DVM Student University of Cornell Ithaca, New York, United States
Abstract:
Background: Fecal samples for microbiota studies in calves are usually collected on a weekly basis. This approach can result in collection of samples from diarrheic calves without considering the time of diarrhea onset.
Objective: Compare the fecal microbiota of healthy calves, calves with diarrhea onset on the day of sampling (D< 24h), and calves having diarrhea for >24 to 48h (D24-48h). Animals: 20 healthy, 20 D< 24h, and 11 D24-48h veal calves of 3-7 days of age.
Methods: Case control study. Calves with loose or watery feces were considered as diarrheic. Fecal samples were collected on day 7 after arrival on farm. Fecal microbiota was characterized by sequencing of 16S ribosomal RNA gene amplicons.
Results: The fecal community membership (Jaccard index) and structure (Yue & Clayton index) of healthy calves were significantly different than those of diarrheic calves (AMOVA, P < 0.001 for both comparisons). Both the bacterial membership and structure differed significantly between D< 24h and D24-48h calves (AMOVA, P < 0.001 for both comparisons). Phocaeicola, Bacteroides, Prevotella, Faecalibacterium, Butyricicoccus, Ruminococcaceae, and Lachnospiraceae were enriched in healthy calves. Enterococcus, Ligilactobacillus, Lactobacillus, and Gallibacterium were enriched in the feces of D< 24h calves, while Enterococcus, Streptococcus, Clostridium sensu stricto and Escherichia/Shigella were enriched in the D24-48h calves.
Conclusions: Rapid changes in fecal microbiota occur during the first 48h of diarrhea. The time from diarrhea onset to sampling affect the bacterial composition of feces of diarrheic calves. Researchers should standardize times for fecal collection based on the time of diarrhea onset rather than convenient times.
