Abstract
The aim of this study was to investigate the effect of feeding milk replacer (MR) with two different antibiotics treatments on the gut microbiota of pre-weaning calves. Twelve (12) Holstein male calves at 1-day-old were randomly assigned to: milk replacer without antibiotics (CON), milk replacer plus low cocktail of antibiotics (LCA) concentration (penicillin 0.024 mg/L, streptomycin 0.025 mg/L, tetracycline 0.1 mg/L, ceftiofur 0.33 mg/L), and milk replacer plus a low concentration of single antibiotic (LSA; ceftiofur 0.33 mg/L). All the calves were harvested at 35-day-old, and the digesta from the ileum and colon was collected in addition to fecal samples. Samples were analyzed by 16S rRNA gene using Illumina MiSeq platform. Results showed that there were significant differences among treatments in the ileum, where LCA significantly reduced the relative abundance of Enterobacteriaceae (P = 0.02) especially Escherichia-coli (P = 0.02), while LSA significantly reduced the relative abundance of Comamonas (P = 0.02). In the colon and rectum, LSA treatment was significantly enriched with the class Bacilli, whereas the control group was significantly enriched with Alloprevotlla (P = 0.03). However, at the family level in the rectum LCA and LSA significantly reduced the relative abundance of Acidaminococcaceae (P = 0.01). Moreover, at the genera level in the colon, LSA significantly increased Prevotellaceae_Ga6A1_ group (P = 0.02), whereas in the rectum both of treatments reduced the relative abundance of Phascolarctobacterium (P = 0.01). In conclusion, the overall low cocktail of antibiotics concentration induced changes at different taxonomic levels; specifically the decrease in Escherichia-coli which might subsequently reduce the incidences of diarrhea in calves.
Highlights
The gastrointestinal tract (GIT) of a young calf is colonized by millions of microbiota immediately after birth [1,2]
After data quality filtering and chimera removal, valid sequences based on 97% similarity were obtained for the ileum (26393 ± 8537), colon (30435 ± 2207), and rectum (23117 ± 8394)
Pereira et al [15] showed that antibiotics affected the microbiota at the genus level only; while our results showed that ingestion of antibiotics induced a shift at higher bacterial taxonomic levels
Summary
The gastrointestinal tract (GIT) of a young calf is colonized by millions of microbiota immediately after birth [1,2]. Deng et al [11] showed that waste milk pre-treatment significantly affected the microbiota composition of pre-weaning calves at genera level. Calves that were fed with medicated MR reported reduced morbidity and calf scours compared to those fed non-medicated MR [12,13,14] This reduction was likely due to modulation of the intestinal and fecal microbiota in the pre-weaning period [15,16,17]. Xie et al [16] and Looft et al [18] reported that in-feed antibiotics led to an increase in the abundance of pathogenic microbes like Escherichia-coli in calves and pigs, respectively. The inconsistent findings on the effect of antibiotics on fecal microbiota are possibly due to the kind of antibiotics, dose of antibiotics, different animals, and different kind of samples
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