Low Concentration of Antibiotics Modulates Gut Microbiota at Different Levels in Pre-Weaning Dairy Calves

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.

Keywords: antibiotics; calf; colon; ileum; microbiota; rectum.

Figure 1

Principal component analysis (PCA) of bacterial community structures in the three treatments of the ileum (A), colon (B) and rectum (C). The percentage of variation explained by the x axis represented by PC1 and the y axis represented by PC2 are indicated in the axis. A = ileum; B = colon and C = rectum. CON = control; LCA = low cocktail of antibiotics concentration; LSA = low concentration of single antibiotic. The percentage of variation explained by PC1 and PC2 are indicated in the axis, and the ellipses represented with 95% confidence. R-values closer to 0 denote groups not significantly different from one another, while values closer to 1 denote a highly different community composition, P value ≤ 0.05 is significantly different.

Figure 2

Effect of feeding milk replacer (MR) with low antibiotics concentration cocktail or single on the phyla composition in the ileum, colon and rectum. A = ileum; B = colon and C = rectum. CON = control; LCA = low cocktail of antibiotics concentration; LSA = low concentration of single antibiotic. The values are the mean plus standard deviation.

Figure 3

Effect of feeding MR with low antibiotics concentration cocktail or single on the family distribution in the ileum, colon and rectum. A = ileum; B = colon and C = rectum. CON = control; LCA = low cocktail of antibiotics concentration; LSA = low concentration of single antibiotic. The values are the mean plus standard deviation.

Figure 4

Effect of feeding MR antibiotics on the predominant genera in the ileum, colon and rectum samples. A = ileum; B = colon; C = rectum; D and E Comparison of the relative abundances of the significantly different genera among treatments in the ileum and rectum respectively. CON = control; LCA = low cocktail of antibiotics concentration; LSA = low concentration of single antibiotic. The values are the mean plus standard deviation. Treatments with different letters are significantly different (P < 0.05).

Figure 5

Linear discriminant analysis (LDA) for the significantly abundant microbes across treatments in the ileum, colon and rectum. Histogram of the LDA scores calculated for differentially abundant genera in the ileum, colon and rectum at the genus level among the different treatments groups (only the genera LDA scores above 2 are shown). A = ileum; B = colon and C = rectum. CON = control; LCA = low cocktail of antibiotics concentration; LSA = low concentration of single antibiotic.