Surface-Enhanced Raman Scattering-Based Surface Chemotaxonomy: Combining Bacteria Extracellular Matrices and Machine Learning for Rapid and Universal Species Identification

Abstract

Rapid, universal, and accurate identification of bacteria in their natural states is necessary for on-site environmental monitoring and fundamental microbial research. Surface-enhanced Raman scattering (SERS) spectroscopy emerges as an attractive tool due to its molecule-specific spectral fingerprinting and multiplexing capabilities, as well as portability and speed of readout. Here, we develop a SERSbased surface chemotaxonomy that uses bacterial extracellular matrices (ECMs) as proxy biosignatures to hierarchically classify bacteria based on their shared surface biochemical characteristics to eventually identify six distinct bacterial species at >98% classification accuracy. Corroborating with in silico simulations, we establish a three-way inter-relation between the bacteria identity, their ECM surface characteristics, and their SERS spectral fingerprints. The SERS spectra effectively capture multitiered surface biochemical insights including ensemble surface characteristics, e.g., charge and biochemical profiles, and molecular-level information, e.g., types and numbers of functional groups. Our surface chemotaxonomy thus offers an orthogonal taxonomic definition to traditional classification methods and is achieved without gene amplification, biochemical testing, or specific biomarker recognition, which holds great promise for point-of-need applications and microbial research.

Quantitative Analysis of Trace Analytes with Highly Sensitive SERS Tags on Hydrophobic Interface

“…With the advancement of nanotechnology, plasmon-enhanced spectroscopy has rapidly progressed, including techniques such as surface-enhanced fluorescence, surface-enhanced infrared spectroscopy, and surface-enhanced Raman scattering (SERS). Among these, SERS has garnered widespread attention due to its potential for sensitive detection as a surface analysis technique. − It combines the principles of Raman spectroscopy with the unique properties of nanostructured metal surfaces, resulting in a significant enhancement of Raman signal intensity. − Since this pioneering discovery, researchers have been dedicated to in-depth exploration and utilization of SERS across various fields including chemical analysis, − bioassays, , environmental monitoring, and materials science. − A pivotal advantage of SERS lies in its ability to provide vibrational spectra akin to fingerprints, offering highly specific information about the chemical composition and structure of molecules. , Furthermore, the integration of SERS with technologies such as microfluidics, , plasmonics, , and nanotechnology has further extended its applicability. For instance, in biomedical research, SERS has been applied for label-free detection of biomolecules, − imaging of cellular processes, − and even in vivo diagnostics .…”

Unmasking Bacterial Identities: Exploiting Silver Nanoparticle ‘Masks’ for Enhanced Raman Scattering in the Rapid Discrimination of Diverse Bacterial Species and Antibiotic-Resistant Strains

“…Although this method can be used for rapid quantitative detection (within 30 min) or classification of bacteria, it can only detect specific bacteria. Recently, Ling et al 13 developed a SERS-based method for surface chemotaxonomy. This method utilizes bacterial extracellular matrices (ECMs) as proxy biomarkers and uses a 4-mercaptopyridine (MPY) smallmolecule SERS probe to obtain different SERS spectra of MPY bacteria to accurately identify six different bacterial species, but this is the signal of the probe and not the signal of the bacteria in situ.…”