Several themes, one lens:

Bacteria don't live in flasks. They navigate physical barriers, compete with neighboring microbes, and constantly fend off viral and immunological predators, all while trying to infect and colonize us. Our research is organized around several interconnected lines of inquiry, united by a single question: what are the rules of bacterial survival, and how do we use those rules to defeat them?

Bacterial Organization & Mechanomicrobiology Bacteria are far more structurally sophisticated than classical models suggested. We discovered how bacteria build cytoskeletons, sculpt their shapes, and sense mechanical forces like fluid flow and surface stiffness, as well as how this physical organization directly regulates virulence. This work helped establish the field of mechano-microbiology: bacteria both use mechanics to shape themselves and actively read their mechanical environment as a core part of how they cause disease. Bartlett et al., Cell 2017 · CrvA links V. cholerae morphology to pathogenesis Ramachandran et al., PNAS 2024 · Free-swimming bacteria transcriptionally respond to shear flow Hallinen et al., PNAS 2025 · Microcolony morphologies tune flow-dependent colonization

Single-Cell Heterogeneity & Host Interactions Bacteria within a clonal population are not identical. Individual cells harbor striking differences in gene expression that determine which ones survive antibiotic treatment, which ones successfully infect a host, and which ones are killed by phages. We developed M3-Seq and Duet-Seq as massively parallel single-cell RNA sequencing platforms to reveal how this individuality shapes bacterial outcomes in ways that bulk measurements entirely miss. Wang et al., Nature Microbiology 2023 · M3-Seq identifies rare antibiotic-surviving subpopulations and single-cell phage responses Yuan et al., submitted · Duet-Seq simultaneously profiles host and pathogen transcriptomes during infection

Phage-Bacteria Conflict & Anti-Infective Discovery Bacteria are not only predators but are prey. We study the regulatory principles of phage-bacteria conflict: how phages recognize and kill bacteria, how bacteria defend themselves, and how these dynamics unfold in 3D environments that better resemble real infections. These same principles guide our therapeutic work: using imaging-based machine learning, we have discovered antibiotics with novel mechanisms that evade resistance entirely as well as novel antibiotics whose spectrum can be tuned from broad to narrow spectrum to selectively spare the host microbiome. Martin et al., Cell 2020 · SCH-79797, dual-mechanism antibiotic that avoids resistance Chain et al., Nature Microbiology 2024 · Fluorofolin exploits metabolic differences for narrow-spectrum targeting Taylor et al., Nature 2025 · Prophages block cell surface receptors to preserve viral progeny