Label-free microscopy enables high-throughput identification of genes controlling biofilm development

Biofilms are structured microbial communities that thrive on diverse surfaces in natural, industrial, and host environments. The biofilm lifestyle underpins microbial survival, shapes ecosystem function, and drives persistent infections; yet, for many microbes, the molecular determinants of biofilm development remain poorly defined. Here, we introduce "label-free analysis of biofilms" (LFAB), an imaging method that integrates time-lapse, low-magnification brightfield microscopy with regional optical density measurements to quantify biofilm biomass. Unlike conventional assays, LFAB enables real-time, non-perturbative, and high-throughput monitoring of biofilm dynamics. We validated LFAB across diverse microbial species and observed a strong correlation with traditional biofilm quantification methods. Applying LFAB to Streptococcus pneumoniae, a major human pathogen whose biofilm lifecycle underpins colonization and infection, we uncovered reproducible patterns of microcolony biofilm expansion and growth. LFAB-enabled screening of a transposon mutant library revealed that biofilm formation in S. pneumoniae is shaped by genes spanning carbohydrate metabolism, cell wall synthesis, adhesion, and surface interactions. Further analysis identified choline-binding protein A (CbpA) and its associated two-component regulator, as well as the peptidoglycan hydrolase LytB, as key drivers of microcolony biofilm dynamics. Together, these findings establish LFAB as a broadly applicable platform for dissecting biofilm biology and reveal new regulators of biofilm development in a clinically important pathogen.

Biofilms are structured communities of microorganisms that attach to surfaces and persist within a self-produced matrix. The biofilm lifestyle underlies microbial survival in nature, contributes to industrial biofouling, and drives many chronic infections. Despite the importance of biofilms, high-throughput measurements of biofilm growth dynamics are challenging using existing tools, which are often disruptive or are not scalable. To overcome this limitation, we developed "label-free analysis of biofilms" (LFAB), a brightfield-based imaging platform that enables real-time, non-perturbative, and scalable quantification of biofilm biomass. LFAB is broadly applicable across species and correlates strongly with traditional assays. Applying LFAB to Streptococcus pneumoniae, a major human pathogen, we performed a mutagenesis screen, uncovering new genetic regulators of biofilm formation in this organism. These findings advance understanding of S. pneumoniae pathogenesis and establish LFAB as a powerful approach for dissecting the molecular basis of microbial community growth.