Genome-scale label-free imaging reveals cellular physiology encoded in bacterial collective architecture
- 1Carnegie Mellon University
Abstract
DNA sequencing unified microbial genotyping into a single, comprehensive readout, yet phenotyping remains a slow and fragmented endeavor. Here, we introduce Microbial Phenotyping Using Low-magnification Label-free Imaging (PULLI), a computer vision platform that extracts microcolony and population-level phenotypes from brightfield timelapses of liquid culture growth. Using PULLI, we screened a genome-scale Vibrio cholerae mutant library, recording more than 200,000 images, which revealed that core bacterial pathways shape community architecture. Functionally related mutants converge in appearance, allowing us to resolve processes as distinct as biofilm formation, motility, central metabolism, cofactor biosynthesis, and envelope composition using a single approach. We further show PULLI can be used to determine a drug target, characterize other pathogens, and classify bacterial species. Our results show that bacterial multicellular development is an interpretable signature of genotype-phenotype relationships, which can be captured from simple brightfield timelapses. We release the PULLI pipeline and an interactive atlas of community forms.
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BibTeX
@misc{mellick2026genomescale,
title = {{Genome-scale label-free imaging reveals cellular physiology encoded in bacterial collective architecture}},
author = {S. N. S. Mellick and J. J. Derringer and D. Boyes and G. Croteau and M. Burke and S. Gifford and D. J. Stark and L. A. Mike and S. Turecki and O. Carja and I. V. Mikheyeva-Bridges and D. A. Bridges},
howpublished = {bioRxiv},
year = {2026},
month = aug,
doi = {10.64898/2026.08.30.748126},
url = {https://www.biorxiv.org/content/10.64898/2026.08.30.748126v1},
note = {CC BY-NC},
}
RIS
TY - UNPB
TI - Genome-scale label-free imaging reveals cellular physiology encoded in bacterial collective architecture
AU - S. N. S. Mellick
AU - J. J. Derringer
AU - D. Boyes
AU - G. Croteau
AU - M. Burke
AU - S. Gifford
AU - D. J. Stark
AU - L. A. Mike
AU - S. Turecki
AU - O. Carja
AU - I. V. Mikheyeva-Bridges
AU - D. A. Bridges
PY - 2026
DA - 2026/08/30
PB - bioRxiv
DO - 10.64898/2026.08.30.748126
UR - https://www.biorxiv.org/content/10.64898/2026.08.30.748126v1
AB - DNA sequencing unified microbial genotyping into a single, comprehensive readout, yet phenotyping remains a slow and fragmented endeavor. Here, we introduce Microbial Phenotyping Using Low-magnification Label-free Imaging (PULLI), a computer vision platform that extracts microcolony and population-level phenotypes from brightfield timelapses of liquid culture growth. Using PULLI, we screened a genome-scale Vibrio cholerae mutant library, recording more than 200,000 images, which revealed that core bacterial pathways shape community architecture. Functionally related mutants converge in appearance, allowing us to resolve processes as distinct as biofilm formation, motility, central metabolism, cofactor biosynthesis, and envelope composition using a single approach. We further show PULLI can be used to determine a drug target, characterize other pathogens, and classify bacterial species. Our results show that bacterial multicellular development is an interpretable signature of genotype-phenotype relationships, which can be captured from simple brightfield timelapses. We release the PULLI pipeline and an interactive atlas of community forms.
ER -