Parenteral long-acting amoxicillin reduces intestinal bacterial community diversity in piglets even 5 weeks after the administration

We investigated the long-term effects of a single intramuscular administration of amoxicillin (15 mg kg-1) 1 day after birth, on piglet intestinal microbiota. Animals received no creep feed before weaning on day 28 of age. For the next 11 days, the piglets received a wheat¿barley-based diet. Colon digesta samples were collected on day 39 and subjected to denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments. DGGE fingerprint diversity indices differed between the group treated with amoxicillin and the untreated group (0.80.19 and 1.030.17, respectively, P=0.012). Reamplification and sequencing of two bands present in all samples revealed that a Roseburia faecalis-related population was strongly reduced in relative abundance (98% identity) in the treated group, while an enterobacterial population with 100% identity to Shigella spp., Escherichia coli and Salmonella enterica serovar Typhi was enriched. A band corresponding to Lactobacillus sobrius was present only in the control group. The protective effect of prophylactic antibiotic administration may be outweighed by the long-lasting disturbance of the gut ecosystem.