PUBLICATIONS

See Lewis core lab publications here

Papers published by CMRF users, using CMRF resources:

2026

Yeh TC, Velez G, Prasad A, Lee SH, Rasmussen DK, Kumar A, Chadha M, Dabaja MZ, Singh AM, Sanislo S, Smith S, Mruthyunjaya P, Montague A, Bassuk AG, Almeida D, Dufour A, Mahajan VB. Multi-omics liquid biopsy identifies mitochondrial dysfunction in geographic atrophy and supports the longevity-associated metabolite alpha-ketoglutarate as a therapeutic strategy. medRxiv [Preprint]. 2026 Mar 19:2026.03.12.26347263. PMID: 41891014; PMCID: PMC13015626.

White-Gloria C, Moorhead GB, Zardini Buzatto A. Lipidomic profiling of Arabidopsis chloroplast protein phosphatase SLP1 mutants reveals altered diurnal lipid remodeling. BBA Adv. 2026 Jan 9;9:100180. doi: 10.1016/j.bbadva.2026.100180. PMID: 41607683; PMCID: PMC12834941.

Wang W, Fortuna R, Mayengbam S, Seerattan RA, Mu C, Rios JL, Abughazaleh N, Vaghef Mehrabani E, Noye Tuplin EW, Hart DA, Sharkey KA, Herzog W, Reimer RA. Multiomics insights into the effects of prebiotics on physical function and metabolism in adults with obesity and knee osteoarthritis. Gut Microbes. 2026 Dec 31;18(1):2679516. doi: 10.1080/19490976.2026.2679516. PMID: 42231528; PMCID: PMC13240952.

Valdes-Tresanco ME, Valdes-Tresanco MS, Wacker S, Brodie NI, Ponce LF, Aburashed R, Mansuri A, Groves RA, Ulke-Lemee A, Lewis IA. MS-MINT: An Open-Source Data Analysis Software for Large-Scale Metabolomics Studies. Anal Chem. 2026. 98 (22). doi: 10.1021/acs.analchem.6c01083.

Phillips K, Arrieta MC, The Preterm Infant Gut Microbiome and Probiotics Influence Growth Rates and Synaptic Development in Gnotobiotic Mice, University of Calgary, June 2026. Masters Thesis.

Dobranowski P, Duan H, Butcher J, Mayne J, Figeys D, Mack DR, Stintzi A. Individual variability shapes ex vivo responses to resistant starch in inflammatory bowel disease derived microbiomes. NPJ Biofilms and Microbiomes. 2026 May 13, 12: 142. PMID: 42129181.

Colter J, Dang T, Gysel E, Young D, Dufour A, Lewis I, Murari K, Kallos MS. Multi-omics reveals mesodermal fate bias and enables predictive cell state control in human pluripotent stem cell biomanufacturing. bioRxiv [Preprint]. 2026 May 26. doi: 10.64898/2026.05.26.727850.

Beg AZ, Fields BL, Chen YT, Wong Fok Lung T, Gowdy G, Talat A, Khan AU, Shah SS, Lewis I, Riquelme SA, Prince A. T6SS mutants exploit itaconate to support infection of phagocytes. bioRxiv [Preprint]. 2026 Mar 13. doi: 10.64898/2026.03.11.711069.

2025

Ye J, Raman M, Taylor LM, Yousuf M, Panaccione R, Turbide C, Sinha SR, Haskey N. Reduced Sulfur Diet Reshapes the Microbiome and Metabolome in Mild-Moderate Ulcerative Colitis. Int J Mol Sci. 2025 May 11;26(10):4596. doi: 10.3390/ijms26104596. PMID: 40429741; PMCID: PMC12111015.

Stykel MG, Siripala SV, Soubeyrand E, Coackley CL, Lu P, Camargo S, Thevasenan S, Figueroa GB, So RWL, Stuart E, Panchal R, Akrioti EK, Joseph JT, Haji-Ghassemi O, Taoufik E, Akhtar TA, Watts JC, Ryan SD. G6PD deficiency triggers dopamine loss and the initiation of Parkinson's disease pathogenesis. Cell Rep. 2025 Jan 28;44(1):115178. doi: 10.1016/j.celrep.2024.115178. PMID: 39772392.

Semper C, Pham TTM, Ram S, Palys S, Evdokias G, Ouedraogo JP, Moisan MC, Geoffrion N, Reid I, Di Falco M, Bailey Z, Tsang A, Benoit-Gelber I, Savchenko A. Global survey of secondary metabolism in Aspergillus niger via activation of specific transcription factors. PNAS Nexus. 2025 Aug 8;4(8):pgaf249. doi: 10.1093/pnasnexus/pgaf249. PMID: 40852424; PMCID: PMC12368960.

Puentes R, Mirzadzare N, Hannawayya R, Perez-Perez L, Dies A, Tiedje K, Derakhshani A, Young D, Johnson F, Golub L, Scaduto J, Dufour A, Cobo ER. A curcumin derivative metalloprotease inhibitor (CMC2.24) mitigates Brachyspira spp.-induced swine dysentery. Int Immunopharmacol. 2025 Aug 1;163:115312. doi: 10.1016/j.intimp.2025.115312. PMID: 40752109.

Lowry D, Reimer R, Early-Life Microbiota and Nutrition: Investigating the Effects of Fiber on Maternal Milk and Offspring Metabolic Outcomes, University of Calgary, November 2025. Masters Thesis.

Li X, Yeganeh M, Sinclair G, Mwenifumbo J, Jacob KJ, Arbour L, Lehman A, Rakic B, Vaz FM, Horvath G, Tarailo-Graovac M, Stockler-Ipsiroglu S. Biallelic variants in BBOX1 cause L-Carnitine deficiency and elevated gamma-butyrobetaine. NPJ Genom Med. 2025 Dec;10(1):64. doi: 10.1038/s41525-025-00523-2.

King MA, Heger KC, Drikic M, Mandwal A, Khan A, Sinasac DS, Pittman K, Huttlin EL, Greenway SC, Lewis IA. Altered Fibroblast Glutamine Metabolism Is Linked to the Severity of Cardiac Dysfunction in DCMA, a Mitochondrial Cardiomyopathy. J Inherit Metab Dis. 2025 Mar;48(2):e70018. doi: 10.1002/jimd.70018. PMID: 40033659; PMCID: PMC11876715.

Hannawayya R, Puentes R, Mirzadzare N, Cirone K, Amin H, Soraisham A, Alshaikh B, Thomas S, Cobo ER. A multidimensional fecal microbial and inflammatory biomarker profiling in preterm and full-term neonates. Pediatr Res. 2025. 98, 278–285. doi: 10.1038/s41390-025-03882-9. PMID: 39856229.

Gutierrez MW, van Tilburg Bernardes E, Ren E, Kalbfleisch KN, Day M, Lameu EL, Glatthardt T, Mercer EM, Sharma S, Zhang H, Al-Azawy A, Chleilat F, Hirota SA, Reimer RA, Arrieta MC. Early-life gut mycobiome core species modulate metabolic health in mice. Nat Commun. 2025 Feb;16(1). doi: 10.1038/s41467-025-56743-8.

Elias EE, Lau A, Belay SG, Derakhshani A, Andonegui G, Jenne CN, Dufour A, Bracey NA, Chun J, Muruve DA. The spleen tyrosine kinase inhibitor entospletinib resolves inflammation to promote repair following acute kidney injury. JCI Insight. 2025;10(16):e189601. doi: 10.1172/jci.insight.189601.

Donald AMH, de Almeida LGN, Dabaja MZ, Orchard I, Ybema K, Tsegai V, Armstrong V, Smith S, Young D, Longman RS, Tyndall AV, Rawling JM, Hill MD, Tsai WH, Agbani EO, Poulin MJ, Dufour A. Longitudinal Proteomic Profiling of Cognition across an Aerobic Exercise Intervention. Ann Neurol. 2025 May;97(5):1007-1018. doi: 10.1002/ana.27210. PMID: 40013367; PMCID: PMC12010053.

DeMichele E, Sosnowski O, Flood D, Taylor CT, Lewis IA, Allain T, Buret AG. Giardia duodenalis stabilizes HIF-1alpha and induces glycolytic alterations in intestinal epithelial cells. Sci Rep. 2025 Aug 7;15:28852. doi: 10.1038/s41598-025-13635-7. PMID: 40770382; PMCID: PMC12328747.

Chen YT, Liu Z, Fucich D, Giulieri SG, Liu Z, Wadhwa R, Rios G, Henschel H, Tyagi N, Olivier FAB, Monk IR, Shah SS, Sridhar SH, Drikic M, Bianco C, Lohia GK, Beg AZ, Planet PJ, Lewis IA, Sebra R, Traven A, Hachani A, Stinear TP, Howden BP, Boyd JM, Riquelme SA, Wang C, Prince A, Wong Fok Lung T. Regulation of airway fumarate by host and pathogen promotes Staphylococcus aureus pneumonia. Nat Commun. 2025 Aug 1;16:7050. doi: 10.1038/s41467-025-62453-y. PMID: 40745169; PMCID: PMC12313914.

Chan CCY, Groves RA, Aburashed R, Rydzak T, Lewis IA. LC-MS System for Collecting Time-Resolved Metabolomics Data of Cultured Cells. Anal Chem. 2025 May 20;97(19):10145-10148. doi: 10.1021/acs.analchem.4c06697. PMID: 40337904.

Chan CCY, Gregson DB, Wildman SD, Bihan DG, Groves RA, Aburashed R, Rydzak T, Pittman K, Van Bavel N, Lewis IA. Metabolomics strategy for diagnosing urinary tract infections. Nat Commun. 2025 Mar 18;16(1):2658. doi: 10.1038/s41467-025-57765-y. PMID: 40102424; PMCID: PMC11920235.

Caballero-Huertas M, Ladisa C, Lopez-Chillaron S, Joly S, Habibi HR, Ribas L. Identifying sex-linked metabolomic biomarkers in fish gonads after bacterial infection. Metabolomics. 2025 Nov 15;21(6):167. doi: 10.1007/s11306-025-02356-7. PMID: 41241706; PMCID: PMC12619773.

Beg AZ, Liu Z, Chen YT, Talat A, Gowdy G, Miller J, Florek L, Dietrich L, Wang C, Lewis I, Wong Fok Lung T, Riquelme SA, Prince A. Sequestration of the phagocyte metabolite itaconate by Pseudomonas aeruginosa RpoN promotes successful pulmonary infection. Nat Commun. 2025 Dec 13;17(1):460. doi: 10.1038/s41467-025-67153-1. PMID: 41387428; PMCID: PMC12800299.

Antomagesh F, Vijayan MM. Stable-isotope tracing reveals the role of corticosteroid receptors in driving cortisol-mediated central and peripheral glucose regulation in zebrafish. Front Endocrinol (Lausanne). 2025 Oct 14;16:1670637. doi: 10.3389/fendo.2025.1670637. eCollection 2025. PMID: 41163681; PMCID: PMC12558738.

Bundalovic-Torma C, Wang G, Kim J, Duytschaever G, Mukorako P, Bruehlmann S, McCoy KD, Andrews CN. Targeted Microbiome Strain Analysis Using SIMBA Capsules Reveals Fecal Sampling May Not Accurately Represent the Relative Abundance of Tyrosine-Decarboxylating (TDC) Bacteria Strains in the Small Intestine for Gut-Brain Axis Research, Gastroenterology. 2025;169(1 Suppl):S-1571. doi: 10.1016/S0016-5085(25)04477-4.

2024

Blanco AM, Antomagesh F, Comesana S, Soengas JL, Vijayan MM. Chronic cortisol stimulation enhances hypothalamus-specific enrichment of metabolites in the rainbow trout brain. Am J Physiol Endocrinol Metab. 2024, 326(3):E382-397. doi:10.1152/ajpendo.00410.2023 

van de Wouw M, Wang Y, Workentine ML, Vaghef-Mehrabani E, Barth D, Mercer EM, Dewey D, Arrieta MC, Reimer RA, Tomfohr-Madsen L, Giesbrecht GF. Cluster-specific association between the gut microbiota and behavioral outcomes in preschool-aged children. Microbiome. 2024, 12:60. doi:10.1186/s40168-024-01773-5

Fortuna R, Wang W, Mayengbam S, Noye Tuplin EW, Sampsell K, Sharkey KA, Hart DA, Reimer RAA. Effect of prebiotic fiber on physical function and gut microbiota in adults, mostly women, with knee osteoarthritis and obesity: a randomized controlled trial. Eur J Nutr. 2024, 63, 2149–2161. doi:10.1007/s00394-024-03415-w

Ponce LF, Bishop SL, Wacker S, Groves RA, Lewis IA. SCALiR: A web application for automating absolute quantification of mass spectrometry-based metabolomics data. Anal Chem. 2024, 96(17):6566-6574. doi:10.1021/acs.analchem.3c04988

Mandwal A, Bishop SL, Castellanos M, Westlund A, Chaconas G, Davidsen J, Lewis IA. MINNO: An open source software for refining metabolic networks and investigating complex netwoek activity using empirical metabolomics data. Anal Chem. 2024, 96(8):3382-3388. doi: 10.1021/acs.analchem.3c04501

Wang G, Bundalovic-Torma C, Menon S, Bruehlmann S, Wilsack L, Rehak R, Bagheri S, Banoei MM, Lou L, Nasser Y, Woo M, Lewis I, McCoy KD, Andrews CN. Clinical sampling of small intestine luminal content for microbiome multi-omics analysis: a performance analysis of the Small Intestine Microbiome Aspiration (SIMBA) capsule and benchmarking against endoscopy. medRxiv [Preprint]. 2024. doi: 10.1101/2024.04.04.24305299.

van Tilburg Bernardes E, Gutierrez MW, Nguyen WNT, Mercer EM, Ramay HR, Glatthardt T, Thomson CA, Halim T, Gopalakrishnan N, Kalbfleish K, Patel KD, McCoy KD, Freedman SB, Arrieta MC. Antibiotic-induced Malassezia spp. expansion in infants promotes early-life immune dysregulation and airway inflammation in mice. Nat Commun. 2024 Apr 24. 17 (5499). doi.org/10.1038/s41467-026-74417-x.

van de Wouw M, Wang Y, Workentine ML, Vaghef-Mehrabani E, Barth D, Mercer EM, Dewey D, Arrieta MC, Reimer RA, Tomfohr-Madsen L, Giesbrecht GF. Cluster-specific associations between the gut microbiota and behavioral outcomes in preschool-aged children. Microbiome. 2024 Mar 21;12(1):60. doi: 10.1186/s40168-024-01773-5. PMID: 38515179; PMCID: PMC10956200.

Urso AC, Prince A. Host Metabolites in Bacterial Infections and Bioenergetics [dissertation]. New York: Columbia University; December 2023. PhD thesis.

Urso A, Monk IR, Cheng YT, Predella C, Wong Fok Lung T, Theiller EM, Boylan J, Perelman S, Baskota SU, Moustafa AM, Lohia G, Lewis IA, Howden BP, Stinear TP, Dorrello NV, Torres V, Prince AS. Staphylococcus aureus adapts to exploit collagen-derived proline during chronic infection. Nat Microbiol. 2024 Oct;9(10):2506-2521. doi: 10.1038/s41564-024-01769-9. PMID: 39134708; PMCID: PMC11445067.

Toppings N, Marshall M, Smirnova AV, Sheremet A, Pasala AS, Nwosu FC, Hepburn M, Lewis I, Coleman NV, Dunfield PF. Ethylene and epoxyethane metabolism in methanotrophic bacteria: comparative genomics and physiological studies using Methylohalobius crimeensis. Microb Genom. 2024 Oct;10(10):001306. doi: 10.1099/mgen.0.001306. PMID: 39453690; PMCID: PMC11507031.

Ngo I, Kumar R, Li L, Kim SW, Kwon M, Ro DK. Identification of clerodane diterpene modifying cytochrome P450 (CYP728D26) in Salvia divinorum - en route to psychotropic salvinorin A biosynthesis. Physiol Plant. 2024 Sep;176(5):e14569. doi: 10.1111/ppl.14569. PMID: 39377159.

Mercer EM, Ramay HR, Moossavi S, Laforest-Lapointe I, Reyna ME, Becker AB, Simons E, Mandhane PJ, Turvey SE, Moraes TJ, Sears MR, Subbarao P, Azad MB, Arrieta MC. Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition. Microbiome. 2024;12(1). doi: 10.1186/s40168-023-01735-3.

Mapar M, Lewis IA. Molecular characterization of clinically important phenotypes of Staphylococcus aureus in a large cohort of bloodstream infections [dissertation]. Calgary: University of Calgary; December 2024. PhD Thesis.

Lacroix R, Kurrasch D. The effect of the herbicide glyphosate on neurodevelopment and its influences on two genetic zebrafish models of autism [dissertation]. Calgary: University of Calgary; December 2024. PhD Thesis.

Gutierrez MW, Arrieta MC. The early-life intestinal mycobiome in obesity development and metabolic inflammation [dissertation]. Calgary: University of Calgary; June 2024. PhD Thesis.

Granato A, Renwick S, Yau C, Kong T, Daigneault MC, Knip M; DIABIMMUNE Study Group; Allen-Vercoe E, Danska JS. Analysis of early childhood intestinal microbial dynamics in a continuous-flow bioreactor. Microbiome. 2024 Dec 5;12(1):255. doi: 10.1186/s40168-024-01976-w. PMID: 39639333; PMCID: PMC11619690.

Fekete E, Allain T, Sosnowski O, Anderson S, Lewis IA, Buret AG. Giardia spp.-induced microbiota dysbiosis disrupts intestinal mucin glycosylation. Gut Microbes. 2024 Jan-Dec;16(1):2412676. doi: 10.1080/19490976.2024.2412676. PMID: 39412866; PMCID: PMC11485787.

Desmonts de Lamache D, Lewis, IA. Systematic survey of the Plasmodium falciparum hemoglobin catabolic pathway in intact cells using the digestomics approach [dissertation]. Calgary: University of Calgary; December 2024. PhD Thesis.

Comesana S, Antomagesh F, Soengas JL, Blanco AM, Vijayan MM. Valine administration in the hypothalamus alters the brain and plasma metabolome in rainbow trout. Am J Physiol Regul Integr Comp Physiol. 2024 Aug;327(2):R261-R273. doi: 10.1152/ajpregu.00056.2024. PMID: 38881412.

Desmonts de Lamache D, Aburashed R, Wacker S, Lewis IA. DigestR: an open-source software tool for visualizing LC-MS proteomics data resulting from natural protein catabolism. bioRxiv [Preprint]. 2024 Oct 8. doi: 10.1101/2024.10.08.617287.

Chan CCY, Lewis IA. The metabolism of uropathogenic bacteria in in vitro human urine cultures [dissertation]. Calgary: University of Calgary; October 2024, PhD Thesis.

Bundalovic-Torma C, Wang G, Menon S, Bruehlmann S, Wilsack L, Rehak R, Bagheri S, Banoei MM, Lou L, Nasser Y, Woo M, McCoy KD, Andrews CN. Targeted and Reproducible Sampling of the Small Intestinal Microbiome with the Small Intestine Microbiome Aspirate Capsule Technology (SIMBA): Clinical Validation Against Endoscopy Aspirates and Fecal Samples in Healthy and GI Disorder. Gastroenterology. 2024;166(5 Suppl):S-608.

Chan CCY, Groves RA, Rydzak T, Lewis IA. Metabolomics survey of uropathogenic bacteria in human urine. Front Microbiol. 2024 Dec 18;15:1507561. doi: 10.3389/fmicb.2024.1507561. PMID: 39744398; PMCID: PMC11688363.

Arzamendi MJ, Habibyan YB, Defaye M, Shute A, Baggio CH, Chan R, Ohland C, Bihan DG, Lewis IA, Sharkey KA, McCoy KD, Altier C, Geuking MB, Nasser Y. Sex-specific post-inflammatory dysbiosis mediates chronic visceral pain in colitis. Gut Microbes. 2024 Jan-Dec;16(1):2409207. doi: 10.1080/19490976.2024.2409207. PMID: 39360560; PMCID: PMC11451282.

2023

Burkhard R, Koegler M, Brown K, Wilson K, Mager LF, Zucoloto AZ, Thomson C, Roopa Hebbandi N, Skalosky I, Ahmadi S, McDonald B, Geuking MB. Intestinal colonization regulates systemic anti-commensal immune sensitivity and hyperreactivity. Front Immunol. 2023. 14:1030395. doi.org/10.3389/fimmu.2023.1030395.

van de Wouw M, Rojas L, Vaghef-Mehrabani E, Wang Y, Fichter C, Workentine ML, Dewey D, Arrieta MC, Reimer RA, Tomfohr-Madsen L, Giesbrecht GF. Exploring associations between the gut microbiota and full-scale intelligence in preschool children. Neurosci Lett. 2023. 810: 137357. doi.org/10.1016/j.neulet.2023.137357

Pormohammad A, Firrinciel A, Salazar-Alemán DA, Mohammadi M, Hansen D, Cappelletti M, Zannoni D, Zarei M, Turner RJ. Insights into the Synergistic Antibacterial Activity of Silver Nitrate with Potassium Tellurite against Pseudomonas aeruginosa. Microbiol Spectr. 2023. 11:e00628-23. doi.org/10.1128/spectrum.00628-23.

van Gelderen TA, Ladisa C, Salazar-Moscoso M, Folgado C, Habibi HR, Ribas L. Metabolomic and transcriptomic profiles after immune stimulation in the zebrafish testes. Genomics. 2023. 115:2, 110581. doi.org/10.1016/j.ygeno.2023.110581.

Arzamendi MJ, Shute A, Chan R, Defaye M, Bihan DG, Lewis IA, Altier C, Sharkey KA, Geuking MB, Nasser Y. Sex-specific gut microbiota differences in post-inflammatory visceral pain. Gastroenterology 2023. 164(6):S-9. doi: 10.1093/jcag/gwac036.052. PMCID: PMC9991246.

Hamed SA, Mohan A, Krishnan SN, Wang A, Drikic M, Prince NL, Lewis IA, Shearer J, Keita AV, Söderholm JD, Shutt TE, McKay DM. Butyrate reduces adherent-invasive E. coli-evoked disruption of epithelial mitochondrial morphology and barrier function: involvement of free fatty acid receptor 3. Gut Microbes. 2023 Dec;15(2):2281011. doi: 10.1080/19490976.2023.2281011. PMID: 38078655; PMCID: PMC10730202.

Brown K, Thomson CA, Wacker S, Drikic M, Groves R, Fan V, Lewis IA, McCoy KD. Microbiota alters the metabolome in an age- and sex- dependent manner in mice. Nat Commun. 2023, 14(1):1348. doi: 10.1038/s41467-023-37055-1. PMID: 36906623

Tomlinson KL, Riquelme SA, Baskota SU, Drikic M, Monk IR, Stinear TP, Lewis IA, Prince AS. Staphylococcus aureus stimulates neutrophil itaconate production that suppresses the oxidative burst. Cell Reports. 2023, 42(2):112064. doi.org/10.1016/j.celrep.2023.112064

Zhao Y, Shutt T. Mitochondrial skeletal disorders provide insight into the effect of mitochondrial proteostatic stress on steroidogenesis [dissertation]. Calgary: University of Calgary; September 2023. PhD Thesis.

Young TC, Shutt T. Municipal wastewater effluent and stormwater impacts the acute stress-induced metabolic rate and plasma metabolome in rainbow trout [dissertation]. Calgary: University of Calgary; September 2023. PhD Thesis.

Sikdar MS, Mahoney D. Microbiome-derived hydroxyphenyl propanoates enhance antitumour immunity [dissertation]. Calgary: University of Calgary; April 2023, PhD Thesis.

Menard J, Bagheri S, Menon S, Yu YT, Goodman LB. Noninvasive sampling of the small intestinal chyme for microbiome, metabolome and antimicrobial resistance genes in dogs, a proof of concept. Anim Microbiome. 2023 Dec 16;5(1):64. doi: 10.1186/s42523-023-00286-0. PMID: 38104116; PMCID: PMC10725013.

Fields BL, Prince A. The role of the Type VI Secretion System in the adaptation of Pseudomonas aeruginosa to the lung [dissertation]. New York: Columbia University; 2023. PhD Thesis.

2022

Valcheva R, Armstrong HK, Kovic O, Bording-Jorgensen M, Veniamin S, Pérez-Muñoz ME, Haskey N, Silva M, Peerani F, Wong K, Kao DH, Veldhuyzen Van Zanten S, Kroeker KI, Gibson DL, Wine E, Gänzle M, Walter J, Dieleman LA. Double blind placebo-controlled trial for the prevention of ulcerative colitis relapses by β-fructan prebiotics: efficacy and metabolomic analysis. MedRxiv [Preprint], 2022. doi.org/10.1101/2022.01.16.22269376

Wang Y, van de Wouw M, Drogos L, Vaghef-Mehrabani E, Reimer RA, Tomfohr-Madsen L, Giesbrecht GF. Sleep and the gut microbiota in preschool aged children. Sleep, 2022. 45:6 zsac020. doi.org/10.1093/sleep/zsac020

Giommi C, Ladisa C, Carnevali O, Maradonna F, Habibi HR. Metabolomic and Transcript Analysis Revealed a Sex-Specific Effect of Glyphosate in Zebrafish Liver. Int J Mol Sci. 2022. 23: 2724. doi.org/10.3390/ijms23052724

Kwon M, Utomo JC, Park L, Pascoe CA, Chiorean S, Ngo I, Pelot KA, Pan CH, Kim SW, Zerbe P, Vederas JC, Ro DK. Cytochrome P450-Catalyzed Biosynthesis of a Dihydrofuran Neoclerodane in Magic Mint (Salvia divinorum). ACS Catal. 2022. 12 (1): 777–782. doi.org/10.1021/acscatal.1c03691 

Samara J, Moossavi S, Alshaikh B, Ortega VA, Pettersen VK, Ferdous T, Hoops SL, Soraisham A, Vayalumkal J, Dersch-Mills D, Gerber JS, Mukhopadhyay S, Puopolo K, Tompkins TA, Knights D, Walter J, Amin H, Arrieta MX. Supplementation with a probiotic mixture accelerates gut microbiome maturation and reduces intestinal inflammation in extremely preterm infants. Cell Host Microbe. 2022. 30(5): P696-711. doi.org/10.1016/j.chom.2022.04.005 

Ladisa C, Ma Y, Habibi HR. Metabolic Changes During Growth and Reproductive Phases in the Liver of Female Goldfish (Carassius auratus). Front Cell Dev Biol. 2022. 10:834688. doi.org/10.3389/fcell.2022.834688 

de Almeida LGN, Young D, Chow L, Nicholas J, Lee A, Poon MC, Dufour A, Agbani EO. Proteomics and Metabolomics Profiling of Platelets and Plasma Mediators of Thrombo-Inflammation in Gestational Hypertension and Preeclampsia. Cells. 2022. 11(8):1256. doi.org/10.3390/cells11081256

Chakraborty A, Rattray JE, Drake SS, Matthews S, Li C, Jørgensen BB, Hubert CRJ. Metabolic responses of thermophilic endospores to sudden heat-induced perturbation in marine sediment samples. Front Microbiol. 2022. 13:958417. doi.org/10.3389/fmicb.2022.958417

Armstrong HK, Bording-Jorgensen M, Santer DM, Zhang Z, Valcheva R, Rieger AM, Sung-Ho Kim J, Dijk SI, Mahmood R, Ogungbola O, Jovel J, Moreau F, Gorman H, Dickner R, Jerasi J, Mander IK, Lafleur D, Cheng C, Petrova A, Jeanson TL, Mason A, Sergi CM, Levine A, Chadee K, Armstrong D, Rauscher S, Bernstein CN, Carroll MW, Huynh HQ, Walter J, Madsen KL, Dieleman LA, Wine E. Unfermented b-fructan Fibers Fuel Inflammation in Select Inflammatory Bowel Disease Patients. Gastroenterology. 2022. 164:2. doi.org/10.1053/j.gastro.2022.09.034

Bishop SL, Drikic M, Wacker S, Chen YY, Kozyrskyj AL,Lewis IA. Moving beyond descriptive studies: harnessing metabolomics to elucidate the molecular mechanisms underpinning host-microbiome phenotypes. Mucosal Immunol. 2022. 15(6): 1071–1084. doi.org/10.1038/s41385-022-00553-4

Mohammadi M, Bishop SL, Aburashed R, Luqman S, Groves RA, Bihan DG, Rydzak T, Lewis IA. Microbial Containment Device (MCD): a platform for comprehensive analysis of microbial metabolism without sample preparation. Front Microbiol. 2022. 13:958785. doi: 10.3389/fmicb.2022.958785

Raman M, Ma C, Taylor LM, Dieleman LA, Gkoutos GV, Vallance JK, McCoy KD, Lewis IA, Jijon H, McKay DM, Mutch DM, Barkema HW, Gibson D, Rauch M, Ghosh S. Crohn's disease therapeutic dietary intervention (CD-TDI): Study protocol for a randomized controlled trial. BMJ Open Gastroenterology 2022. 9(1):e00841. doi: 10.1136/bmjgast-2021-000841. PMID: 35046093; PMCID: PMC8772401.

Mapar M, Rydzak T, Groves RA, Lewis IA. Biomarker Enrichment Medium (BEM): A Defined Medium for Metabolomic Analysis of Microbial Pathogens. Front Microbiol. 2022. 13:957158. doi.org/10.3389/fmicb.2022.957158,.

Shute A, Bihan DG, Lewis IA, Nasser Y. Metabolomics: the key to unravelling the role of the microbiome in visceral pain neurotransmission. Front Neurosci, 2022. 16:917197. doi: 10.3389/fnins.2022.917197. PMID: 35812241; PMCID: PMC9260117.

Groves RA, Mapar M, Aburashed R, Ponce LF, Bishop SL, Rydzak T, Drikic M, Bihan DG, Benediktsson H, Clement F, Gregson DB, Lewis IA. Methods for quantifying the metabolic boundary fluxes of cell cultures in large cohorts by high resolution hydrophilic liquid chromatography mass spectrometry. Anal Chem. 94(25): 8874–8882 (2022).

Rydzak T, Groves RA, Zhang R, Pushpker R, Mapar M, Lewis IA. Metabolic Preference Assay for Rapid Diagnosis of Bloodstream Infections. Nat Commun. 2022 Apr 28;13(1):2332. doi: 10.1038/s41467-022-30048-6. PMID: 35484129; PMCID: PMC9050716.

Bihan DG, Rydzak T, Wyss M, Pittman K, McCoy KD, Lewis IA. Method for absolute quantification of short chain fatty acids via reverse phase chromatography mass spectrometry. PLoS One, 2022. 17(4): e0267093. doi.org/10.1371/journal.pone.0267093.

Wong Fok Lung T, Charytonowicz D, Beaumont KG, Shah SS, Sridhar SH, Gorrie CL, Mu A, Hofstaedter CE, Varisco D, McConville TH, Drikic M, Fowler B, Urso A, Shi W, Fucich D, Annavajhala MK, Khan IN, Oussenko I, Francoeur N, Smith ML, Stockwell BR, Lewis IA, Hachani A, Upadhyay Baskota S, Uhlemann AC, Ahn D, Ernst RK, Howden BP, Sebra R, Prince A. Klebsiella pneumoniae induces host metabolic stress that promotes tolerance to pulmonary infection. Cell Metab. 2022 May 3. 34(5):761-774.e9. doi: 10.1016/j.cmet.2022.03.009. PMID: 35413274; PMCID: PMC9081115.

Vicentini FA, Szamosi JC, Rossi L, Griffin L, Nieves K, Bihan DG, Lewis IA, Pittman QJ, Swain MG, Surette MG, Hirota SA, Sharkey KA. Colitis-associated microbiota drives changes in behaviour in male mice in the absence of inflammation. Brain Behav Immun. 2022. 102: 266-278. doi.org/10.1016/j.bbi.2022.03.001.

Lau A, Rahn JJ, Chappellaz M, Chung H, Benediktsson H, Bihan DG, von Mässenhausen A, Linkermann A, Jenne CN, Robbins SM, Senger DL, Lewis IA, Chun J, Muruve DA. Dipeptidase-1 governs renal inflammation during ischemia reperfusion injury. Sci Adv. 2022 Feb 4;8(5):eabm0142. doi: 10.1126/sciadv.abm0142. PMID: 35108057; PMCID: PMC8809686.

2021

Michi AN, Yipp BG, Dufour A, Lopes F, Proud D. PGC-1α mediates a metabolic host defense response in human airway epithelium during rhinovirus infections. Nat Commun. 2021. 12, 3669. doi.org/10.1038/s41467-021-23925-z

Shute A, Callejas BE, Li S, Wang A, Jayme TS, Ohland C, Lewis IA, Layden BT, Buret AG, McKay DM. Cooperation between host immunity and the gut bacteria is essential for helminth-evoked suppression of colitis. Microbiome. 2021. 9(1): 186. doi.org/10.1186/s40168-021-01146-2.

Baggio G, Groves RS, Chignola R, Piacenza E, Presentato A, Lewis IA, Lampis S, Vallini G, Turner RJ. Untargeted metabolomics investigation on selenite reduction to elemental selenium by Bacillus mycoides SeITE01. Front Microbiol. 2021 Sep 16;12:711000. doi: 10.3389/fmicb.2021.711000. PMID: 34603239; PMCID: PMC8481872.

Voigt AL, Kondro DA, Powell D, Valli-Pulaski H, Ungrin M, Stukenborg JB, Klein C, Lewis IA, Orwig KW, Dobrinski I. Metabolic Phenotype of Early Prepubertal Spermatogonia and its Transition during Maturation. FASEB J. 2021 May;35(5):e21513. doi: 10.1096/fj.202002799R. PMID: 33811704; PMCID: PMC8212869.

Almblad H, Randall TE, Rich JD, Liu F, Leblanc K, Groves RA, Lou Y, Fournier N, Groizeleau J, Granton E, Jennings LK, Singletary LA, Kittichotirat W, Winsor GL, Brinkman FSL, Winstone TML, Good NM, Bumgarner RE, Hynes MF, Tseng BS, Singh M, Stietz MS, Kumar A, Brassinga AK, Parsek MR, Lewis IA, MacCallum K, Yipp BG, Harrison JJ. Bacterial cyclic diguanylate signaling networks sense temperature. Nat Commun. 2021. Mar 31;12(1):1986. doi: 10.1038/s41467-021-22176-2. PMID: 33790266; PMCID: PMC8012707.

Tomlinson KL, Wong Fok Lung T, Dach F, Annavajhala MK, Gabryszewski SJ, Groves RA, Drikic M, Francoeur NJ, Sridhar SH, Smith ML, Khanal S, Britto CJ, Sebra R, Lewis IA, Uhlemann AC, Kahl BC, Prince AS, Riquelme SA. Staphylococcus aureus induces an itaconate-dominated immunometabolic response that drives biofilm formation. Nat Commun. 2021. 12(1399). doi.org/10.1038/s41467-021-21718-y.

McCubbin K, Anholt RM, de Jong E, Ida J, Nobrega DB, Conly J, Gotte M, McAllister TA, Orsel K, Lewis IA, Jackson L, Plastow G, Wieden HJ, McCoy KD, Myles L, Robinson J, Hardcastle L, Hollis A, Ashbolt N, Checkley SL, Tyrrell G, Buret A, Rennert-May E, Goddard E, Otto S, Geransar R, Barkema H. Knowledge gaps in the understanding of antimicrobial resistance in Canada. Front Public Health. 2021. 9:726484. doi: 10.3389/fpubh.2021.726484. PMID: 34778169; PMCID: PMC8582488.

2020

van Tilburg Bernardes E, Kuchařová Pettersen V, Gutierrez MW, Laforest-Lapointe I, Jendzjowsky NG, Cavin JB, Vicentini FA, Keenan CM, Ramay HR, Samara J, MacNaughton WK, Wilson RJA, Kelly MM, McCoy KD, Sharkey KA, Arrieta MC. Intestinal fungi are causally implicated in microbiome assembly and immune development in mice. Nat Commun. 2020. 11, 2577. doi.org/10.1038/s41467-020-16431-1 

Monych NK, Turner RJ. Multiple Compounds Secreted by Pseudomonas aeruginosa Increase the Tolerance of Staphylococcus aureus to the Antimicrobial Metals Copper and Silver. mSystems 2020. 5:10.1128/msystems.00746-20. doi.org/10.1128/mSystems.00746-20 

Riquelme SA, Liimatta K, Wong Fok Lung T, Fields B, Ahn D, Chen D, Lozano C, Sáenz Y, Uhlemann AC, Kahl BC, Britto CJ, DiMango E, Prince A. Pseudomonas aeruginosa utilizes host-derived itaconate to redirect its metabolism to promote biofilm formation. Cell Metab. 2020. 31:6. doi.org/10.1016/j.cmet.2020.04.017 

Dong X, Rattray JE, Campbell DC, Webb J, Chakraborty A, Adebayo O, Matthews S, Li C, Fowler M, Macdonald A, Groves RA, Lewis IA, Wang SH, Mayumi D, Greening C, Hubert CRJ. Thermogenic hydrocarbons sustain diverse subseafloor microbial communities in deep sea cold seep sediments. Nat Commun, 2020. 11(1):1-14.

Mager LFM, Burkhard R, Cooke N, Brown K, Groves RA, Lewis IA, Geuking MB, McCoy KD. Microbiome-derived inosine modulates response to checkpoint inhibitor immunotherapy. Science, 2020. 369:6510, 1481-1489. PMID: 32792462

Esquerre N, Basso L, Defaye M, Vicentini FA, Cluny N, Bihan DG, Hirota SA, Schick A, Jijon HB, Lewis IA, Geuking MB, Sharkey KA, Altier C, Nasser Y. Colitis-Induced Microbial Perturbation Promotes Postinflammatory Visceral Hypersensitivity. Cell Mol Gastroenterol Hepatol. 2020. 10, 2:225-244. PMID: 32289500

Marmont LS, Whitfield GB, Pfoh R, Williams RJ, Randall TE, Ostaszewski A, Razvi E, Groves RA, Robinson H, Nitz M, Parsek MR, Lewis IA, Whitney JC, Harrison JJ, Howell PL. PelX is a UDP- N-acetylglucosamine C4-epimerase involved in Pel polysaccharide-dependent biofilm formation. J Biol Chem. 2020. 295(34):11949-11962. PMID: 32601062

2019

Faught E, Vijayan MM. Loss of the glucocorticoid receptor in zebrafish improves muscle glucose availability and increases growth. Am J Physiol Endocrinol Metab. 2019. 2;316(6):E1093-E1104. doi.org/10.1152/ajpendo.00045.2019 

Nguyen TD, Kwon M, Kim SU, Fischer C, Ro DK. 2019. Catalytic plasticity of germacrene A oxidase underlies sesquiterpene lactone diversification. Plant Physiology. 2019. 181:3. doi.org/10.1104/pp.19.00629 

Banoei MM, Iupe I, Dowlatabadi Bazaz R, Campos M, Vogel HJ, Winston BW, Mirsaeidi M. Metabolomic and metallomic profile differences between Veterans and Civilians with Pulmonary Sarcoidosis. Scientific reports. 2019. 9, 19584. doi.org/10.1038/s41598-019-56174-8

Riquelme SA, Lozano C, Moustafa AM, Liimatta K, Tomlinson KL, Britto C, Khanal S, Gill SK, Narechania A, Azcona-Gutiérrez JM, DiMango E, Saénz Y, Planet P, Prince A. CFTR-PTEN–dependent mitochondrial metabolic dysfunction promotes Pseudomonas aeruginosa airway infection. Sci Transl Med. 2019. 11,eaav4634. doi.org/10.1126/scitranslmed.aav4634

Seow CH, Jijon H, Groves RA, Sharifi N, Bindra GK, Panaccione R, Swain MG, Beck PL, Lewis IA, McCoy KD. Urine metabolomic signatures differentiate pregnancy from the non-pregnant state and differ in pregnant patients with Crohn's disease compared with ulcerative colitis. Gastroenterology. 2019. 156(6):S-891.

Allain T, Groves RA, Lewis IA, Buret A. 2019. Giardia sp. Metabolome: Towards the identification of new virulence factors. J Can Assoc Gastroenterol. 2019. 2:323-323.

Taylor MR, Flannigan KL, Rahim H, Mohamud A,Lewis IA, Hirota SA, Greenway SC. Vancomycin Relieves Mycophenolate Mofetil-Induced Gastrointestinal Toxicity by Eliminating Gut Bacterial β-Glucuronidase Activity. Sci Adv. 2019. 5(8). PMID: 31457102

Dong X, Greening C, Rattray JE, Chakraborty A, Chuvochina M, Mayumi D, Dolfing J, Li C, Brooks J, Bernard B, Groves RA, Lewis IA, Hubert CRJ. Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments. Nat Commun, 2019. 10(1):1816. PMID: 31000700

2018

Moges R, Desmonts De Lamache D, Sajedy S, Renaux BS, Hollenberg MD, Muench G, Abbott EM, Buret AG. 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. 2018. 5:57. doi.org/10.3389/fvets.2018.00057 

Gauthier PR, Evenset A, Christensen GN, Jorgensen EH, Vijayan MM. Lifelong exposure to PCBs in the remote Norwegian Arctic disrupts the plasma stress metabolome in arctic charr. Environ Sci Technol. 2018. 52 (2): 868–876. doi.org/10.1021/acs.est.7b05272