Metabolic Screening of Gut Microbiota by Fourier-Transform Infrared Spectroscopy

Short-chain fatty acids (SCFAs) are bacterial metabolites with crucial roles in host homeostasis and immune system modulation. Given their benefits, they have been proposed as markers of healthy microbiota. However, accurate SCFA quantification typically requires gas chromatography coupled with mass spectrometry (GC-MS), which is time-consuming, expensive, and requires specialized personnel and equipment, limiting its routine use for stool quality assessment in clinical contexts. In this initial feasibility study, we explored the use of Fourier transform infrared (FT-IR) spectroscopy as a rapid metabolic screening approach for stool samples. Analysis of SCFA-associated spectral windows enhanced discrimination between healthy and dysbiotic stool samples with Clostridioides difficile infection using principal component analysis. FT-IR is not intended to replace GC-MS for precise SCFA quantification but rather to provide a rapid screening of metabolically relevant differences. Although additional validation is still needed, the present study provides a robust proof-of-concept demonstrating the feasibility of applying FT-IR spectroscopy to clinical stool samples. Combined with the widespread availability of this technology in most hospitals, these advantages highlight its potential for future development as a tool for routine screening in clinical laboratories.