Abstract

The intestinal microbiota plays a major role in growth as well as maintenance of the health of animals. Traditionally, the microorganisms present in the intestine of animals were identified by bacteriological culture methods. In this study, the microbial community of caecal content of chicken was identified by sequencing genomic material directly from the caecum.Deoxyribonucleic acid (DNA) was extracted directly from the caecal microbial content of broiler chicken. 16S recombinant deoxyribonucleic acid (DNA) sequence is a hyper-variable region which is conserved in almost all prokaryotes. Using universal primers, the 16S rDNA sequence was amplified, cloned into PCR⁽⁴⁾ TOPO vector and transformed in Escherichia coli DH₅ α cells, the plasmid from clones containing target 16S rDNA sequence was sequenced. All the sequences were subjected to BLAST search against prokaryote genomic database to identify similar sequences. Cloned sequences exhibited high level of sequence similarity (> 95%) with Stenotrophomonas maltophilia (strain D1, AUX077, CCF00024, 776), uncultured bacterium P4D1-70, 87% with uncultured eubacterium clone GL178.1, S. maltophilia (strain HB, B2A, 776), Nanobacterium spp. nanoU, 94% with S. maltophilia(strain D1, AUX077), uncultured bacterium clone P4D7-617. Based on the similarity search and phylogenetic tree construction it was identified that the bacterial community present in the caecal content of broiler chicken belongs to Bacillus spp group and it exhibits the evolutionary relationship with Nanobacterium spp, Stenotrophomonas spp and unculturable microorganism.

Key words: 16S rDNA, cecal content, broiler chicken, universal primers.