Fecal Microbiota Dysbiosis and Diarrhea-Associated Bacterial Taxa in Post-Weaning Dairy Calves

Post-weaning diarrhea is a prevalent gastrointestinal disorder in intensive dairy calf production, causing impaired growth, elevated mortality and widespread excessive antimicrobial use. While fecal microbiota dysbiosis is well implicated in diarrhea pathogenesis, specific microbial signatures linked to post-weaning diarrhea remain incompletely defined. In this case–control study, we performed 16S rRNA gene amplicon sequencing to characterize and compare fecal microbiota of 101 diarrheic and 101 clinically healthy female Holstein calves at 7 days post-weaning. Diarrheic calves exhibited significantly higher species richness (Chao1 index, p = 8.7 × 10−21) but reduced community evenness (Simpson index, p = 2.3 × 10−10), a distinct pattern from most neonatal calf diarrhea reports. Microbial community structure differed significantly between groups (PERMANOVA, Bray–Curtis dissimilarity, R2 = 0.084, p = 0.001). Four genera including Faecousia (fold change = 1.40) were enriched in diarrheic calves, while six genera including Duncaniella (fold change = 0.34) were depleted after FDR correction and validated by complementary statistical methods. PICRUSt2 functional prediction revealed downregulated carbohydrate metabolism and energy biosynthesis pathways in diarrheic calves, alongside upregulated xenobiotic degradation and stress response pathways. This study identifies high-confidence bacterial biomarkers for post-weaning calf diarrhea, providing a solid microbial basis for developing targeted microbiota-based prevention and intervention strategies.