Publications

Explore publications from the Phage Foundry team.

2025

  1. Anand A, Arkin A, Dukes F, Mageeney C, Mukundan H, Mutalik V. Bridging the gap: pathway programs for inclusion and persistence in microbiology. Trends Microbiol 2025. https://doi.org/10.1016/j.tim.2024.12.007. 

2024

  1. Rotman E, McClure S, Glazier J, Fuerte-Stone J, Foldi J, Erani A, McGann R, Arnold J, Lin H, Valaitis S, Mimee M. Rapid design of bacteriophage cocktails to suppress the burden and virulence of gut-resident carbapenem-resistant Klebsiella pneumoniae. Cell Host Microbe 2024. https://doi.org/10.1016/j.chom.2024.09.004. 
  2. Roux S, Mutalik VK. Tapping the treasure trove of atypical phages. Curr Opin Microbiol 2024;82:102555. https://doi.org/10.1016/j.mib.2024.102555. 

2023 and Previous Years

  1. Denish Piya, Nicholas Nolan, Madeline L Moore,  Luis A Ramirez Hernandez, Brady F Cress, Ry Young, Adam P Arkin*, Vivek K Mutalik*. “Genome-wide CRISPRi knockdown to map gene essentiality landscape in coliphages lambda and P1” PLoS Biology, Dec 4, 2023 https://doi.org/10.1371/journal.pbio.3002416
  2. Hans K Carlson*, Denish Piya, Madeline L Moore,  Roniya T Magar, Nathalie H Elisabeth, Adam M Deutschbauer, Adam P Arkin, Vivek K Mutalik*. “Geochemical constraints on bacteriophage infectivity in terrestrial environments”. ISME communications, 3, p78, 2023
  3. Strathdee SA, Hatfull GF, Mutalik VK, Schooley RT. “Phage therapy: From biological mechanisms to future directions”. Cell. 2023 Jan 5;186(1):17-31. PubMed Central PMCID: PMC9827498.
  4. Benjamin A. Adler, Karthik Chamakura, Heloise Carion, Jonathan Krog, Adam M Deutschbauer, Ryland F Young, Vivek K. Mutalik*, Adam P. Arkin*. ”Multicopy suppressor screens reveal convergent evolution of single-gene lysis proteins” Nature Chemical Biology, 1-8, 2023 
  5. *Adler, B. A., *Al-Shimary, M. J., Patel, J. R., Ambruster, E., Colognori, D., Charles, E. J., … Doudna, J. A. & Cress, B. F. (2023). Genome-wide Characterization of Diverse Bacteriophages Enabled by RNA-Binding CRISPRi. bioRxiv, 2023-09. doi: 10.1101/2023.09.18.558157
  6. Piya D, Nolan N, Moore ML, Ramirez Hernandez LA, Cress BF, Young R, Arkin AP, Mutalik VK. Systematic and scalable genome-wide essentiality mapping to identify nonessential genes in phages. PLoS Biol. 2023 Dec 4;21(12):e3002416. doi: 10.1371/journal.pbio.3002416. PMID: 38048319; PMCID: PMC10695390.
  7. Adler, B.A., Hessler, T., Cress, B.F. et al. Broad-spectrum CRISPR-Cas13a enables efficient phage genome editing. Nat Microbiol 7, 1967–1979 (2022). https://doi.org/10.1038/s41564-022-01258-x
  8. Vivek K. Mutalik*, Adam P. Arkin*. “A phage foundry framework to systematically develop viral countermeasures to combat antibiotic-resistant bacterial pathogens”  iScience 25, 104121, April 15, 2022  
  9. Adler B, Hessler T, Cress B, Lahiri A, Mutalik V, Barrangou R, Banfield J, Doudna J. “Broadspectrum CRISPR-Cas13a enables efficient phage genome editing”. Nature Microbiology. 2022 October 31; 7(12):1967-1979.
  10. Rubin BE, Diamond S, Cress BF, Crits-Christoph A, Lou YC, Borges AL, Shivram H, He C, Xu M, Zhou Z, Smith SJ, Rovinsky R, Smock DCJ, Tang K, Owens TK, Krishnappa N, Sachdeva R, Barrangou R, Deutschbauer AM, Banfield JF, Doudna JA. Species- and site-specific genome editing in complex bacterial communities. Nat Microbiol. 2022 Jan;7(1):34-47. doi: 10.1038/s41564-021-01014-7. Epub 2021 Dec 6. PMID: 34873292; PMCID: PMC9261505.
  11. Vivek K. Mutalik*, Benjamin A. Adler, Harneet S. Rishi, Denish Piya, Crystal Zhong, Britt Koskella, Elizabeth Kutter, Richard Calendar, Pavel Novichkov, Morgan N. Price, Adam M. Deutschbauer, Adam P. Arkin*. “High-throughput mapping of the phage resistance landscape in E. coli”. PLoS Biology 2021, 18(10): e3000877 https://doi.org/10.1371/journal.pbio.3000877
  12. Sean Carim, Ashley L. Azadeh, Alexey E. Kazakov, Morgan N. Price, Peter J. Walian, Romy Chakraborty, Adam M. Deutschbauer, Vivek K. Mutalik*, Adam P. Arkin*. “Systematic discovery of Pseudomonad genetic factors involved in sensitivity to tailocins”. ISME Journal 2021 Mar 1. doi: 10.1038/s41396-021-00921-1 (work highlighted in LBNL News, Bio-IT World)
  13. Benjamin A. Adler, Crystal Zhong, Hualan Liu, Elizabeth Kutter, Adam M. Deutschbauer, Vivek K. Mutalik* and Adam P. Arkin*. “The Genetic Basis of phage susceptibility, cross-resistance and host-range in Salmonella”. Microbiology, 2021, 167 (12) 001126
  14. Vivek K. Mutalik*, Pavel S. Novichkov, Morgan N. Price, Trenton K. Owens, Mark Callaghan, Sean Carim, Adam M. Deutschbauer and Adam P. Arkin*, “Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria”. Nature Communication. 2019 Jan 18;10(1):308.
  15. Plattner M, Shneider MM, Arbatsky NP, Shashkov AS, Chizhov AO, Nazarov S, Prokhorov NS, Taylor NMI, Buth SA, Gambino M, Gencay YE, Brøndsted L, Kutter EM, Knirel YA, Leiman PG. Structure and Function of the Branched Receptor-Binding Complex of Bacteriophage CBA120. J Mol Biol. 2019 Sep 6;431(19):3718-3739. doi: 10.1016/j.jmb.2019.07.022. Epub 2019 Jul 17. PMID: 31325442.
  16. Rotman E, Kouzminova E, Plunkett G, Kuzminov A. 2012. Genome of Enterobacteriophage Lula/phi80 and Insights into Its Ability To Spread in the Laboratory Environment. J Bacteriol 194:. https://doi.org/10.1128/jb.01353-12
  17. Unauthorized Horizontal Spread in the Laboratory Environment: The Tactics of Lula, a Temperate Lambdoid Bacteriophage of Escherichia coli Rotman E, Amado L, Kuzminov A (2010) Unauthorized Horizontal Spread in the Laboratory Environment: The Tactics of Lula, a Temperate Lambdoid Bacteriophage of Escherichia coli. PLOS ONE 5(6): e11106. https://doi.org/10.1371/journal.pone.0011106