Multi-omics insights into gut microbiota-metabolite interactions under probiotic intervention in a developmental cafeteria diet model

The developmental phase is a pivotal biological period for the maturation of the gut microbiota and the establishment of lifelong metabolic health. During these period, dietary patterns that induce dysbiosis, such as the high-fat, low-fiber “cafeteria diet,” disrupt the production of key metabolites in the gut-metabolite axis, including short chain fatty acids (SCFAs) and indole-3-propionic acid (IPA). This study employs a multi-omics approach to examine the impact of cafeteria diet exposure during the developmental period (days 21–56) in 21-day-old male Wistar rats on microbiota composition, SCFA, and IPA levels, and to assess the extent to which concurrent probiotic administration can mitigate these disruptions. The cafeteria diet led to a marked reduction in alpha diversity indices (Shannon p = 0.021; Simpson p = 0.034) and altered the Firmicutes/Bacteroidetes ratio (p = 0.015). Beta diversity analysis indicated a distinct separation between groups (PERMANOVA p = 0.002). Metabolite analysis revealed significant reductions in acetic acid (p = 0.004), isobutyric acid (p = 0.094), butyric acid (p = 0.0014), valeric acid (p = 0.0001), heptanoic acid (p = 0.0125), and IPA (p = 0.002), whereas probiotic administration largely restored these levels. At the species level, cafeteria diet markedly increased Segatella copri, while probiotic intervention partially restored beneficial taxa such as Faecalibacterium prausnitzii and butyrate-producing genera (Anaerostipes hadrus, Intestinimonas butyriciproducens, Blautia wexlerae, and Flintibacter sp. KGMB00164), as evidenced primarily by shotgun metagenomics. Correlation analysis further revealed strong positive associations between butyrate and F. prausnitzii (ρ = 0.65, p = 0.003) and between IPA and B. longum (ρ = 0.68, p = 0.002). Collectively, these results highlight the protective role of probiotic intervention against diet-induced dysbiosis by reinforcing microbiota metabolite interactions. By integrating metagenomic and metabolomic analyses, this multi-omics study demonstrates that exposure to a high-fat cafeteria diet during the developmental period disrupts microbiota composition and metabolite production, whereas concurrent probiotic administration largely prevent these effects, serving a protective role in the gut-metabolite axis. The study underscores the potential of early-life probiotic intervention, supports SCFA and IPA production, as a critical strategy to optimize microbiota-metabolite interactions and promote long-term gut and systemic health.