Microbial signature of calf diarrheic gut

Neonatal calf diarrhea is a common disease, leading to a major economic loss for cattle producers worldwide. Several infectious and non-infectious factors are implicated in calf diarrhea, but disease control remains problematic because of the multifactorial etiology of the disease. To gain insight into the dysbiotic signature of the gut microbiome in calf diarrhea, we conducted diagnostic multiplex PCR assay and meta-omics analysis (16S rRNA gene-based metagenomics and untargeted transcriptional profiling) of rectal content of normal and diarrheic beef calves (n = 18). In the diarrheic calf gut, we detected both microbial compositional dysbiosis (i.e., increased abundances of the family Enterobacteriaceae members and their lytic bacteriophages) and functional dysbiosis (i.e., elevated levels of aerobic respiration and virulence potential). Longitudinal analysis of the gut microbiota in intermittently diarrheic calves (n = 5) revealed a positive correlation between the abundance of Enterobacteriaceae and the incidence of diarrhea.