Microbial community composition of the ileum and cecum of broiler chickens as revealed by molecular and culture-based techniques

Danish Institute for Food and Veterinary Research, Arhus N. lob@dfvf.dk

The microbial communities of the ileum and cecum of broiler chickens from a conventional and an organic farm were investigated using conventional culture techniques as well as cloning and sequencing of 16S rRNA genes. Eighty-five percent of the 557 cloned sequences were <97% related to known cultured species. The chicken ileum was dominated by lactobacilli, whereas the cecum harbored a more diverse microbial community. The cecum was dominated by a large group of bacteria with hitherto no close cultured relatives but most closely related to Faecalibacterium prausnitzii. Approximately 49 and 20% of the cecal clones belonged to this cluster in conventional and organic broiler chickens, respectively. We were, however, able to recover a number of these phylotypes by cultivation, and the isolates were shown to be butyric acid producers. The investigation was a descriptive rather than a comparative study of 2 different rearing systems; however, several differences were observed. For instance, Clostridium perfringens was found in significantly higher numbers in the birds from the organic farm compared with the conventional broilers, probably due to the addition of salinomycin to the conventional feed. In the ileum, the abundance of the different Lactobacillus species differed between the 2 broiler types. The culture-based and culture-independent techniques complemented each other well. Strengths and limitations of the different methods are discussed.

This article has been cited by other articles:

				D. P. Stephenson, R. J. Moore, and G. E. Allison Comparison and Utilization of Repetitive-Element PCR Techniques for Typing Lactobacillus Isolates from the Chicken Gastrointestinal Tract Appl. Envir. Microbiol., November 1, 2009; 75(21): 6764 - 6776. [Abstract] [Full Text] [PDF]

				P. Janczyk, B. Halle, and W. B. Souffrant Microbial community composition of the crop and ceca contents of laying hens fed diets supplemented with Chlorella vulgaris Poult. Sci., November 1, 2009; 88(11): 2324 - 2332. [Abstract] [Full Text] [PDF]

				E. Grilli, M. R. Messina, E. Catelli, M. Morlacchini, and A. Piva Pediocin A improves growth performance of broilers challenged with Clostridium perfringens Poult. Sci., October 1, 2009; 88(10): 2152 - 2158. [Abstract] [Full Text] [PDF]

				A. De Cesare, G. Borilova, I. Svobodova, V. Bondioli, and G. Manfreda Clostridium perfringens occurrence and ribotypes in healthy broilers reared in different European countries Poult. Sci., September 1, 2009; 88(9): 1850 - 1857. [Abstract] [Full Text] [PDF]

				R. Chevrot, A. Carlotti, V. Sopena, P. Marchand, and E. Rosenfeld Megamonas rupellensis sp. nov., an anaerobe isolated from the caecum of a duck Int J Syst Evol Microbiol, December 1, 2008; 58(12): 2921 - 2924. [Abstract] [Full Text] [PDF]

				M. J. Rothrock Jr., K. L. Cook, J. G. Warren, and K. Sistani The Effect of Alum Addition on Microbial Communities in Poultry Litter Poult. Sci., August 1, 2008; 87(8): 1493 - 1503. [Abstract] [Full Text] [PDF]