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bioRxiv · 10.1101/2025.09.09.675137

A ratiometric pH sensor for Gram-positive and Gram-negative bacteria

Kossmann, D.·Iizuka, A.·Khanna, N.·Rivera-Fuentes, P.
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Abstract

Fluctuating environments can lead to phenotypic heterogeneity within a monoclonal bacterial population, especially in response to antibiotics or the human immune system. Methods are required to analyze the physiology of single cells to understand how individual cells interact with their environment and adapt to pH stress. We report a ratiometric, fluorescent probe to sense cytoplasmic pH in bacteria. Our probes are based on hemicyanine dyes and are taken up into both Gram-positive and Gram-negative bacteria. The probes react preferentially with OH- over other nucleophiles in biological systems. The response to pH changes is reversible and rapid, allowing for the real-time tracking of pH fluctuations. The sensing of these probes was tuned to allow for monitoring fluctuations around neutrality and biologically relevant acidifications. These probes were validated for cytoplasmic pH sensing in Escherichia coli, Staphylococcus epidermidis, and a clinically isolated methicillin-resistant Staphylococcus aureus (MRSA) strain. Furthermore, the probes enabled the identification of pH-sensitive phenotypes and monitored phagocytosis of virulent clinical strains in immune cells. Our probes are a promising tool for detecting phenotypic heterogeneity within bacterial populations and may help unravel the physiological state of resistant or persistent strains of clinical relevance.

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Kossmann, D., Iizuka, A., Khanna, N., Rivera-Fuentes, P.. 2025-09-09. A ratiometric pH sensor for Gram-positive and Gram-negative bacteria. https://doi.org/10.1101/2025.09.09.675137

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