Effect of time of sample collection after onset of diarrhea on fecal microbiota composition of calves

BACKGROUND: The effect of time of sample collection after onset of diarrhea on the fecal microbiota composition of calves is unknown. OBJECTIVE: Compare the fecal microbiota of calves with diarrhea onset on the day of sampling (D <24h), and calves having had diarrhea for >24 to 48 hours (D 24‐48h). ANIMALS: Thirty‐one diarrheic calves (20 D <24h and 11 D 24‐48h), 3 to 7 days of age. METHODS: Cross‐sectional study. Diarrhea was defined as a calf with loose feces or watery feces. Assessment of the fecal microbiota was performed by sequencing of 16S ribosomal RNA gene amplicons. RESULTS: Richness and diversity were not statistically different between D <24h and D 24‐48h (P > .05), but bacterial membership and structure differed significantly (AMOVA, P < .001 for both comparisons). Linear discriminant analysis effect size (LefSe) showed an enrichment of Faecalibacterium, Phocaeicola, Lachnospiracea, and Lactobacillus in the feces of D <24h calves, whereas Escherichia/Shigella, Ligilactobacillus, Clostridium_Sensu_Stricto, Clostridium_Incerta_Sedis, and Enterococcus were enriched in the D 24‐48h calves. CONCLUSION AND CLINICAL IMPORTANCE: Rapid changes in fecal microbiota occur during the first 48 hours of diarrhea with an enrichment of lactic acid‐producing bacteria in D <24h followed by an enrichment in Escherichia/Shigella and Clostridium spp. in D 24‐48h. The time from diarrhea onset to sampling appears to affect the bacterial composition. Researchers should standardize times for fecal collection based on the time of diarrhea.