Microflora ecology of the chicken intestine using 16S ribosomal DNA primers

Poult Sci. 2004 Jul;83(7):1093-8. doi: 10.1093/ps/83.7.1093.


The microflora in the gastrointestinal tract of broiler chickens influences digestion, health, and wellbeing. Analysis of chicken gut microflora has been mainly by culture-based methods. Studies using these techniques have been useful for identification and analysis of specific groups of bacteria, however, the use of enrichment medium precludes even relative quantitation of bacterial species. Recent advances in ribosomal DNA-based molecular techniques make it possible to identify different bacterial populations in environmental samples without cultivation. In this study, the intestinal microflora was examined using 16S ribosomal DNA (rDNA) targeted probes from bacterial DNA isolated from intestinal and cecal contents of chickens at 4, 14, and 25 d of age. The ribosomal gene sequence was amplified using PCR with universal primers to determine total bacterial DNA and specific primers directed at 6 bacterial species: Lactobacillus, Bifidobacterium, Salmonella, Campylobacter, Escherichia coli, and Clostridium. The use of universal primers extends these methods to allow determination of relative proportions of different bacterial species. The results indicated that in young chicks the major species present in the small intestines and ceca was Lactobacilli, with a Bifidobacteria population becoming more dominant in the ceca at older age. Clostridium was detected in some segments of the small intestine in young chicks. In older chickens, Salmonella, Campylobacter, and E. coli species were found in the ceca. This study has demonstrated the use of molecular techniques for determining relative proportions of bacterial species and monitoring pathogens in the chick gastrointestinal tract.

MeSH terms

  • Aging
  • Animals
  • Bifidobacterium / genetics
  • Bifidobacterium / isolation & purification
  • Campylobacter / genetics
  • Campylobacter / isolation & purification
  • Cecum / microbiology
  • Chickens / microbiology*
  • Clostridium / genetics
  • Clostridium / isolation & purification
  • DNA Primers*
  • DNA, Bacterial / analysis*
  • DNA, Ribosomal / genetics*
  • Escherichia coli / genetics
  • Escherichia coli / isolation & purification
  • Intestines / microbiology*
  • Lactobacillus / genetics
  • Lactobacillus / isolation & purification
  • Polymerase Chain Reaction
  • RNA, Ribosomal, 16S / genetics*
  • Salmonella / genetics
  • Salmonella / isolation & purification


  • DNA Primers
  • DNA, Bacterial
  • DNA, Ribosomal
  • RNA, Ribosomal, 16S