Precision probiotic development based on gut microbial biomarkers: from mechanistic insights to clinical translation

Abstract

The intricate interplay between individualized differences in gut microbiota and host health has garnered significant attention in contemporary biomedical research. This review elucidates the complex mechanisms governing the development of personalized gut microbial ecosystems and examines innovative modulation strategies, underscoring the imperative to transcend conventional “one-size-fits-all” paradigms in probiotic therapeutics. The gastrointestinal tract harbors a complex consortium of trillions of microorganisms. The enterotype paradigm categorizes the gut microbiota into three predominant clusters: Bacteroides-dominant, Prevotella-dominant, and Ruminococcus-dominant configurations. However, an individual's unique microbial signature is influenced by a multifactorial interplay of host genetics, dietary habits, birth modality, and environmental exposures, resulting in a microbial complexity that defies simplistic enterotype classification. Contemporary research has revealed that traditional dietary interventions for the modulation of gut microbiota often lack specificity and fail to account for individual microbial variations. In contrast, emerging probiotic and prebiotic approaches offer promising avenues for targeted microbial manipulation. To establish effective, individualized probiotic and prebiotic interventions, a comprehensive methodological framework is essential. This framework should integrate in vitro gut simulation models to replicate microbial ecosystems, in vivo studies to assess microbial colonization dynamics and metabolic impacts, and advanced computational approaches combining machine learning algorithms with multi-omics data analysis. Such an integrated approach facilitates the identification of gut microbial biomarkers and the development of precision probiotics, while requiring further refinement of algorithm-driven outcome prediction models and establishment of cross-population validation protocols, thereby accelerating the translation of gut microbiome research into personalized therapeutic strategies and advancing the frontier of precision medicine in gastrointestinal health.