The Transformative Role of Biophotonics in Rapid, Real-Time, and in Situ Studies of Microbial Structure, Cellular Processes, and Interactions

Abstract

Photonics and optical technologies provide powerful, noninvasive means to study microorganisms, including those that remain unculturable, by detecting light signals arising from specific structural and biochemical features. These include intrinsic chromophores such as aromatic amino acids, nicotinamide adenine dinucleotide hydride, and flavins; spectral signatures of functional groups in proteins, lipids, and nucleic acids; refractive index contrasts from cell walls and organelles; and scattering patterns shaped by microbial morphology. This review synthesizes current advances in applying optical and photonic methods to microbial research, with the explicit aim of showing how these tools enable in situ, real-time characterization of microbial structure, metabolic state, behavior, and interactions. We overview high-resolution imaging modalities (confocal, multiphoton, and super-resolution microscopy) for visualizing morphology and dynamics, spectroscopic techniques (Raman, surface-enhanced Raman scattering, Fourier transform infrared spectroscopy, fluorescence) for label-free molecular fingerprinting, and biosensors (fiber-optic, plasmonic, lab-on-chip) for rapid detection. We also examine light-based manipulation strategies (optogenetics, optical tweezers, laser ablation) that allow precise control of microbial processes and discuss emerging integrations with artificial intelligence analytics, quantum sensing, and space-adapted photonics. By linking the physical principles of signal generation to microbial targets, we highlight how photonics is transforming microbial ecology, diagnostics, and biotechnology and identify the technical challenges driving the development of next-generation optical tools.

Received: 1 August 2025 | Revised: 20 October 2025 | Accepted: 28 November 2025

Conflicts of Interest

The authors declare that they have no conflicts of interest to this work.

Data Availability Statement

Data sharing is not applicable to this article as no new data were created or analyzed in this study.

Author Contribution Statement

Abdul Rafay Rafiq: Conceptualization, Methodology, Software, Validation, Formal analysis, Investigation, Resources, Data curation, Writing – original draft, Writing – review & editing, Visualization, Supervision, Project administration. Muhammad Abdullah Farooq: Conceptualization, Methodology, Software, Formal analysis, Investigation, Data curation, Writing – original draft, Writing – review & editing, Visualization. Hamza Tariq: Conceptualization, Methodology, Software, Formal analysis, Investigation, Data curation, Writing – original draft, Writing – review & editing, Visualization. Ahsan Raza: Conceptualization, Methodology, Software, Formal analysis, Investigation, Data curation, Writing – original draft, Writing – review & editing, Visualization. Zeeshan Zafar Iqbal: Conceptualization, Methodology, Software, Formal analysis, Investigation, Data curation, Writing – original draft, Writing – review & editing, Visualization.