Scott H. Wang, Daisuke Mayumi, Chris Greening, Casey R. J. Hubert. 2020. Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep. Nature Communications https://doi.org/10.1038/s41467-020-19648-2
Leili Rohani, Breanna S. Borys, Golsa Razian, Pooyan Naghsh, Shiying Liu, Adiv A. Johnson, Pranav Machiraju, Heidrun Holland, Ian A. Lewis, Ryan A. Groves, Derek Toms, Paul M. K. Gordon, Joyce W. Li, Tania So, Tiffany Dang, Michael S. Kallos, Derrick E. Rancourt. 2020. Stirred suspension bioreactors maintain naive pluripotency of human pluripotent stem cells. Communications Biology https://doi.org/10.1038/s42003-020-01218-3
Lindsey S. Marmont, Gregory B. Whitfield, Roland Pfoh, Rohan J. Williams, Trevor E. Randall, Alexandra Ostaszewski, Erum Razvi, Ryan A. Groves, Howard Robinson, Mark Nitz, Matthew R. Parsek, Ian A. Lewis, John C. Whitney, Joe J. Harrison, Lynne P. Howell. 2020. TI PelX is a UDP-N-acetylglucosamine C4-epimerase involved in Pel polysaccharide-dependent biofilm formation. J Biological Chemistry https://doi.org/10.1074/jbc.RA120.014555
Nicolas Esquerre, Lilian Basso, Manon Defaye, Fernando A. Vicentini, Nina Cluny, Dominique Bihan, Simon A. Hirota, Alana Schick, Humberto B. Jijon, Ian A. Lewis, Markus B. Geuking, Keith A. Sharkey, Christophe Aitier, Yasmin Nasser. 2020. Colitis-Induced Microbial Perturbation Promotes Postinflammatory Visceral Hypersensitivity. Cellular and Molecular Gastroenterology and Hepatology https://doi.org/10.1016/j.jcmgh.2020.04.003
Breanna S. Borys, Tania So, James Colter, Tiffany Dang, Erin L. Roberts, Tamas Revay, Leila Larijani, Roman Krawetz, Ian Lewis, Bob Argiropoulos, Derrick E. Rancourt, Sunghoon Jung, Yas Hashimura, Brian Lee, Michael S. Kallos. 2020. Optimized serial expansion of human induced pluripotent stem cells using low-density inoculation to generate clinically relevant quantities in vertical-wheel bioreactors. Stem Cells Translational Medicine https://doi.org/10.1002/sctm.19-0406
Madeleine Wyss, Kirsty Brown, Carolyn A. Thomson, Mia Koegler, Fernanda Terra, Vina Fan, Francesca Ronchi, Dominique Bihan, Ian Lewis, Markus B. Geuking, Kathy D. McCoy. 2020. Using Precisely Defined in vivo Microbiotas to Understand Microbial Regulation of IgE. Frontiers in Immunology https://doi.org/10.3389/fimmu.2019.03107
2019
Michael R. Taylor, Kyle L. Flannigan, Hannah Rahim, Amina Mohamud, Ian A. Lewis, Simon A. Hirota, Steven C. Greenway. 2019. Vancomycin relieves mycophenolate mofetil-induced gastrointestinal toxicity by eliminating gut bacterial beta-glucuronidase activity. Science Advances https://doi.org/10.1126/sciadv.aax2358
Xiyang Dong, Chris Greening, Jayne E. Rattray, Anirban Chakraborty, Maria Chuvochina, Daisuke Mayumi, Jan Dolfing, Carmen Li, James M. Brooks, Bernie B. Bernard, Ryan A. Groves, Ian A. Lewis, Casey R. J. Hubert. 2019. Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments. Nature Communications https://doi.org/10.1038/s41467-019-09747-0
Erin Faught and Mathilakath M. Vijayan. 2019. Loss of the glucocorticoid receptor in zebrafish improves muscle glucose availability and increases growth. Am J Physiol Endocrinol Metab. https://doi.org/10.1152/ajpendo.00045.2019
Trinh-Don Nguyen, Moonhyuk Kwon, Soo-Un Kim, Conrad Fischer, Dae-Kyun Ro. 2019. Catalytic plasticity of germacrene A oxidase underlies sesquiterpene lactone diversification. Plant Physiology https://doi.org/10.1104/pp.19.00629
Mohammad Mehdi Banoei, Isabella Iupe, Reza Dowlatabadi Bazaz, Michael Campos, Hans J. Vogel, Brent W. Winston & Mehdi Mirsaeidi. 2019. Metabolomic and metallomic profile differences between Veterans and Civilians with Pulmonary Sarcoidosis. Scientific reports https://doi.org/10.1038/s41598-019-56174-8
Sebastián A. Riquelme, Carmen Lozano, Ahmed M. Moustafa, Kalle Liimatta, Kira L. Tomlinson, Clemente Britto, Sara Khanal, Simren K. Gill, Apurva Narechania, Jose M. Azcona-Gutiérrez, Emily DiMango, Yolanda Saénz, Paul Planet, and Alice Prince. 2019. CFTR-PTEN–dependent mitochondrial metabolic dysfunction promotes Pseudomonas aeruginosa airway infection. Sci. Transl. Med. https://doi.org/10.1126/scitranslmed.aav4634
2018
Andrew H. Lee, Satish K. Dhingra, Ian A. Lewis, Maneesh K. Singh, Amila Siriwardana, Seema Dalal, Kelly Rubiano, Matthias S. Klein, Katelynn S. Baska, Sanjeev Krishna, Michael Kiemba, Paul D. Roepe, Manuel Linas, Ceilia R. S. Garcia, David A. Fidock. 2018. Evidence for Regulation of Hemoglobin Metabolism and Intracellular Ionic Flux by the Plasmodium falciparum Chloroquine Resistance Transporter. Scientific Reports https://doi.org/10.1038/s41598-018-31715-9
Kyle L. Flannigan, Michael R. Taylor, Sheldon K. Pereira, Jimena Rodriguez-Arguello, Andrew W. Moffat, Laurie Alston, Xuemei Wang, Karen K. Poon, Paul L. Beck, Kevin P. Rioux, Mahesh Jonnalagadda, Prasanth K. Chelikani, Heather J. Galipeau, Ian A. Lewis, Matthew L. Workentine, Steven G. Greenway, Simon A. Hirota. 2018. An intact microbiota is required for the gastrointestinal toxicity of the immunosuppressant mycophenolate mofetil. J Heart and Lung Transplantation https://doi.org/10.1016/j.healun.2018.05.002
Jean-Paul Motta, Thibault Allain, Luke E. Green-Harrison, Ryan A. Groves, Troy Feener, Hena Ramay, Paul L. Beck, Ian A. Lewis, John L. Wallace, Andre G. Buret. 2018. Iron Sequestration in Microbiota Biofilms As A Novel Strategy for Treating Inflammatory Bowel Disease. Inflammatory Bowel Diseases https://doi.org/10.1093/ibd/izy116
Ruth Moges, Dimitri Desmonts De Lamache, Saman Sajedy, Bernard S. Renaux, Morley D. Hollenberg, Gregory Muench, Elizabeth M. Abbott, and Andre G. Buret. 2018. Anti-inflammatory benefits of antibiotics: Tylvalosin induces apoptosis of porcine neutrophils and macrophages, promotes Efferocytosis, and inhibits Pro-Inflammatory CXCL-8, IL1α, and LTB4 Production, While Inducing the Release of Pro-Resolving Lipoxin A4 and Resolvin D1. Front. Vet. Sci. https://doi.org/10.3389/fvets.2018.00057
Patrick T. Gauthier, Anita Evenset, Guttorm N. Christensen, Even H. Jorgensen, and Mathilakath M. Vijayan. 2018. Lifelong exposure to PCBs in the remote Norwegian Arctic disrupts the plasma stress metabolome in arctic charr. Environ. Sci. Technol. https://doi.org/10.1021/acs.est.7b05272