We believe that the role of science in improving the quality of life of all societies must be facilitated through collaboration between researchers and shared knowledge. The primary goal of our Centre is to help the scientific community achieve the research goals, but also disseminate knowledge in the form of public outreach. The diverse and complementary expertise of our members promotes microbiome research across many scientific domains. Check out some examples by exploring the left menu.
2025
1. Cai W, Haddad M, Haddad R, Kesten I, Hoffman T, Laan R, Westfall S, Defaye M, Abdullah NS, Wong C, Brown N, Tansley S, Lister KC, Hooshmandi M, Wang F, Lorenzo LE, Hovhannisyan V, Ho-Tieng D, Kumar V, Sharif B, Thurairajah B, Fan J, Sahar T, Clayton C, Wu N, Zhang J, Bar-Yoseph H, Pitashny M, Krock E, Mogil JS, Prager-Khoutorsky M, Séguéla P, Altier C, King IL, De Koninck Y, Brereton NJB, Gonzalez E, Shir Y, Minerbi A, Khoutorsky A. The gut microbiota promotes pain in fibromyalgia.Neuron. 2025 Apr 18:S0896-6273(25)00252-1. doi: 10.1016/j.neuron.2025.03.032. Online ahead of print.PMID: 40280127
2. Westfall S, Gentile ME, Olsen TM, Karo-Atar D, Bogza A, Röstel F, Pardy RD, Mandato G, Fontes G, Herbert D, Melichar HJ, Abadie V, Richer MJ, Vinh DC, Koenig JFE, Harrison OJ, Divangahi M, Weis S, Gregorieff A, King IL. A type 1 immune-stromal cell network mediates disease tolerance against intestinal infection. Cell. 2025 Apr 22:S0092-8674(25)00395-2. doi: 10.1016/j.cell.2025.03.043. Online ahead of print.PMID: 40267906
3. Pidgeon R, Mitchell S, Shamash M, Suleiman L, Dridi L, Maurice CF, Castagner B. Diet-derived urolithin A is produced by a dehydroxylase encoded by human gut Enterocloster species. Nat Commun. 2025 Jan 24;16(1):999. doi: 10.1038/s41467-025-56266-2.PMID: 39856097
4. Shamash M, Sinha A, Maurice CF. Improving gut virome comparisons using predicted phage host information. mSystems. 2025 May 20;10(5):e0136424. doi: 10.1128/msystems.01364-24. Epub 2025 Apr 8.PMID: 40197051
5. Prattico C, Gonzalez E, Dridi L, Jazestani S, Low KE, Abbott DW, Maurice CF, Castagner B. Identification of novel fructo-oligosaccharide bacterial consumers by pulse metatranscriptomics in a human stool sample. mSphere. 2025 Jan 28;10(1):e0066824. doi: 10.1128/msphere.00668-24. Epub 2024 Dec 19.PMID: 39699190
6. Beauchemin ET, Hunter C, Maurice CF. Dextran sodium sulfate-induced colitis alters the proportion and composition of replicating gut bacteria. mSphere. 2025 Jan 28;10(1):e0082524. doi: 10.1128/msphere.00825-24. Epub 2024 Dec 26.PMID: 39723822
7. Gonzalez E, Sahar T, Haddad M, Toupin S, Zioud R, Zoabi M, Eyal Waldman L, Leshinsky ZT, Ben Sasson M, Kumar V, Marom Y, Midbari A, Brereton NJB, Shir Y, Minerbi A. Altered Gut Microbiome Composition and Function in Individuals with Complex Regional Pain Syndrome. Anesthesiology. 2025 May 3. doi: 10.1097/ALN.0000000000005435. Online ahead of print.PMID: 40042519
8. Feng Z, Lorenc N, O'Brien B, Sun G, Li Z, Jung D, Ronholm J. Deep culturing the fecal microbiota of healthy laying hens. Anim Microbiome. 2025 Mar 28;7(1):32. doi: 10.1186/s42523-025-00395-y.PMID: 40148927
9. Lorenc N, Leadbeater S, Wang J, Ronholm J, Liu X. A pilot study on the effects of in-feed probiotic Lactobacillus rhamnosus ATCC 53103 (LGG) on vaccinated Atlantic salmon (Salmo salar): microbiomes and Aeromonas salmonicida challenge resilience.Can J Microbiol. 2025 Jan 1;71:1-10. doi: 10.1139/cjm-2024-0130. Epub 2025 Jan 17.PMID: 39819033
10. Lu Y, Hui F, Zhou G, Xia J. MicrobiomeNet: exploring microbial associations and metabolic profiles for mechanistic insights. Nucleic Acids Res. 2025 Jan 6;53(D1):D789-D796. doi: 10.1093/nar/gkae944.PMID: 39441071
11. Minerbi A, Khoutorsky A, Shir Y. Decoding the connection: unraveling the role of gut microbiome in fibromyalgia. Pain Rep. 2024 Dec 24;10(1):e1224. doi: 10.1097/PR9.0000000000001224. eCollection 2025 Feb.PMID: 39726854
12. Wojciuk B, Falcone EL, Lawson R. Editorial: Microbiome in an immunocompromised host- a jungle of challenges or a glacier of hidden opportunities? Front Cell Infect Microbiol. 2025 Apr 23;15:1569842. doi: 10.3389/fcimb.2025.1569842. eCollection 2025.PMID: 40337450
13. Chandrasekaran P, Krausz M, Han Y, Mitsuiki N, Gabrysch A, Nöltner C, Proietti M, Heller T, Grou C, Calderon V, Subramanian P, Jones DR, Siu Y, Deming C, Conlan S, Holland SM, Segre JA, Uzel G, Grimbacher B, Falcone EL. The intestinal microbiome and metabolome discern disease severity in cytotoxic T-lymphocyte-associated protein 4 deficiency. Microbiome. 2025 Feb 11;13(1):51. doi: 10.1186/s40168-025-02028-7.PMID: 39934899
14. Zhang XS, Wang Y, Sun H, Zerbe C, Falcone E, Bhattacharya S, Zhang M, Gao Z, Diaz-Rubio ME, Bharj D, Patel D, Pan S, Ro G, Grenard J, Armstrong A, Yin YS, Dominguez-Bello MG, Holland S, Su X, Blaser MJ. Gut microbiota phospholipids regulate intestinal gene expression and can counteract the effects of antibiotic treatment. bioRxiv [Preprint]. 2025 Jan 28:2025.01.28.633906. doi: 10.1101/2025.01.28.633906.PMID: 39975029
15. Chandrasekaran P, Krausz M, Han Y, Mitsuiki N, Gabrysch A, Nöltner C, Proietti M, Heller T, Grou C, Calderon V, Subramanian P, Jones DR, Siu Y, Deming C, Conlan S, Holland SM, Segre JA, Uzel G, Grimbacher B, Falcone EL. Correction: The intestinal microbiome and metabolome discern disease severity in cytotoxic T-lymphocyte-associated protein 4 deficiency. Microbiome. 2025 Mar 15;13(1):74. doi: 10.1186/s40168-025-02069-y.PMID: 40089763
16. Joos R, Boucher K, Lavelle A, Arumugam M, Blaser MJ, Claesson MJ, Clarke G, Cotter PD, De Sordi L, Dominguez-Bello MG, Dutilh BE, Ehrlich SD, Ghosh TS, Hill C, Junot C, Lahti L, Lawley TD, Licht TR, Maguin E, Makhalanyane TP, Marchesi JR, Matthijnssens J, Raes J, Ravel J, Salonen A, Scanlan PD, Shkoporov A, Stanton C, Thiele I, Tolstoy I, Walter J, Yang B, Yutin N, Zhernakova A, Zwart H.; Human Microbiome Action Consortium; Doré J, Ross RP. Examining the healthy human microbiome concept. Nat Rev Microbiol. 2025 Mar;23(3):192-205. doi: 10.1038/s41579-024-01107-0. Epub 2024 Oct 23.PMID: 39443812
17. Shkoporov AN, Hill C. A hypermobile prophage in the genome of a key human gut bacterium. PLoS Biol. 2025 Apr 1;23(4):e3003071. doi: 10.1371/journal.pbio.3003071. eCollection 2025 Apr.PMID: 40168365
18. Ríos Colombo NS, Paul Ross R, Hill C. Synergistic and off-target effects of bacteriocins in a simplified human intestinal microbiome: implications for Clostridioides difficile infection control. Gut Microbes. 2025 Dec;17(1):2451081. doi: 10.1080/19490976.2025.2451081. Epub 2025 Jan 16.PMID: 39817466
19. Iliev ID, Ananthakrishnan AN, Guo CJ. Microbiota in inflammatory bowel disease: mechanisms of disease and therapeutic opportunities. Nat Rev Microbiol. 2025 Mar 10. doi: 10.1038/s41579-025-01163-0. Online ahead of print.PMID: 40065181
20. Galipeau HJ, Verdu EF. Is the microbiome important in celiac disease? J Can Assoc Gastroenterol. 2025 Feb 21;8(Suppl 2):S51-S55. doi: 10.1093/jcag/gwae047. eCollection 2025 Mar.PMID: 39990507
2024
1. Pidgeon Mitchell S, Shamash M, Suleiman L, Dridi L, Maurice CF, Castagner B. The dietary ellagitannin metabolite urolithin A is produced by a molybdenum-dependent dehydroxylase encoded by prevalent human gut Enterocloster spp. In review at Nature Communications, and on Biorxiv: https://www.biorxiv.org/content/10.1101/2024.02.08.579493v2
2. Vigano M, Kubal S, Lu Y, Habib S, Samarani S, Cama G, Viau C, Farzin H, Koudieh N, Xia J, Ahmad A, Vigano A, Costiniuk CT. Impact of Cannabidiol and Exercise on Clinical Outcomes and Gut Microbiota for Chemotherapy-Induced Peripheral Neuropathy in Cancer Survivors: A Case Report .Pharmaceuticals (Basel). 2024 Jun 25;17(7):834. doi: 10.3390/ph17070834.PMID: 39065685.
3. Logel M, El-Zein M, Franco EL, Gonzalez E.J. Species-level characterization of the cervicovaginal microbiota and its role in human papillomavirus-associated cervical carcinogenesis. Med Virol. 2024 Jun;96(6):e29764. doi: 10.1002/jmv.29764.PMID: 38923577.
4. Bogza A, King IL, Maurice CF. Worming into infancy: Exploring helminth-microbiome interactions in early life. Cell Host Microbe. 2024 May 8;32(5):639-650. doi:10.1016/j.chom.2024.04.009.PMID: 38723604.
5. Ding W, Chen L, Xia J, Dong G, Song B, Pei B, Li X. Causal relationships between gut microbiome and digestive system diseases: A two-sample Mendelian randomization study. Medicine (Baltimore). 2024 Apr 26;103(17):e37735. doi: 10.1097/MD.0000000000037735.PMID: 38669367.
6. Ajeeb TT, Gonzalez E, Solomons NW, Vossenaar M, Koski KG. Human milk microbiome: associations with maternal diet and infant growth. Front Nutr. 2024 Mar 11;11:1341777. doi: 10.3389/fnut.2024.1341777. eCollection 2024.PMID: 38529196.
2023
1. Lu Y, Zhou G, Ewald J, Pang Z, Shiri T, Xia J. MicrobiomeAnalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data. Nucleic Acids Res. 2023 May 11:gkad407. doi: 10.1093/nar/gkad407. Online ahead of print.PMID: 37166960.
2. Stockdale SR, Hill C. Incorporating plasmid biology and metagenomics into a holistic model of the human gut microbiome. Curr Opin Microbiol. 2023 Mar 30;73:102307. doi: 10.1016/j.mib.2023.102307. Online ahead of print.PMID: 37002975 Free article. Review.
3. Madi N, Chen D, Wolff R, Shapiro BJ, Garud NR. Community diversity is associated with intra-species genetic diversity and gene loss in the human gut microbiome. Elife. 2023 Feb 9;12:e78530. doi: 10.7554/eLife.78530.PMID: 36757364 Free PMC article.
4. Dridi L, Altamura F, Gonzalez E, Lui O, Kubinski R, Pidgeon R, Montagut A, Chong J, Xia J, Maurice CF, Castagner B. Identifying glycan consumers in human gut microbiota samples using metabolic labeling coupled with fluorescence-activated cell sorting. Nat Commun. 2023 Feb 7;14(1):662. doi: 10.1038/s41467-023-36365-8.PMID: 36750571 Free PMC article.
5. Lui O, Dridi L, Gonzalez E, Yasmine S, Kubinski R, Billings H, Bohlmann J, Withers SG, Maurice C, Castagner B. Characterizing the Effect of Amylase Inhibitors on Maltodextrin Metabolism by Gut Bacteria Using Fluorescent Glycan Labeling. ACS Chem Biol. 2023 Feb 17;18(2):356-366. doi: 10.1021/acschembio.2c00791. Epub 2023 Feb 2.PMID: 36728836 Free article.
6. Minerbi A, Gonzalez E, Brereton N, Fitzcharles MA, Chevalier S, Shir Y. Altered serum bile acid profile in fibromyalgia is associated with specific gut microbiome changes and symptom severity. Pain. 2023 Feb 1;164(2):e66-e76. doi: 10.1097/j.pain.0000000000002694. Epub 2022 May 19.PMID: 35587528.
7. Majumder S, Sackey T, Viau C, Park S, Xia J, Ronholm J, George S. Genomic and phenotypic profiling of Staphylococcus aureus isolates from bovine mastitis for antibiotic resistance and intestinal infectivity. BMC Microbiol. 2023 Feb 20;23(1):43. Doi: 10.1186/s12866-023-02785-1.
8. Sutcliffe SG, Reyes A, Maurice CF. Bacteriophages playing nice: Lysogenic bacteriophage replication stable in the human gut microbiota. iScience. 2023 Jan 18;26(2):106007. doi: 10.1016/j.isci.2023.106007. eCollection 2023 Feb 17.PMID: 36798434 Free PMC article.
2022
1. Hajjar R, Gonzalez E, Fragoso G, Oliero M, Alaoui AA, Calvé A, Vennin Rendos H, Djediai S, Cuisiniere T, Laplante P, Gerkins C, Ajayi AS, Diop K, Taleb N, Thérien S, Schampaert F, Alratrout H, Dagbert F, Loungnarath R, Sebajang H, Schwenter F, Wassef R, Ratelle R, Debroux E, Cailhier JF, Routy B, Annabi B, Brereton NJB, Richard C, Santos MM. Gut microbiota influence anastomotic healing in colorectal cancer surgery through modulation of mucosal proinflammatory cytokines. Gut. 2023 Jun;72(6):1143-1154. doi: 10.1136/gutjnl-2022-328389. Epub 2022 Dec 30.PMID: 36585238.
2. Ajeeb TT, Gonzalez E, Solomons NW, Koski KG. Human milk microbial species are associated with infant head-circumference during early and late lactation in Guatemalan mother-infant dyads. Front Microbiol. 2022 Nov 16;13:908845. doi: 10.3389/fmicb.2022.908845. eCollection 2022.PMID: 36466698 Free PMC article.
3. Lopez Leyva L, Gonzalez E, Solomons NW, Koski KG. Human milk microbiome is shaped by breastfeeding practices.Front Microbiol. 2022 Sep 8;13:885588. doi: 10.3389/fmicb.2022.885588. eCollection 2022.PMID: 36160202 Free PMC article.
4. Sinha A, Li Y, Mirzaei MK, Shamash M, Samadfam R, King IL, Maurice CF. Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates the severity of DSS colitis. Microbiome. 2022 Jul 8;10(1):105. doi: 10.1186/s40168-022-01275-2.PMID: 35799219 Free PMC article.
5. Shkoporov AN, Turkington CJ, Hill C. Mutualistic interplay between bacteriophages and bacteria in the human gut. Nat Rev Microbiol. 2022 Dec;20(12):737-749. doi: 10.1038/s41579-022-00755-4. Epub 2022 Jun 30.PMID: 35773472 Review.
6. Klassen L, Reintjes G, Li M, Jin L, Amundsen C, Xing X, Dridi L, Castagner B, Alexander TW, Abbott DW. Fluorescence activated cell sorting and fermentation analysis to study rumen microbiome responses to administered live microbials and yeast cell wall derived prebiotics. Front Microbiol. 2023 Mar 3;13:1020250. doi: 10.3389/fmicb.2022.1020250. eCollection 2022.PMID: 36938132 Free PMC article. Review.
7. Shamash M, Maurice CF. Phages in the infant gut: a framework for virome development during early life. ISME J. 2022 Feb;16(2):323-330. doi: 10.1038/s41396-021-01090-x. Epub 2021 Aug 20.PMID: 34417565 Free PMC article. Review. No abstract available.
8. Galipeau HJ, Verdu EF. The double-edged sword of gut bacteria in celiac disease and implications for therapeutic potential. Mucosal Immunol. 2022 Feb;15(2):235-243. doi: 10.1038/s41385-021-00479-3. Epub 2022 Jan 14.PMID: 35031683 Free article. Review.
9. Shimbori C, De Palma G, Baerg L, Lu J, Verdu EF, Reed DE, Vanner S, Collins SM, Bercik P. Gut bacteria interact directly with colonic mast cells in a humanized mouse model of IBS. Gut Microbes. 2022 Jan-Dec;14(1):2105095. doi: 10.1080/19490976.2022.2105095.PMID: 35905313 Free PMC article.
10. Jin Z, Ng A, Maurice CF, Juncker D. The Mini Colon Model: a benchtop multi-bioreactor system to investigate the gut microbiome. Gut Microbes. 2022 Jan-Dec;14(1):2096993. doi: 10.1080/19490976.2022.2096993.PMID: 35844189 Free PMC article.