In order to ensure precision in the use of probiotics, it is crucial to address the inherent heterogeneity present in probiotic strains, hosts, and their microbiomes. This comprehensive review aims to discuss the strategies necessary to mechanistically identify the most suitable probiotic strain of Bifidobacterium and/or Lactobacillus for targeting specific pathologies and comorbidities in individual patients. These strategies take into account the genetic and phenotypic characteristics of the strain, allowing for a personalized approach to probiotic selection. The integration of multi-omics approaches, such as genomics, transcriptomics, metabolomics, and proteomics, plays a vital role in elucidating the intricate metabolic and intermicrobial interactions associated with individual probiotic strains. By employing these techniques, it becomes possible to reconstruct metabolic networks and study the cross-feeding and production of molecular effectors by probiotics. These findings hold significant potential in modulating the ecological balance of metabolic networks within the host's microbial consortia. Specifically, this review will focus on the crucial role of Bifidobacteria and Lactobacillus as integral members of the human microbiota. It will delve into their potential as precision probiotics, aimed at preventing and treating various diseases.