Publications

Explore publications from the Phage Foundry team.

2026

  1. Yang S, Cress BF. Disarming a pathogen with programmable phage-derived particles. Trends Microbiol 2026;0. https://doi.org/10.1016/j.tim.2026.07.013.
  2. [Preprint] Selvakumar H, Noonan AJC, Rotman E, Alayouni M, Piya D, Maucourt F, Koderi Valappil S, Svab M, Orihuela B, Cowser G, Murray I, Bousliman C, Kazakov A, Deutschbauer AM, Roux S, Mimee M, Arkin AP, Mutalik VK. A comprehensive phage-bacteria interaction atlas links phage lineage and capsule serotype to genome-guided machine learning prediction in Klebsiella pneumoniae. bioRxiv 2026:2026.08.12.744533. https://doi.org/10.64898/2026.08.12.744533.
  3. 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. Cross-family and phage-specific gene requirements for Klebsiella infection revealed by scalable RB-TnSeq genetic screens. PLoS Genet 2026;22:e1012233. https://doi.org/10.1371/journal.pgen.1012233.
  4. [Preprint] Englert F, Valappil SK, Kubilius J, Jones SK Jr, Mutalik VK, Beisel CL, Patinios C. Targeted DNA nicking enables efficient, single-step and counterselection-free editing of bacteriophage genomes. bioRxiv 2026:2026.06.25.734514. https://doi.org/10.64898/2026.06.25.734514.
  5. Trinh J, Mutalik VK, Mageeney CM. Discovery, induction, and screening of prophages in clinical Acinetobacter baumannii isolates. Phage (New Rochelle) 2026. https://doi.org/10.1177/26416549261461823.
  6. [Preprint] Piya D, Noonan AJC, Selvakumar H, Alayouni M, Valappil SK, Maucourt F, Murray I, Svab M, Bousliman C, Heidenblut M, Orihuela B, Kazakov A, Carlson H, Yao Y, Smith E, Roux S, Deutschbauer A, Inman J, Arkin AP, Mutalik VK. Comprehensive interaction profiling and machine learning prediction of bacteriophage infectivity across clinically diverse Pseudomonas aeruginosa. bioRxiv 2026:2026.05.19.726084. https://doi.org/10.64898/2026.05.19.726084.
  7. [Preprint] Patel J, Swartz SE, Oromi-Bosch A, Yong L, LaTurner ZW, Demaray JE, Voelker A, Ono R, Vu P, Rao P, Luskin H, Andrade P, Cui ML, Mchedlishvili G, Hayes MM, Aluwihare N, Iglesias-Aguirre CE, MacKenzie EC, Rodriguez CI, Devkota S, Diamond S, Cress BF. Bridge recombinase enables versatile rewriting of bacterial genomes. bioRxiv 2026:2026.04.29.721476. https://doi.org/10.64898/2026.04.29.721476.
  8. González-Delgado A, Bonillo-Lopez L, Johnson MS, Knödlseder N, Ko C-C, Lekbach Y, Oh J-H, Selvakumar H, Wold MC, Yu Z, Aragón V, Gralnick JA, Güell M, Hatfull GF, Keitz BK, Koskella B, Mutalik VK, van Pijkeren J-P, Shipman SL. Genome editing of phylogenetically distinct bacteria using cross-species retron-mediated recombineering. Nat Biotechnol 2026:1–13. https://doi.org/10.1038/s41587-026-03076-6.
  9. [Preprint] Moriniere L, Noonan AJC, Kazakov A, Pena M, Svab M, Rivera-Lopez EO, Maucourt F, Johnson MS, Roux S, Koskella B, Deutschbauer AM, Dudley EG, Mutalik VK, Arkin AP. Enabling the prediction of phage receptor specificity from genome data. bioRxiv 2026:2026.04.02.716166. https://doi.org/10.64898/2026.04.02.716166.
  10. Mutalik VK, Inman JL, Chang H, Arkin A, Mao J-H. Phage therapy in oncology: opportunities for cancer prevention and treatment. Trends Mol Med 2026;0. https://doi.org/10.1016/j.molmed.2026.02.001.

2025

  1. [Preprint; accepted in Nature Microbiology] Noonan AJC, Moriniere LC, Rivera-López EO, Patel K, Pena M, Svab M, Kazakov A, Deutschbauer A, Dudley EG, Mutalik VK, Arkin AP. Phylogeny-agnostic strain-level prediction of phage-host interactions from genomes. bioRxiv 2025:2025.11.15.688630. https://doi.org/10.1101/2025.11.15.688630.
  2. Adler BA, Al-Shimary MJ, Patel JR, Armbruster EG, Colognori D, Charles EJ, Miller KV, Lahiri A, Cui ML, Oromí-Bosch A, Voelker A, Trinidad M, Lee J, Beurnier S, Boger R, Nomburg J, Barrangou R, Mutalik VK, Schoeniger JS, Pogliano JA, Savage DF, Doudna JA, Cress BF. CRISPRi-ART enables functional genomics of diverse bacteriophages using RNA-binding dCas13d. Nat Microbiol 2025;10:694–709. https://doi.org/10.1038/s41564-025-01935-7. OSTI: 2551792
  3. 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. OSTI: 2500395

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. OSTI: 2502080
  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. OSTI: 2477758

Relevant Reading from 2023 and Earlier

Phage Foundry member names are bolded.

  1. Piya D, Nolan N, Moore ML, Ramirez Hernandez LA, Cress BF, Young R, Arkin A, Mutalik VK. Systematic and scalable genome-wide essentiality mapping to identify nonessential genes in phages. PLoS Biol 2023;21:e3002416. https://doi.org/10.1371/journal.pbio.3002416. 
  2. Adler BA, Al-Shimary MJ, Patel JR, Armbruster E, Colognori D, Charles EJ, Miller KV, Lahiri A, Trinidad M, Boger R, Nomburg J, Beurnier S, Cui ML, Barrangou R, Mutalik VK, Schoeniger JS, Pogliano JA, Savage DF, Doudna JA, Cress BF. Genome-wide Characterization of Diverse Bacteriophages Enabled by RNA-Binding CRISPRi. BioRxiv 2023. https://doi.org/10.1101/2023.09.18.558157. 
  3. Carlson HK, Piya D, Moore ML, Magar RT, Elisabeth NH, Deutschbauer AM, Arkin AP, Mutalik VK. Geochemical constraints on bacteriophage infectivity in terrestrial environments. ISME Commun 2023;3:78. https://doi.org/10.1038/s43705-023-00297-7. 
  4. Adler BA, Chamakura K, Carion H, Krog J, Deutschbauer AM, Young R, Mutalik VK, Arkin AP. Multicopy suppressor screens reveal convergent evolution of single-gene lysis proteins. Nat Chem Biol 2023;19:759–66. https://doi.org/10.1038/s41589-023-01269-7. 
  5. Strathdee SA, Hatfull GF, Mutalik VK, Schooley RT. Phage therapy: From biological mechanisms to future directions. Cell 2023;186:17–31. https://doi.org/10.1016/j.cell.2022.11.017. 
  6. Adler BA, Hessler T, Cress BF, Lahiri A, Mutalik VK, Barrangou R, Banfield J, Doudna JA. Broad-spectrum CRISPR-Cas13a enables efficient phage genome editing. Nat Microbiol 2022;7:1967–79. https://doi.org/10.1038/s41564-022-01258-x. 
  7. Mutalik VK, Arkin AP. A Phage Foundry framework to systematically develop viral countermeasures to combat antibiotic-resistant bacterial pathogens. iScience 2022;25:104121. https://doi.org/10.1016/j.isci.2022.104121. 
  8. 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;7:34–47. https://doi.org/10.1038/s41564-021-01014-7. 
  9. Adler BA, Kazakov AE, Zhong C, Liu H, Kutter E, Lui LM, Nielsen TN, Carion H, Deutschbauer AM, Mutalik VK, Arkin AP. The genetic basis of phage susceptibility, cross-resistance and host-range in Salmonella. Microbiology 2021;167. https://doi.org/10.1099/mic.0.001126. 
  10. Carim S, Azadeh AL, Kazakov AE, Price MN, Walian PJ, Lui LM, Nielsen TN, Chakraborty R, Deutschbauer AM, Mutalik VK, Arkin AP. Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins. ISME J 2021;15:2289–305. https://doi.org/10.1038/s41396-021-00921-1. 
  11. Mutalik VK, Adler BA, Rishi HS, Piya D, Zhong C, Koskella B, Kutter EM, Calendar R, Novichkov PS, Price MN, Deutschbauer AM, Arkin AP. High-throughput mapping of the phage resistance landscape in E. coli. PLoS Biol 2020;18:e3000877. https://doi.org/10.1371/journal.pbio.3000877. 
  12. 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;431:3718–39. https://doi.org/10.1016/j.jmb.2019.07.022. 
  13. Mutalik VK, Novichkov PS, Price MN, Owens TK, Callaghan M, Carim S, Deutschbauer AM, Arkin AP. Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria. Nat Commun 2019;10:308. https://doi.org/10.1038/s41467-018-08177-8. 
  14. Rotman E, Kouzminova E, Plunkett G 3rd, Kuzminov A. Genome of Enterobacteriophage Lula/phi80 and insights into its ability to spread in the laboratory environment. J Bacteriol 2012;194:6802–17. https://doi.org/10.1128/JB.01353-12. 
  15. Rotman E, Amado L, Kuzminov A. Unauthorized horizontal spread in the laboratory environment: the tactics of Lula, a temperate lambdoid bacteriophage of Escherichia coli. PLoS One 2010;5:e11106. https://doi.org/10.1371/journal.pone.0011106.