Pensinger DA, Fisher AT, Dobrila HA, Van Treuren W, Gardner JO, Higginbottom SK, Carter MM, Schumann B, Bertozzi CR, Anikst V, Martin C, Robilotti EV, Chow J, Buck RH, Tompkins LS, Sonnenburg JL, Hryckowian AJ (2023). Butyrate differentiates permissiveness to Clostridioides difficile infection and influences growth of diverse C. difficile isolates. Infection & Immunity. doi:


Hanson L, VandeVusse L, Forgie M, Malloy E, Singh M, Scherer M, Kleber D, Dixon J, Hryckowian AJ, Safdar N (2022). A randomized controlled trial of an oral probiotic to reduce antepartum Group B Streptococcus colonization and gastrointestinal symptoms. American Journal of Obstetrics & Gynecology Maternal Fetal Medicine. doi:

Lynch JB, Bennett BD, Merrill BD, Ruby EG, Hryckowian AJ (2022). Independent host- and bacterium-based determinants protect a model symbiosis from phage predation. Cell Reports. doi: 

Pruss KM, Enam F, Battaglioli EJ, DeFeo M, Diaz OR, Higginbottom SK, Fischer CR, Hryckowian AJ, Van Treuren W, Dodd D, Kashyap P, Sonnenburg JL (2022). Oxidative ornithine metabolism supports non-inflammatory C. difficile colonization. Nature Metabolism doi:


*Gregory AL, *Pensinger DA, Hryckowian AJ (2021). A short chain fatty acid-centric view of Clostridioides difficile pathogenesis. PLoS Pathogens doi: *Co-first

Flaherty KE, Grembi JA, Ramachandran VV, Haque F, Khatun S, Rahman M, Maples S, Becker TK, Spormann AM, Schoolnik GK, Hryckowian AJ, Nelson EJ (2021). High-throughput low-cost nl-qPCR for enteropathogen detection: A proof-of-concept among hospitalized patients in Bangladesh. PLoS ONE doi: 

Hryckowian AJ (2021). Microbiome Management for the 21st Century and Beyond. mSystems doi:

Shkoporov AN, Khokhlova EV, Stephens N, Hueston C, Seymore S, Hryckowian AJ, Scholz D, Ross RP, Hill C (2021). Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis. BMC Biology doi:


*^Hryckowian AJ, *Merrill DB, Porter NT, Van Treuren W, Nelson EJ, Garlena RA, Russell DA, Martens EC, ^Sonnenburg JL (2020). Bacteroides thetaiotaomicron-infecting bacteriophage isolates inform sequence-based host range predictions. Cell Host & Microbe doi: *Co-first, ^Co-corresponding

Featured in Cell Host & Microbe Preview: Phage-bacteria Associations: Analyze. Match. Develop Therapies. 

Nelson EJ, Grembi JA, Chao DL, Andrews JR, Alexandrova L, Rodriguez PH, Ramachandran VV, Sayeed MdA, Wamala WJ, Debes AK, Sack DA, Hryckowian AJ, Haque F, Khatun S, Rahman M, Chien A, Spormann AM, Schoolnik GK (2020). Gold-standard cholera diagnostics are tarnished by lytic bacteriophage. Journal of Clinical Microbiology doi:

*Porter NT, *^Hryckowian AJ, Merrill BD, Fuentes JJ, Gardner JO, Glowacki RWP, Singh S, Crawford RD, Snitkin ES, Sonnenburg JL, ^Martens EC (2020). Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron. Nature Microbiology doi: *Co-first, ^Co-corresponding

Garland M, Hryckowian AJ, Tholen M, Loscher S, Van Treuren W, Oresic-Bender K, Sonnenburg JL, Bogyo M (2020). The clinical drug candidate ebselen attenuates inflammation and promotes microbiome recovery after antibiotic treatment for Clostridium difficile infection. Cell Reports Medicine doi:

Before 2020

Alexandrova L, Haque F, Rodriguez P, Marrazzo AC, Grembi JA, Ramachandran V, Hryckowian AJ, Adams CM, Siddique SA, Khan AI, Qadri F, Andrews JR, Rahman M, Spormann AM, Schoolnik GK, Chien A, Nelson EJ (2019). Identification of widespread antibiotic exposure in cholera patients correlates with clinically relevant microbiota changes. The Journal of Infectious Diseases doi:

Napier BA, Andres-Terre M, Mattis LM, Hryckowian AJ, Higginbottom SK, Cumnock K, Casey KM, Lugo KA, Schneider DS, Sonnenburg JS, Monack DM (2019). Western diet regulates immune status and the response to LPS-driven sepsis independent of the microbiome. Proceedings of the National Academy of Science doi:

Hryckowian AJ, Van Treuren W, Smits SA, Davis NM, Gardner JO, Bouley DM, Sonnenburg JL (2018). Microbiota accessible carbohydrates suppress Clostridium difficile infection in a murine model. Nature Microbiology doi:10.1038/s41564-018-0150-6

Dodd D, Spitzer MH, Van Treuren W, Merrill BD, Hryckowian AJ, Higginbottom SK, Le A, Cowan TM, Nolan GP, Fischbach MA, Sonnenburg JL (2017). A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites. Nature 551, 648-652 doi:10.1038/nature24661

*Hryckowian AJ, *Pruss KM, Sonnenburg JL (2017). The emerging metabolic view of Clostridium difficile pathogenesis. Current Opinion in Microbiology 35, 42-47. doi:10.1016/j.mib.2016.11.006, *Co-first

Oresic-Bender K, Garland M, Ferreyra JA, Hryckowian AJ, Child MA, Puri AW, Solow-Cordero DE, Higginbottom SK, Segal E, Banaei N, Shen A, Sonnenburg JL, Bogyo M (2015). Identification of a small molecule anti-virulence agent for the treatment of Clostridium difficile infection. Science Translational Medicine 7(306):306ra148. doi:10.1126/scitranslmed.aac9103

Hryckowian AJ, Baisa GA, Schwartz KJ, Welch RA (2015). dsdA does not affect colonization of the murine urinary tract by Escherichia coli CFT073. PLoS ONE 10(9):e0138121. doi:10.1371/journal.pone.0138121

Ferreyra JA, Wu K, Hryckowian AJ, Bouley D, Weimer B, Sonnenburg JL (2014). Gut microbiota-produced succinate promotes Clostridium difficile infection after antibiotic treatment or motility disturbance. Cell Host & Microbe 16, 770-777. doi:10.1016/j.chom.2014.11.003

Hryckowian AJ, Battesti A, Lemke JJ, Meyer ZC, Welch RA (2014). IraL is an RssB anti-adaptor that stabilizes RpoS during logarithmic phase growth in Escherichia coli and Shigella. mBio 5(3). doi:10.1128/mBio.01043-14

Hryckowian AJ, Welch RA (2013). RpoS contributes to phagocyte oxidase-mediated stress resistance during urinary tract infection by Escherichia coli CFT073. mBio 4(1). doi:10.1128/mBio.00023-13

Battaglioli EJ, Baisa GA, Weeks AE, Schroll RA, Hryckowian AJ, Welch RA (2011). Isolation of generalized transducing bacteriophages for uropathogenic strains of Escherichia coli. Applied and Environmental Microbiology 77(18):6630-5. doi:10.1128/AEM.05307-11

Hatfull GF, Jacobs-Sera D, Lawrence JG, Pope WH, Russell DA, Ko CC, Weber RJ, Patel MC, Germane KL, Edgar RH, Hoyte NN, Bowman CA, Tantoco AT, Paladin EC, Myers MS, Smith AL, Grace MS, Pham TT, O’Brien MB, Vogelsberger AM, Hryckowian AJ, Wynalek JL, Donis-Keller H, Bogel MW, Peebles CL, Cresawn SG, Hendrix RW (2010). Comparative genomic analysis of sixty mycobacteriophage genomes: genome clustering, gene acquisition and gene size. Journal of Molecular Biology 397, 119-143. doi:10.1016/j.jmb.2010.01.011

Hatfull GF, Pedulla ML, Jacobs-Sera D, Cichon PM, Foley A, Ford ME, Gonda RM, Houtz JM,Hryckowian AJ, Kelchner VA, Namburi S, Pajcini KV, Popovich MG, Schleicher DT, Simanek BZ, Smith AL, Zdanowicz GM, Kumar V, Peebles CL, Jacobs WR Jr, Lawrence JG, Hendrix RW (2006). Exploring the mycobacteriophage metaproteome: Phage genomics as an educational platform. PLoS Genetics Vol. 2, No. 6, e92. doi:10.1371/journal.pgen.0020092