LAUSR

BACKGROUND Antimicrobial-associated diarrhoea is a common adverse effect of antimicrobial treatment in horses and has been reported following the administration of oral doxycycline. The administration of antimicrobials has also been associated with changes in the equine intestinal microbiota diversity yet has not been explored under doxycycline treatment. OBJECTIVES To describe the dynamics of the faecal microbial diversity following a 5-day oral administration of doxycycline in healthy horses with Streptococcus zooepidemicus infected tissue chambers. STUDY DESIGN Experimental prospective cohort study in a single horse group. METHODS Seven healthy adult horses with S. zooepidemicus infected tissue chambers received oral doxycycline at 10 mg/kg q 12h for 5-days following the tissue chamber inoculation. Faeces were collected prior to the tissue chamber inoculation and until 28-days post inoculation. Faecal microbiota was characterised by high throughput sequencing of the V4 region of the 16S rRNA gene on the Illumina MiSeq sequencing platform. Bioinformatic analysis was performed with Mothur and statistical analysis were conducted on R Studio. RESULTS A significant decrease in alpha diversity, characterised by a decrease of richness and diversity, and a decrease in beta diversity, characterised by changes in relative abundance, occurred after initiation of and during the administration of doxycycline. A decrease in Verrucomicrobia and increase in Firmicutes:Bacteroidetes ratio occurred following the initiation of treatment, with a return to initial Firmicutes:Bacteroidetes ratio during the treatment. It took 23 days after discontinuing the treatment for the faecal microbiota to return close to the initial state. MAIN LIMITATIONS Lack of control population within the study. CONCLUSIONS Transitory intestinal dysbiosis occurs under oral administration of doxycycline in horses.