How wastewater composition and isolation workflow shape Raman-based bacterial phenotyping

Wastewater represents a structurally and chemically heterogeneous environment in which suspended particulates and polymeric organic matter influence microbial recovery and measurable phenotype. Here, we systematically examined how matrix architecture and sample handling affect single-cell Raman phenotyping. Using defined synthetic wastewater supplemented with either agarose (structurally stable) or tapioca (dynamic, particulate-rich) matrices, we demonstrate that matrix structure influences bacterial recoverability and redistributes Raman-detectable biochemical phenotypes across five clinically relevant species (Pseudomonas aeruginosa, Escherichia coli, Acinetobacter baumannii, Enterococcus faecalis, and Enterococcus faecium). We further establish that filtration-based isolation constitutes a pre-analytical bias factor, by shaping both the recovered cell fraction and the resulting spectral profiles. Despite these influences, PCA-LDA maintained robust intra- and inter-species discrimination, indicating that the observed Raman spectral variation reflects not only species-associated differences but also matrix- and workflow-related effects. Together, these findings position matrix-aware standardization as a prerequisite for translating Raman-based surveillance from controlled settings to real-world wastewater monitoring.