Examination of the microbial ecology of the avian intestine in vivo using bromodeoxyuridine

Bromodeoxyuridine, a thymidine analogue that can be incorporated into the DNA of actively dividing cells, has been used in vivo to identify intestinal bacteria that are metabolically active in 3-week-old turkey poults during an acute period of feed withdrawal. Automated ribosomal intergenic spacer analysis was used to identify amplicons unique to animals subjected to feed withdrawal. One amplicon was unique to fasted birds while two amplicons were present in 60% of fasted birds and absent in all fed birds. Sequence analysis of 16S ribosomal genes indicated the caecal communities of all birds were dominated by Clostridiaceae while also harbouring low levels of metabolically active gamma-proteobacteria and Bacteroides. Twenty per cent of clones from the fasted animals were identified as belonging to the genus Papillibacter, suggesting these microbes may be specifically dividing in response to environmental conditions present in the caeca of fasted birds.