Short communication. Effects of antibiotics (oxytetracycline, florfenicol or tulathromycin) on neonatal calves’ faecal microbial diversity.

In this study, we used barcoded pyrosequencing of the 16S rRNA gene to characterise the effects of antibiotic treatment upon the faecal microbiota of neonatal calves. Eleven pre-weaned calves were treated for pneumonia or otitis using one of three antibiotics (oxytetracycline, florfenicol or tulathromycin) and were matched for age /date of birth and sex with eleven control calves. All calves were born and reared at the same farm. Faecal microbial diversity data were obtained by barcoded pyrosequencing of the 16S rRNA gene one week pre-treatment, and one and two weeks post treatment for both treated and control calves. Using multivariate discriminant analysis we were able to show that antibiotic treatment has a substantial effect on faecal samples’ microbial composition one week after administration; this effect was no longer observed two weeks after administration. The effect of oxytetracycline treatment on Lactobacillus spp. was shown to be significant but many other important species appeared to be unaffected. The small number of calves used in the study prohibited quantitative comparisons of the effects of individual antibiotics compared to others on Chao1 richness index; despite this, however, some interesting numerical differences were apparent. In conclusion, our study serves to illustrate that change occurs in the gut microbiome of the young ruminant in response to antimicrobial administration. Given the limitations of our study we suggest that further similar studies are necessary