Phage Biology & Bacterial Immunity

We explore the fascinating battle between bacteria and their viruses (phages), focusing on how CRISPR-Cas and other bacterial immune systems evolve and function. By combining experimental and computational approaches, we uncover the molecular mechanisms driving these complex systems, answering fundamental biological questions and inspiring novel biotechnologies.

Bacteria shown in a graphic and artistic expression

 

 

 

 

 

Like all living organisms, bacteria face the constant threat of infection and have evolved sophisticated immune systems to detect and neutralise their viruses (phages). Studying these systems has led to revolutionary biotechnologies such as restriction enzymes and CRISPR–Cas, and is crucial for developing future phage therapy strategies against antibiotic-resistant infections. Recent discoveries reveal that the bacterial immune arsenal is far more diverse and complex than once thought, with surprising evolutionary links to eukaryotic immune pathways and many systems awaiting discovery.

We use a combination of research approaches, including bacterial genetics, phage biology, bioinformatics, and molecular biology, to study the evolution and diversification of bacterial immunity systems and to dissect their underlying molecular mechanisms. We are also interested in the other side of the co-evolutionary arms race, investigating how phages counteract bacterial defences. Our long-term goal is to answer fundamental questions in microbiology and immunology while building a foundation for future biomedical and industrial applications.

 

Discover our software solutions designed to support research in microbial immunity and phage biology.

 

 

Discover our latest breakthroughs in the phage–bacteria arms race:

 

 

 

 

 

 

 

2025

  • Kuehn JA, Pinilla-Redondo R. (Hai)Long Story Short: Phages Trip the DNA Wire—Snap! Molecular Cell. 2025;85(13):2460–2461.
  • Zeng Z, Hu Z, Zhao R, Rao J, Mestre MR, Liu Y, Liu S, Feng H, Chen Y, He H, Chen N, Zheng J, Peng D, Luo M, She Q, Pinilla-Redondo R, Han W. Base-modified nucleotides mediate immune signaling in bacteria. Science (New York, N.Y.). 2025;388(6745):eads6055. 19 p.

2024

  • Čepaitė R, Klein N, Mikšys A, et al. Structural variation of types IV-A1- and IV-A3-mediated CRISPR interference. Nature Communications. 2024;15:9306. https://doi.org/10.1038/s41467-024-53778-1
  • Mayo-Muñoz D, Li H, Mestre MR, Pinilla-Redondo R. The role of noncoding RNAs in bacterial immunity. Trends in Microbiology. 2025 Feb;33(2):208–222. doi:10.1016/j.tim.2024.09.006. Epub 2024 Oct 12. PMID: 39396887.
  • Payne L, Jackson S, Pinilla-Redondo R. Supramolecular assemblies in bacterial immunity: an emerging paradigm. Trends in Microbiology. 2024;32(9):828–831. 4 p.
  • Benz F, Camara-Wilpert S, Russel J, Wandera KG, Čepaitė R, Ares-Arroyo M, Gomes-Filho JV, Englert F, Kuehn JA, Gloor S, Mestre MR, Cuénod A, Aguilà-Sans M, Maccario L, Egli A, Randau L, Pausch P, Rocha EPC, Beisel CL, Madsen JS, et al. Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans. Cell Host and Microbe. 2024;32(6):875–886.e9. 12 p.

2023

  • Mayo-Muñoz D, Pinilla-Redondo R, Birkholz N, Fineran PC. A host of armor: Prokaryotic immune strategies against mobile genetic elements. Cell Reports. 2023;42(7):112672. 14 p.
  • Camara-Wilpert S, Mayo-Muñoz D, Russel J, Fagerlund RD, Madsen JS, Fineran PC, Sørensen SJ, Pinilla-Redondo R. Bacteriophages suppress CRISPR–Cas immunity using RNA-based anti-CRISPRs. Nature. 2023;623(7987):601–607. 7 p.

2022

  • Zeng Z, Chen Y, Pinilla-Redondo R, Shah SA, Zhao F, Wang C, Hu Z, Wu C, Zhang C, Whitaker RJ, She Q, Han W. A short prokaryotic Argonaute activates membrane effector to confer antiviral defense. Cell Host and Microbe. 2022;30(7):930–943.e6. 21 p.
  • Marino ND, Pinilla-Redondo R, Bondy-Denomy J. CRISPR-Cas12a targeting of ssDNA plays no detectable role in immunity. Nucleic Acids Symposium Series. 2022;50(11):6414–6422. 9 p.
  • Pinilla-Redondo R, Russel J, Mayo-Muñoz D, Shah SA, Garrett RA, Nesme J, Madsen JS, Fineran PC, Sørensen SJ. CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids. Nucleic Acids Research. 2022;50(8):4315–4328.

2020

  • Marino ND, Pinilla-Redondo R, Csörgő B, Bondy-Denomy J. Anti-CRISPR protein applications: natural brakes for CRISPR-Cas technologies. Nature Methods. 2020;17(5):471–479. 9 p.
  • Pinilla-Redondo R, Shehreen S, Marino ND, Fagerlund RD, Brown CM, Sørensen SJ, Fineran PC, Bondy-Denomy J. Discovery of multiple anti-CRISPRs highlights anti-defense gene clustering in mobile genetic elements. Nature Communications. 2020;11:5652. 11 p.
  • Pinilla-Redondo R, Mayo-Muñoz D, Russel J, Garrett RA, Randau L, Sørensen SJ, Shah SA. Type IV CRISPR-Cas systems are highly diverse and involved in competition between plasmids. Nucleic Acids Research. 2020;48(4):2000–2012. doi:10.1093/nar/gkz1197. PMID: 31879772; PMCID: PMC7038947.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Our research group is supported by:

 

 

Excited about joining us? Job opening or not, please reach out − we’d love to explore options for MSc projects or hosting visiting PhDs/Postdocs.

Please email us with a short explanation of why you’d like to join our lab, and include your CV, transcripts, and references.

 

 

 

 

 

 

 

 

 

 

Rafael Pinilla Redondo

Group leader

Rafael Pinilla-Redondo
Principal Investigator

Phone +45 35 32 80 49
rafael.pinilla@bio.ku.dk

Section of Microbiology

Group members

Name Title Phone E-mail
Haotian Zheng PhD Student +4535324106 E-mail
Huijuan Li PhD Student E-mail
Johannes Anton Kühn PhD Fellow +4535334642 E-mail
Leighton James Paýne Postdoc +4535337634 E-mail
Mario Rodríguez Mestre PhD Fellow +4535327618 E-mail
Rafael Pinilla Redondo Assistant Professor +4535328049 E-mail
Ruiliang Zhao PhD Student +4535333920 E-mail

Master Students

Name Title Contact
Dennis Zhang Visiting MSc Student ORC-ID
Josepha Klas MSc Student ORC-ID
Nanna Wagner MSc student LinkedIn