Pattern-based rapid and robust profiling of gut microbiota and its metabolism with a single fluorescent probe

Abstract

The gut microbiota and the associated metabolism play a pivotal role in maintaining human health, yet their assessment is challenging due to their inherent diversity, variety, and complexity. Herein, we developed a multichannel sensor array based on a single fluorescent probe, allowing for rapid and robust profiling gut microbiota and their key metabolites including cysteine (Cys), glutathione (GSH), and homocysteine (Hcy). The assay leverages the single fluorescent probe that is with multiple binding sites and the cross-reactive sensing principle to specifically recognize different biological thiols. By analyzing the pattern of biological thiols, the assay is capable of rapidly identifying six gut-derived bacteria including probiotics, neutral, and pathogenic strains based on fluorescent fingerprints within 5 min, and also discriminating bacteria and their mixtures with different composition. Using the assay that enables the simultaneous measurement of multiple gut-derived bacteria and their metabolites, the designed array achieved an accuracy of 0.99 when discriminating colorectal cancer (CRC) patient feces samples from healthy individuals. Remarkably, the as-prepared sensor array can also be used to identify various stages of CRC. The simplicity, rapidness, and cost-effectiveness of our approach render it a robust platform for the analysis of gut microbiota.