This paper (Liu et al., 2025) provides a high-level review of the Gut–Brain Axis (GBA) as a target for precision nutraceutical interventions in the management of malnutrition, emphasizing the role of the microbiome as a predictive indicator of metabolic health. Centrally, it highlights how short-chain fatty acids (SCFAs) the primary metabolites of probiotic fermentation (such as by Lactobacillus strains) act as critical signaling ligands that modulate systemic inflammation, energy expenditure, and neuroendocrine responses. From a technical standpoint, the authors detail the interaction between these microbial metabolites and their cognate G-protein coupled receptors (GPR41, GPR43, and GPR109A), illustrating a pathway where nutrient-driven microbial shifts can suppress pro-inflammatory cytokines like TNF-α and IL-6. By integrating omics technologies (metagenomics and metabolomics) with nutraceutical quality assessments, the study proposes a shift toward “tailored interventions” where specific prebiotic substrates such as high-fiber fruit powders and probiotic consortia are used to optimize the host’s metabolic fingerprint and restore homeostatic signaling across the gut-brain and, by extension, the gut-bone axes.