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

Abstract

Abstract 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 24 to 48 hours (D 24‐48h). Animals Thirty‐one diarrheic calves (20 D .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.

Keywords

• Clostridium
• dysbiosis
• Escherichia coli
• Lactobacillus
• scours