Supplementation with Propionibacterium freudenreichii fermented second cheese whey modulates the composition of faecal microbiota in weanling lambs

Abstract Background Weaning represents a critical transition period during which dietary interventions may exert long-lasting effects on gut ecosystem structure and immune maturation. In small ruminants, nutritional management during weaning is a key determinant of gastrointestinal health and productive performance. Second cheese whey is a largely underutilized dairy industry by-product that, upon fermentation with Propionibacterium freudenreichii , undergoes enrichment in short-chain fatty acids and secondary metabolites known to modulate gut microbiota composition and host immune responses. With the aim of assessing the suitability of P. freudenreichii -fermented second cheese whey as a functional feed additive in early-life nutritional strategies for small ruminants, this study evaluated its effects on growth performance, haematological parameters, and faecal microbiota composition in weanling lambs. Results Twenty-one Sarda female lambs (58–60 days old) were randomly assigned to three groups ( n = 7): fermented second cheese whey (50 mL/day), unfermented second cheese whey (50 mL/day), and a non-supplemented control, for 14 days. Fermented second cheese whey supplementation had no effect on body weight gain. Haematological analysis revealed significant variations in red blood cell count ( p = 0.016) and mean corpuscular volume ( p = 0.02), although all values remained within the physiological range for the ovine species. Faecal microbiota analysis showed increased bacterial alpha diversity in the fermented group, as evidenced by higher richness and diversity indices ( p < 0.05). Beta-diversity analysis revealed a distinct microbial community structure in fermented-supplemented lambs. At the taxonomic level, fermented second cheese whey supplementation reduced by 56.2%, the abundance of Escherichia-Shigella , a genus that includes potentially pathogenic strains. This was accompanied by a 5.08-fold enrichment of obligately anaerobic Firmicutes, including Acetitomaculum , Blautia , Lachnospiraceae_NK3A20 _group, and Ruminococcus_ga uvreauii_ group. No comparable changes were observed in the unfermented group. Exploratory multivariate analysis highlighted Aspergillus, Malassezia, and Coprinellus as candidate discriminatory fungal genera across treatments. Conclusions Supplementation with P. freudenreichii- fermented second cheese whey effectively modulated the faecal microbiota of weanling lambs, enriching potentially beneficial taxa while reducing the relative abundance of Escherichia-Shigella . These findings suggest that fermented second cheese whey represents a viable strategy for the valorisation of dairy industry by-products, with potential implications for environmental hygiene in livestock production systems.