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Uyeno and others (2010) and Oikonomou and others (2013) identified dynamic changes in the faecal microbiota of dairy calves during the first 12 weeks and first 7 weeks of life, respectively; their findings suggested that diet and gut development may drive these changes. Antibiotics are commonly used in the treatment of bacterial infections in all animal species but the effects of antibacterial drugs upon the microbial communities of the gut are poorly understood. Studies in human beings and other monogastric species have demonstrated changes in the gut microbiota subsequent to antimicrobial administration (Suchodolski and others 2009, Panda and others 2014). However, to the best of the authors’ knowledge, the effects of antibiosis upon the gut microbiota characterised with the use of a culture-independent metagenomic approach in ruminant species and particularly neonatal calves have not been examined yet.
The data used in the study described here were collected in a prospective cohort study (Oikonomou and others 2013) that described faecal microbial diversity in 61 female preweaned Holstein calves during their first seven weeks of life. Faecal samples were collected at birth then weekly and kept frozen until used for bacterial DNA extraction. Farm management, sample collection, DNA extraction, PCR and pyrosequencing are described in detail by Oikonomou and others (2013). Eleven of these calves contracted pneumonia or otitis during the study, and were treated with systemic antibiotics. Seven calves were treated with oxytetracycline (‘Biomycin’ Boehringer-Ingleheim, single intramuscular injection of 20 mg/kg of bodyweight), one calf was treated with tulathromycin (‘Draxxin’, Zoetis, single subcutaneous injection of 2.5 mg/kg of bodyweight) and three calves were treated with florfenicol (‘Nuflor’ Schering-Plough, single subcutaneous injection of 40 mg/kg of bodyweight). This enabled the retrospective …