Assessing the Effects of Farm Management Systems and Diarrhea on Gut Microbiota and Metabolites in Dairy Calves in Indonesia

Dairy production in Indonesia relies on two contrasting calf-rearing systems: concentrate-driven commercial dairy systems (CDS) and smallholder farms (SH). As these systems differ in feeding practices, they may influence gut development in calves. This study examined how farm management affects the fecal microbiota and metabolites in healthy and diarrhea post-weaning calves. Fecal samples were collected from 11 and 14 calves from CDS and SH facilities, respectively. Gut bacterial communities were analyzed using 16S rRNA gene amplicon sequencing, and metabolites were characterized using untargeted gas chromatography-mass spectrometry (GC-MS). Microbial diversity, metabolite profiles, and correlation networks were compared between the farm types and diarrhea status. Our results showed that farm management strongly shaped microbial community structure and metabolic outputs, but did not alter microbial richness. Although diarrhea is typically associated with reduced microbial richness, it did not affect the microbial community structure, suggesting that it primarily impacted microbial function, particularly the metabolic environment. Correlation network analysis revealed stronger linkages between microbes and metabolites in SH calves, especially under healthy conditions. Overall, these findings indicate that dietary structure is a key determinant of fermentation stability, with CDS calves showing greater metabolic instability. In contrast, SH calves maintain a more resilient, fiber-driven functional state.