The human gut microbiota exerts profound effects on host physiology, metabolism, and immune function, positioning commensal bacteria as promising agents for microbiota-based therapeutics. However, a key barrier to clinical translation remains the limited mechanistic understanding of how specific microbes contribute to defined biochemical functions. To address this challenge, we established a function-focused approach that links microbial identity with enzymatic activity at molecular resolution. We developed and applied a phenotype-selection platform integrating activity-based probe fluorescence-assisted cell sorting (ABP-FACS), microbial culturing, and real-time biochemical assays. Using a fluorescent β-galactosidase-selective probe, we labeled, isolated, and characterized live bacterial subpopulations from human fecal samples. Fluorescence-based sorting enabled the enrichment of β-galactosidase-producing microbial consortia, which were subsequently validated by enzymatic activity assays showing significantly higher β-galactosidase activity compared to flow-through fraction. 16S rRNA gene sequencing revealed that the enriched communities were phylogenetically diverse, with select members of the families Bifidobacteriaceae and Lachnospiraceae among the most enriched taxa. Interestingly, these functionally enriched populations were not among the most abundant members of the bulk community, underscoring both the specificity of our probes and the novelty of this function-based isolation strategy. Together, these findings demonstrate a direct and selective link between microbial function and identity in complex gut communities. Our platform not only provides mechanistic insights into microbial functions but also establishes a foundation for developing targeted, safe, and compatible live microbiota-based therapeutics aimed at restoring lost functions in the human gut. This work advances the field of microbiota-centered therapy by enabling functional discovery beyond abundance-based approaches.