Dr. Emrah Şimşek === University of Florida === October 2025 - Present
Inferring microbial community composition from absorbance spectra:
The project's aim is to use mathematical modeling to determine community composition based souly on absorbance spectra collected by a UV-VIS-NIR spectrometer. We first aimed to identify if monocultures were able to be predicted based on the spectra, which revealed which monocultures had a unique spectra. Currently we are in the process of forming pairwise communities using strains which revealed to have unique spectra and dermining if the composition of the pairwise community can be determined using the absorbance spectra.I executed large-scale experiments across 12 strains, including both mono and pairwise communities, collecting and normalizing optical density data using spectrophotometers and microplate readers. Throughout this work, I safely conducted experiments on BSL-2 organisms, including Pseudomonas aeruginosa, using biosafety cabinets and established sterile technique, while also training graduate and undergraduate peers in experimental protocols, data handling practices, and lab safety procedures. To analyze the resulting large experimental datasets, I applied signal-to-noise metrics and statistical methods, as well as machine learning dimensionality reduction techniques such as principal component analysis (PCA) and linear discriminant analysis (LDA) to interpret high-dimensional data.
