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).

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

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

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. 2023. The infant gut virome is associated with preschool asthma risk independently of bacteria. Nat Med doi:10.1038/s41591-023-02685-x. 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

Cornuault JK, Moineau S. 2021. Induction and Elimination of Prophages Using CRISPR Interference. CRISPR J. 4:549-557. Abstract

Mosterd C, Moineau S. 2021. Primed CRISPR-Cas Adaptation and Impaired Phage Adsorption in Streptococcus mutans. mSphere. 6:e00185-21. Abstract

Pastuszka A, Beauruelle C, Camiade E, Rousseau GM, Moineau S, Mereghetti L, Horvath P, Lanotte P. 2021. Functional Study of the Type II-A CRISPR-Cas System of Streptococcus agalactiae Hypervirulent Strains. CRISPR J. 4:233-242. Abstract

Doré L, Pageau G, Bourque-Leblanc F, Dupuis MÈ, Lessard-Hurtubise R, Lacasse G, Plante PL, Labrie S, P Jolicoeur A, Rousseau GM, Tremblay DM, Moineau S. 2021. Complete Genome Sequences of 10 Lactococcal Skunavirus Phages Isolated from Cheddar Cheese Whey Samples in Canada. Microbiol Resour Announc. 10:e00098-21. Abstract

Achigar R, Scarrone M, Rousseau GM, Philippe C, Machado F, Duvós V, Campot MP, Dion MB, Shao Y, Pianzzola MJ, Moineau S. 2021. Ectopic Spacer Acquisition in Streptococcus thermophilus CRISPR3 Array. Microorganisms. 9:512. Abstract

Hoikkala V, Ravantti J, Díez-Villaseñor C, Tiirola M, Conrad RA, McBride MJ, Moineau S, Sundberg LR. 2021. Cooperation between Different CRISPR-Cas Types Enables Adaptation in an RNA-Targeting System. mBio. 12:e03338-20. Abstract

Jungblut AD, Raymond F, Dion MB, Moineau S, Mohit V, Nguyen GQ, Déraspe M, Francovic-Fontaine É, Lovejoy C, Culley AI, Corbeil J, Vincent WF. 2021. Genomic diversity and CRISPR-Cas systems in the cyanobacterium Nostoc in the High Arctic. Environ Microbiol. 23:2955-2968. Abstract

Dion MB, Plante PL, Zufferey E, Shah SA, Corbeil J, Moineau S. 2021. Streamlining CRISPR spacer-based bacterial host predictions to decipher the viral dark matter. Nucleic Acids Res. 49:3127-3138. Abstract

Philippe C, Moineau S. 2021. The endless battle between phages and CRISPR-Cas systems in Streptococcus thermophilus. Biochem Cell Biol doi:10.1139/bcb-2020-0593. Abstract

Mosterd C, Rousseau GM, Moineau S. 2021. A short overview of the CRISPR-Cas adaptation stage. Can J Microbiol 67:1-12. Abstract

Fage C, Lemire N, Moineau S. 2020. Delivery of CRISPR-Cas systems using phage-based vectors. Curr Opin Biotechnol 68:174-180. Abstract

Yousfi K, Usongo V, Berry C, Khan RH, Tremblay DM, Moineau S, Mulvey MR, Doualla-Bell F, Fournier E, Nadon C, Goodridge L, Bekal S. 2020. Source Tracking Based on Core Genome SNV and CRISPR Typing of Salmonella enterica Serovar Heidelberg Isolates Involved in Foodborne Outbreaks in Quebec, 2012. Front Microbiol 11:1317. Abstract

Teusink B, Kuipers OP, Moineau S. 2020. Symposium on Lactic Acid Bacteria-reading while waiting for a meeting. FEMS Microbiol Rev Abstract

Jolicoeur AP, Shao Y, Lemay M-L, Moineau S. 2020. CRISPR-Cas Systems in Starter Cultures, Reference Module in Food Science Abstract

Das PS, Gagnon-Turcotte G, Ouazaa K, Bouzid K, Hosseini SN, Bharucha E, Tremblay D, Moineau S, Messaddeq Y, Corbeil J, Gosselin B. 2020. The EcoChip 2: An Autonomous Sensor Platform for Multimodal Bio-environmental Monitoring of the Northern Habitat. Annu Int Conf IEEE Eng Med Biol Soc 2020:4101-4104. Abstract

Kot W, Olsen NS, Nielsen TK, Hutinet G, de Crécy-Lagard V, Cui L, Dedon PC, Carstens AB, Moineau S, Swairjo MA, Hansen LH. 2020. Detection of preQ0 deazaguanine modifications in bacteriophage CAjan DNA using Nanopore sequencing reveals same hypermodification at two distinct DNA motifs. Nucleic Acids Res 48:10383-10396. Abstract

Spinelli S, Tremblay D, Moineau S, Cambillau C, Goulet A. 2020. Structural Insights into Lactococcal Siphophage p2 Baseplate Activation Mechanism. Viruses 12. Abstract

Lemay ML, Maaß S, Otto A, Hamel J, Plante PL, Rousseau GM, Tremblay DM, Shi R, Corbeil J, Gagné SM, Becher D, Moineau S. 2020. A Lactococcal Phage Protein Promotes Viral Propagation and Alters the Host Proteomic Response During Infection. Viruses 12. Abstract

Yousfi K, Usongo V, Berry C, Khan RH, Tremblay DM, Moineau S, Mulvey MR, Doualla-Bell F, Fournier E, Nadon C, Goodridge L, Bekal S. 2020. Source Tracking Based on Core Genome SNV and CRISPR Typing of Salmonella enterica Serovar Heidelberg Isolates Involved in Foodborne Outbreaks in Québec, 2012. Front Microbiol 11:1317. Abstract

Mosterd C, Moineau S. 2020. Characterization of a Type II-A CRISPR-Cas System in Streptococcus mutans. mSphere 5. Abstract

Mosterd C, Rousseau GM, Moineau S. 2020. A short overview of the CRISPR-Cas adaptation stage. Can J Microbiol doi:10.1139/cjm-2020-0212:1-12. Abstract

de Melo AG, Rousseau GM, Tremblay DM, Labrie SJ, Moineau S. 2020. DNA tandem repeats contribute to the genetic diversity of Brevibacterium aurantiacum phages. Environ Microbiol 22:3413-3428. Abstract

Gao R, Naushad S, Moineau S, Levesque R, Goodridge L, Ogunremi D. 2020. Comparative genomic analysis of 142 bacteriophages infecting Salmonella enterica subsp. enterica. BMC Genomics 21:374. Abstract

Philippe C, Levesque S, Dion MB, Tremblay DM, Horvath P, Lüth N, Cambillau C, Franz C, Neve H, Fremaux C, Heller KJ, Moineau S. 2020. Novel Genus of Phages Infecting Streptococcus thermophilus: Genomic and Morphological Characterization. Appl Environ Microbiol 86. Abstract

Cornuault, J.K., and S. Moineau. 2020. A Jumbo Formation in the Viral Game Plan. Crispr J. 3:14-17. Abstract

Dion, M.B., F. Oechslin, and S. Moineau. 2020. Phage diversity, genomics and phylogeny. Nat Rev Microbiol. Abstract

Mathieu, A., M. Dion, L. Deng, D. Tremblay, E. Moncaut, S.A. Shah, J. Stokholm, K.A. Krogfelt, S. Schjorring, H. Bisgaard, D.S. Nielsen, S. Moineau, and M.A. Petit. 2020. Virulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than temperate coliphages. Nat. Commun. 11:378. Abstract

Agudelo, D., S. Carter, M. Velimirovic, A. Duringer, J.F. Rivest, S. Levesque, J. Loehr, M. Mouchiroud, D. Cyr, P.J. Waters, M. Laplante, S. Moineau, A. Goulet, and Y. Doyon. 2020. Versatile and robust genome editing with Streptococcus thermophilus CRISPR1-Cas9. Genome Res. Abstract

Makarova, K.S., Y.I. Wolf, J. Iranzo, S.A. Shmakov, O.S. Alkhnbashi, S.J.J. Brouns, E. Charpentier, D. Cheng, D.H. Haft, P. Horvath, S. Moineau, F.J.M. Mojica, D. Scott, S.A. Shah, V. Siksnys, M.P. Terns, C. Venclovas, M.F. White, A.F. Yakunin, W. Yan, F. Zhang, R.A. Garrett, R. Backofen, J. van der Oost, R. Barrangou, and E.V. Koonin. 2019. Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol. Abstract

Hutinet, G., W. Kot, L. Cui, R. Hillebrand, S. Balamkundu, S. Gnanakalai, R. Neelakandan, A.B. Carstens, C. Fa Lui, D. Tremblay, D. Jacobs-Sera, M. Sassanfar, Y.J. Lee, P. Weigele, S. Moineau, G.F. Hatfull, P.C. Dedon, L.H. Hansen, and V. de Crecy-Lagard. 2019. 7-Deazaguanine modifications protect phage DNA from host restriction systems. Nat. Commun. 10:5442. Abstract

Fuchsbauer, O., P. Swuec, C. Zimberger, B. Amigues, S. Levesque, D. Agudelo, A. Duringer, A. Chaves-Sanjuan, S. Spinelli, G.M. Rousseau, M. Velimirovic, M. Bolognesi, A. Roussel, C. Cambillau, S. Moineau, Y. Doyon, and A. Goulet. 2019. Cas9 Allosteric Inhibition by the Anti-CRISPR Protein AcrIIA6. Mol. Cell. Abstract

Labrie, S.J., C. Mosterd, S. Loignon, M.E. Dupuis, P. Desjardins, G.M. Rousseau, D.M. Tremblay, D.A. Romero, P. Horvath, C. Fremaux, and S. Moineau. 2019. A mutation in the methionine aminopeptidase gene provides phage resistance in Streptococcus thermophilus. Sci Rep 9:13816. Abstract

Fong, K., D.M. Tremblay, P. Delaquis, L. Goodridge, R.C. Levesque, S. Moineau, C.A. Suttle, and S. Wang. 2019. Diversity and Host Specificity Revealed by Biological Characterization and Whole Genome Sequencing of Bacteriophages Infecting Salmonella enterica. Viruses 11. Abstract

Deng, L., R. Silins, J.L. Castro-Mejia, W. Kot, L. Jessen, J. Thorsen, S. Shah, J. Stokholm, H. Bisgaard, S. Moineau, and D.S. Nielsen. 2019. A Protocol for Extraction of Infective Viromes Suitable for Metagenomics Sequencing from Low Volume Fecal Samples. Viruses 11. Abstract

Levesque, S., A.G. de Melo, S.J. Labrie, and S. Moineau. 2019. Mobilome of Brevibacterium aurantiacum Sheds Light on Its Genetic Diversity and Its Adaptation to Smear-Ripened Cheeses. Front Microbiol 10:1270. Abstract

Paquet, V.E., A.T. Vincent, S. Moineau, and S.J. Charette. 2019. Beyond the A-layer: adsorption of lipopolysaccharides and characterization of bacteriophage-insensitive mutants of Aeromonas salmonicida subsp. salmonicida. Mol. Microbiol. Abstract

Bondy-Denomy, J., A.R. Davidson, J.A. Doudna, P.C. Fineran, K.L. Maxwell, S. Moineau, X. Peng, E.J. Sontheimer, and B. Wiedenheft. 2018. A unified resource for tracking anti-CRISPR names. The CRISPR Journal. 1:304-305. Abstract

Davies, K., and S. Moineau. 2018. The phage whisperer: An interview with Sylvain Moineau. The CRISPR Journal. 1:363-366. Abstract

Vincent, A.T., V.E. Paquet, S. Moineau, and S.J. Charrette. 2019. Would bacteriophages be a new old complement to antibiotics in aquaculture? In Microbial Communities in Aquaculture Ecosystems (N. Derome, Editor). Springer. In Press.

Lemay, M.-L., and S. Moineau. 2019. How are genomes modified ? – Cross breeding, mutagenesis and CRISPR-Cas9. In: Genetically modified and irradiated food: Controversial issues – facts versus perceptions. Ed. V. Andersen. Elsevier. In Press.

Lemay, M.-L., A. Otto, S. Maaß, K. Plate, D. Becher, and S. Moineau. 2019. Investigating Lactococcus lactis MG1363 response to phage p2 infection at the proteome level. Molecular & Cellular Proteomics. In press

Ngazoa-Kakou, S., Y. Shao, G. Rousseau, A.A. Addablah, D.M. Tremblay, G. Hutinet, N. Lemire, P.-L. Plante, J. Corbeil, A. Koudou, B.K. Soro, D.N. Coulibaly, S. Aoussi, M. Dosso, and S. Moineau. 2019. Complete genome of Escherichia coli siphophage BRET. Microbiology Resource Announcements. In press

Chabas, H., A. Nicot, S. Meaden, E. Westra, D. Tremblay, L. Pradier, S. Lion, S. Moineau, and S. Gandon. 2019. Variability in the durability of CRISPR-Cas immunity. Philos. Trans. R. Soc. Lond. B Biol. Sci. In press

Liu, H., H. Geagea, G.M. Rousseau, S.J. Labrie, D.M. Tremblay, X. Liu, and S. Moineau. 2018. Characterization of the Escherichia coli virulent Myophage ST32. Viruses 10:616. In press

Dion, M.B., S.J. Labrie, S.A. Shah, and S. Moineau. 2018. CRISPRStudio: A user-friendly software for rapid CRISPR array visualization. Viruses 10:602. In press

Sylvain, M., F. Lehoux, S. Morency, F. Faucher, E. Bharucha, D.M. Tremblay, F. Raymond, D. Sarrazin, M. Allard, S. Moineau, J. Corbeil, Y. Messaddeq, and B. Gosselin. 2018. The EcoChip: a wireless multi-sensor platform for comprehensive environmental monitoring. IEEE Trans Biomed Circuits Syst. doi:10.1109/TBCAS.2018.2878404. In press

da Silva Xavier, A., J.C.F. de Almeida, A.G. de Melo, G.M. Rousseau, D.M. Tremblay, R.R. de Rezende, S. Moineau, and P. Alfenas-Zerbini. 2018. Characterization of CRISPR-Cas systems in the Ralstonia solanacearum species complex. Molecular plant pathology. doi:10.1111/mpp.12750. In press

Chabas, H., S. Lion, A. Nicot, S. Meaden, S. van Houte, S. Moineau, L.M. Wahl, E.R. Westra, and S. Gandon. 2018. Evolutionary emergence of infectious diseases in heterogeneous host populations. PloS Biology. In press

Croteau F.R., G.M. Rousseau, and S. Moineau. 2018. Le système CRISPR-Cas : Au-delà de l’édition génomique. Médecine/Sciences. In press

Millen, A.M., J.E. Samson, D. Tremblay, A.H. Magadán, G.M. Rousseau, S. Moineau, and D.A. Romero. 2018. Lactococcus lactis type III-A CRISPR-Cas system cleaves bacteriophage RNA. RNA Biology. In press

Hynes, A.P., G.M. Rousseau, D. Agudelo, A. Goulet, B. Amigues, J. Loehr, D.A. Romero, C. Fremaux, P. Horvath, Y. Doyon, C. Cambillau, and S. Moineau. 2018. Widespread anti-CRISPR proteins in virulent bacteriophages inhibit a range of Cas9 proteins. Nature Communications. 9:2919. Abstract

El Haddad, L., M.-J. Lemay, G.E. Khalil, S. Moineau, and C.P. Champagne. 2018. Microencapsulation of a Staphylococcus phage for concentration and long-term storage. Food Microbiology. 76:304-309. Abstract

Ngazoa-Kakou S, C. Philippe, D.M. Tremblay, S. Loignon,A. Koudou, A. Abole, D. Ngolo Coulibaly, S. Kan Kouassi,M. Kouamé Sina, S. Aoussi, M. Dosso, and S. Moineau. 2018. Complete genome sequence of Ebrios, a novel T7virus isolated from the Ebrie Lagoon in Abidjan, Côte d’Ivoire. Genome Announc. 6:e00280-18. Abstract

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