Exploratory Shotgun Metagenomic Analysis of the Fecal Microbiome and Antimicrobial-Resistance Potential in Simmental Calves with Different Diarrheal Statuses

Calf diarrhea is frequently accompanied by disruption of the gastrointestinal microbiota, but the relationships between clinical status and microbial community composition, gene-content functional potential, and antimicrobial-resistance-associated features remain incompletely characterized. This exploratory study aimed to characterize these features in calves with different diarrheal statuses using shotgun metagenomics. Six approximately 2-month-old Simmental calves from Chahar Right Middle Banner, Inner Mongolia, were included, comprising two healthy calves, two calves with mild diarrhea, and two calves with severe diarrhea. Read-based taxonomic profiling was complemented by gene-abundance-weighted taxonomic annotation, and microbial functional potential was characterized using eggNOG/COG, KEGG, and CAZy annotations, together with conservatively screened CARD-associated sequence-homology candidates. The two severe-diarrhea samples exhibited lower bacterial richness and Shannon diversity, although PCoA did not show clear separation according to clinical severity. These two samples showed high representation of Proteobacteria and Enterobacteriaceae-related taxa, particularly Escherichia-related assignments, together with lower representation of Ruminococcaceae, Faecalibacterium, and Prevotella. Gene-content profiles showed higher representation of selected functions related to transport, environmental sensing, motility, secretion, and bacterial cell-envelope processes, whereas several glycan- and complex-carbohydrate-associated functions showed lower representation. Selected CARD-associated candidates were also more abundant in the severe-diarrhea samples. Within this small exploratory cohort, the two severe-diarrhea samples therefore showed concordant taxonomic and gene-content differences; however, these observations should not be interpreted as a general severity-specific microbiome signature and require validation in larger longitudinal cohorts.