Aptasensors for specific quantification of the health-relevant gut bacterium Prevotella copri in faecal samples of young and old mice
Age-associated remodelling of the gut microbiome is increasingly recognized as a key determinant of metabolic health, inflammation and frailty. However, most microbiome studies rely on sequencing-based relative abundance profiling, which lacks rapid, species-resolved and absolute quantification in complex biological samples. Here, we report the development of a species-specific, aptamer-based reduced graphene oxide field-effect transistor (rGO-FET) biosensor for quantitative detection of Prevotella copri, a metabolically relevant gut bacterium associated with aging and inflammatory phenotypes. Using FluCell-SELEX against intact P. copri cells combined with iterative counter-selection against co-occurring gut anaerobes, a highly enriched polyclonal aptamer library (AptPC10) as generated. Fluorescence-based assays demonstrated strong specificity and quantitative discrimination of P. copri in mixed bacterial suspensions. Binding analysis yielded a dissociation constant (KD) of 4.2 nM, confirming high-affinity target recognition. Integration of AptPC10 into an rGO-FET platform enabled label-free, real-time electronic detection. The sensor remained specific under competitive conditions and exhibited linear signal responses proportional to P. copri concentration. Application to faecal samples from young and old mice allowed quantitative determination of endogenous P. copri abundance, revealing relative proportions of 14.8% and 10.9%, without need of next-generation sequencing (NGS). Together, this study establishes a rapid, amplification-free and species-selective biosensing strategy for absolute bacterial quantification in complex microbiome samples. The AptPC10-functionalized rGO-FET platform provides a scalable framework for targeted microbiome monitoring in aging research and translational diagnostics.