In our laboratory, we are studying bacteriophages (or phages).

It is now recognized that phages are the most abundant biological entities on the planet. These viruses specifically infect bacteria. They are found in the same environments as their bacterial hosts and play a key role in maintaining the balance of ecosystems. Phages are also excellent viral models applicable to various research areas.

Bacteriophages can be both friends and foes. Friends since they suppress bacterial populations with harmful properties, including pathogenic bacteria. These phages can have industrial and medical applications as biocontrol agents. Foes because they can destroy bacteria that play an important role in food fermentations.

Our main goal is to increase knowledge of phage biology. We favor an integrative approach (combining data from genomics, transcriptomics, proteomics, and structural biology) to understand the interactions between phages and bacteria. New tools are also developed to remove bacteriophages in dairy fermentations and to favor their use as antibacterial agents in various industrial sectors and public health.

To know more about our research projects, visit this website (In French): Research

Our laboratory also houses the largest public collection of bacteriophages in the world (www.phage.ulaval.ca).

Gittrich MR, Sanderson CM, Noel CM, Babusci E, Selbes SC, Svab M, Murray I, Bousliman C, Fofana A, Daboul A, Leopold J, Gonçalves de Melo A, Urvoy M, Moineau S, Mutalik VK, Sullivan MB. 2026. Cross-family and phage-specific gene requirements for Klebsiella infection revealed by scalable RB-TnSeq genetic screens. PLoS Genet 22:e1012233. Abstract

Marangon, A.M., S.A. Pujato, G.M. Rousseau, D.M. Tremblay, G.A. Lugli, M. Ventura, J. Mahony, S. Moineau, A. Quiberoni, and D.M. Guglielmotti. 2026. Temporal dynamics of the S. thermophilus phage population in a yogurt production facility. Int. J. Food Microbiol. Abstract

Morency C, Rousseau GM, Morneau Z, Moineau S. 2026. Phage satellites induced by virulent phages are mobilized by natural competence leading to phage resistance in a new host. Nat Commun doi:10.1038/s41467-026-72928-1. Abstract

Leprince A, Somerville V, Addablah AA, Morency C, Moineau S. 2026. Phage host range: determinants, dynamics and applications. Nat Rev Microbiol doi:10.1038/s41579-026-01306-x. Abstract

Byatt G, Goffard C, Cornuault JK, Lemieux M, De Koninck P, Paquet ME, Moineau S. 2026. Optimization of bacterial colonization in the gut of axenic and conventional zebrafish larvae using live food. Microbiol Spectr doi:10.1128/spectrum.02853-25:e0285325. Abstract

Mejia Bohorquez B, Vincent T, Tremblay D, Moineau S, Garnier A. 2026. Identification of chalcopyrite-binding peptides for flotation applications using phage display and deep sequencing. J Biotechnol 414:8-18. Abstract

Makarova KS, Shmakov SA, Wolf YI, Mutz P, Altae-Tran H, Beisel CL, Brouns SJJ, Charpentier E, Cheng D, Doudna J, Haft DH, Horvath P, Moineau S, Mojica FJM, Pausch P, Pinilla-Redondo R, Shah SA, Siksnys V, Terns MP, Tordoff J, Venclovas Č, White MF, Yakunin AF, Zhang F, Garrett RA, Backofen R, van der Oost J, Barrangou R, Koonin EV. 2025. An updated evolutionary classification of CRISPR-Cas systems including rare variants. Nat Microbiol 10:3346-3361. Abstract

Leprince A, Lefrançois J, Millen AM, Magill D, Horvath P, Romero DA, Rousseau GM, Moineau S. 2025. Strengthening phage resistance of Streptococcus thermophilus by leveraging complementary defense systems. Nat Commun 16:7142. Abstract

Scarrone M, Turner D, Wittmann J, Rohde C, Labrie SJ, Tremblay DM, Moineau S. 2025. Complete genome of five Acinetobacter baumannii phages. Microbiol Resour Announc 14:e0046325. Abstract

Leprince A, Moineau S. 2025. CRISPR-Cas in the Cheese Industry. Annu Rev Virol doi:10.1146/annurev-virology-092623-111016. Abstract

Fremaux, C., P. Horvath, A. Cochu-Blachère, D. Romero, S. Moineau, ans S. Labrie. 2025. Lactic acid bacterium with a reduction of sensitivity to cos-type bacteriophages. US Patent 12,268,219. Abstract

Scarrone M, Turner D, Dion M, Tremblay D, Moineau S. 2025. In silico and in vitro comparative analysis of 79 Acinetobacter baumannii clinical isolates. Microbiol Spectr doi:10.1128/spectrum.02849-24:e0284924. Abstract

Zhang Y, Castro-Mejía JL, Deng L, Shah SA, Thorsen J, Leal Rodríguez C, Jessen LE, Dion MB, Chawes B, Bønnelykke K, Sørensen SJ, Bisgaard H, Moineau S, Petit MA, Stokholm J, Nielsen DS. 2025. The influence of early life exposures on the infant gut virome. Gut Microbes 17:2501194. Abstract

Mosterd C, Moineau S. 2025. Insight into crRNA Processing in Streptococcus mutans P42S and Application of SmutCas9 in Genome Editing. Int J Mol Sci 26. Abstract

Pitot TM, Girard C, Rapp JZ, Somerville V, Culley AI, Vincent WF, Moineau S, Roux S. 2025. Viral niche-partitioning: comparative genomics of giant viruses across environmental gradients in a high Arctic freshwater-saltwater lake. ISME Commun 5:ycae155. Abstract

Fort C, Bareha Y, Pham TTH, Lai TT, Brouillette F, Njamen G, Tolnai B, Moineau S, Barnabe S. 2024. Lifespan and bioactivity improvement of bacteriophages immobilized on carboxymethylcellulose - Cationic starch-coated paper for food packaging. Int. J. Biol. Abstract

Resch G, Brives C, Debarbieux L, Hodges FE, Kirchhelle C, Laurent F, Moineau S, Martins AFM, Rohde C. 2024. Between Centralization and Fragmentation: The Past, Present, and Future of Phage Collections. PHAGE 5:22-29.

Morneau Z, Moineau S. 2024. The double play of a phage HTH regulator. Trends Microbiol 2024 Sep 25:S0966-842X(24)00231-2. Abstract

Addablah AA, Ngazoa-Kakou SE, Adioumani EA, Labrie SJ, Tremblay DM, Gunathilake D, Moineau S. 2024. Complete genome of Escherichia phages Carena and JoYop. Microbiol Resour Announc 13:e0123323. Abstract

Dion MB, Shah SA, Deng L, Thorsen J, Stokholm J, Krogfelt KA, Schjørring S, Horvath P, Allard A, Nielsen DS, Petit MA, Moineau S. 2024. Escherichia coli CRISPR arrays from early life fecal samples preferentially target prophages. ISME J 18. Abstract

Gandon S, Guillemet M, Gatchitch F, Nicot A, Renaud AC, Tremblay DM, Moineau S. 2024. Building pyramids against the evolutionary emergence of pathogens. Proc Biol Sci 291:20231529. Abstract

Oechslin F, Zhu X, Morency C, Somerville V, Shi R, Moineau S. 2024. Fermentation Practices Select for Thermostable Endolysins in Phages. Mol Biol Evol 41. Abstract

de Melo AG, Morency C, Moineau S. 2024. Virulence-associated factors as targets for phage infection. Curr Opin Microbiol 79:102471. Abstract

Hosseini N, Chehreghani M, Moineau S, Charette SJ. 2024. Centroid of the bacterial growth curves: a metric to assess phage efficiency. Commun Biol 7:673. Abstract

Bayat F, Hilal A, Thirugnanasampanthar M, Tremblay D, Filipe CDM, Moineau S, Didar TF, Hosseinidoust Z. 2024. High throughput platform technology for rapid target identification in personalized phage therapy. Nat Commun 15:5626. Abstract

Gunathilake KMD, Makumi A, Loignon S, Tremblay D, Labrie S, Svitek N, Moineau S. 2024. Diversity of Salmonella enterica phages isolated from chicken farms in Kenya. Microbiol Spectr 12:e0272923. Abstract

Leal Rodriguez C, Shah SA, Rasmussen MA, Thorsen J, Boulund U, Pedersen CT, Castro-Mejia JL, Poulsen CE, Poulsen CS, Deng L, Larsen FAN, Widdowson M, Zhang Y, Sorensen SJ, Moineau S, Petit MA, Chawes B, Bonnelykke K, Nielsen DS, Stokholm J. 2024. The infant gut virome is associated with preschool asthma risk independently of bacteria. Nat Med doi:10.1038/s41591-023-02685-x. Abstract

Philippe C, Cornuault JK, de Melo AG, Morin-Pelchat R, Jolicoeur AP, Moineau S. 2023. The never-ending battle between lactic acid bacteria and their phages. FEMS Microbiol Rev 47. Abstract

Pastuszka A, Rousseau GM, Somerville V, Levesque S, Fiset JP, Goulet A, Doyon Y, Moineau S. 2023. Dairy phages escape CRISPR defence of Streptococcus thermophilus via the anti-CRISPR AcrIIA3. Int J Food Microbiol 407:110414. Abstract

Hosseini N, Paquet VE, Marcoux PE, Alain CA, Paquet MF, Moineau S, Charette SJ. 2023. MQM1, a bacteriophage infecting strains of Aeromonas salmonicida subspecies salmonicida carrying Prophage 3. Virus Res 334:199165. Abstract

de Melo AG, Lemay ML, Moineau S. 2023. The impact of Brevibacterium aurantiacum virulent phages on the production of smear surface-ripened cheeses. Int J Food Microbiol 400:110252. Abstract

Jolicoeur AP, Lemay ML, Beaubien E, Bélanger J, Bergeron C, Bourque-Leblanc F, Doré L, Dupuis M, Fleury A, Garneau JE, Labrie SJ, Labrie S, Lacasse G, Lamontagne-Drolet M, Lessard-Hurtubise R, Martel B, Menasria R, Morin-Pelchat R, Pageau G, Samson JE, Rousseau GM, Tremblay DM, Duquenne M, Lamoureux M, Moineau S. 2023. Longitudinal Study of Lactococcus Phages in a Canadian Cheese Factory. Appl Environ Microbiol doi:10.1128/aem.00421-23:e0042123. Abstract

Alizadeh Sahraei A, Mejia Bohorquez B, Tremblay D, Moineau S, Garnier A, Larachi F, Lagüe P. 2023. Insight into the Binding Mechanisms of Quartz-Selective Peptides: Toward Greener Flotation Processes. ACS Appl Mater Interfaces 15:17922-17937. Abstract

Campbell ZA, Njiru N, Mhone AL, Makumi A, Moineau S, Svitek N. 2023. Gender-Responsive Design of Bacteriophage Products to Enhance Adoption by Chicken Keepers in Kenya. Viruses 15. Abstract

Shah SA, Deng L, Thorsen J, Pedersen AG, Dion MB, Castro-Mejía JL, Silins R, Romme FO, Sausset R, Jessen LE, Ndela EO, Hjelmsø M, Rasmussen MA, Redgwell TA, Leal Rodríguez C, Vestergaard G, Zhang Y, Chawes B, Bønnelykke K, Sørensen SJ, Bisgaard H, Enault F, Stokholm J, Moineau S, Petit MA, Nielsen DS. 2023. Expanding known viral diversity in the healthy infant gut. Nat Microbiol doi:10.1038/s41564-023-01345-7. Abstract

Rasmussen TS, Koefoed AK, Deng L, Muhammed MK, Rousseau GM, Kot W, Sprotte S, Neve H, Franz C, Hansen AK, Vogensen FK, Moineau S, Nielsen DS. 2023. CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic mice. ISME J 17:432-442. Abstract

Nielsen TK, Forero-Junco LM, Kot W, Moineau S, Hansen LH, Riber L. 2023. Detection of nucleotide modifications in bacteria and bacteriophages: Strengths and limitations of current technologies and software. Mol Ecol doi:10.1111/mec.16679. Abstract

Kejzar N, Laanto E, Rissanen I, Abrishami V, Selvaraj M, Moineau S, Ravantti J, Sundberg LR, Huiskonen JT. 2022. Cryo-EM structure of ssDNA bacteriophage ΦCjT23 provides insight into early virus evolution. Nat Commun 13:7478. Abstract

Lai TT, Pham TTH, van Lingen M, Desaulniers G, Njamen G, Tolnai B, Jabrane T, Moineau S, Barnabé S. 2022. Development of Antimicrobial Paper Coatings Containing Bacteriophages and Silver Nanoparticles for Control of Foodborne Pathogens. Viruses 14. Abstract

Xavier ADS, de Melo AG, Hendrich CG, Tremblay DM, Rousseau GM, Plante PL, Forest KT, Alfenas-Zerbini P, Allen C, Moineau S. 2022. In through the Out Door: A Functional Virulence Factor Secretion System Is Necessary for Phage Infection in Ralstonia solanacearum. mBio 13:e0147522. Abstract

Mhone AL, Makumi A, Odaba J, Guantai L, Gunathilake KMD, Loignon S, Ngugi CW, Akhwale JK, Moineau S, Svitek N. 2022. Salmonella Enteritidis Bacteriophages Isolated from Kenyan Poultry Farms Demonstrate Time-Dependent Stability in Environments Mimicking the Chicken Gastrointestinal Tract. Viruses 14. Abstract

Philippe C, Morency C, Plante PL, Zufferey E, Achigar R, Tremblay DM, Rousseau GM, Goulet A, Moineau S. 2022. A truncated anti-CRISPR protein prevents spacer acquisition but not interference. Nat Commun 13:2802. Abstract

Oechslin F, Zhu X, Dion MB, Shi R, Moineau S. 2022. Phage endolysins are adapted to specific hosts and are evolutionarily dynamic. PLoS Biol 20:e3001740. Abstract

Mhone AL, Makumi A, Odaba J, Guantai L, Gunathilake KMD, Loignon S, Ngugi CW, Akhwale JK, Moineau S, Svitek N. 2022. Salmonella Enteritidis Bacteriophages Isolated from Kenyan Poultry Farms Demonstrate Time-Dependent Stability in Environments Mimicking the Chicken Gastrointestinal Tract. Viruses 14. Abstract

Gunathilake KMD, Tremblay DM, Plante PL, Jensen EC, Nickerson KW, Moineau S. 2022. Genome Sequence of SN1, a Bacteriophage That Infects Sphaerotilus natans and Pseudomonas aeruginosa. Microbiol Resour Announc 11:e0047822. Abstract

Guillemet M, Chabas H, Nicot A, Gatchich F, Ortega-Abboud E, Buus C, Hindhede L, Rousseau GM, Bataillon T, Moineau S, Gandon S. 2022. Competition and coevolution drive the evolution and the diversification of CRISPR immunity. Nat Ecol Evol doi:10.1038/s41559-022-01841-9. Abstract

Hosseini N, Paquet VE, Chehreghani M, Moineau S, Charette SJ. 2021. Phage Cocktail Development against Aeromonas salmonicida subsp. salmonicida Strains Is Compromised by a Prophage. Viruses 13. Abstract

Cornuault JK, Byatt G, Paquet ME, De Koninck P, Moineau S. 2022. Zebrafish: a big fish in the study of the gut microbiota. Curr Opin Biotechnol. 73:308-313. Abstract

See all the publications