Percent G+C Profiling Accurately Reveals Diet-Related Differences in the Gastrointestinal Microbial Community of Broiler Chickens

Abstract

Broiler chickens from eight commercial farms in Southern Finland were analyzed for the structure of their gastrointestinal microbial community by a nonselective DNA-based method, percent G؉C-based profiling. The bacteriological impact of the feed source and in-farm whole-wheat amendment of the diet was assessed by percent G؉C profiling. Also, a phylogenetic 16S rRNA gene (rDNA)-based study was carried out to aid in interpretation of the percent G؉C profiles. This survey showed that most of the 16S rDNA sequences found could not be assigned to any previously known bacterial genus or they represented an unknown species of one of the taxonomically heterogeneous genera, such as Ruminococcus or Clostridium. The data from bacterial community profiling were analyzed by t-test, multiple linear regression, and principal-component statistical approaches. The percent G؉C profiling method with appropriate statistical analyses detected microbial community differences smaller than 10% within each 5% increment of the percent G؉C profiles. Diet turned out to be the strongest determinant of the cecal bacterial community structure. Both the source of feed and local feed amendment changed the bacteriological profile significantly, whereas profiles of individual farms with identical feed regimens hardly differed from each other. This suggests that the management of typical Finnish farms is relatively uniform or that hygiene on the farm, in fact, has little impact on the structure of the cecal bacterial community. Therefore, feed compounders should have a significant role in the modulation of gut microflora and consequently in prevention of gastrointestinal disorders in farm animals.Previous studies showed that there is a relationship between the gastrointestinal (GI) tract microflora and health of animals (6, 36). To date, most attempts to control GI tract microflora have relied on the use of broad-spectrum antibiotics. The recent and widening introduction of bans on the prophylactic use of many antibiotics due to concerns over dissemination of antibiotic resistance traits will likely end most or all such practices. Hence, there is an increasing interest in developing alternative methods of controlling the GI tract microflora. It has been known for a long time that diet can significantly influence the composition and metabolic activity of the GI tract microflora (20,32,36). Feed ingredients conducive to the growth of beneficial GI tract bacteria, as well as direct introduction of bacterial populations that favor good health and nutrition in animals (i.e., probiotics), can be used to manage the GI tract microbial community (6,11,13,15,19,21). So far, the development of alternate management strategies for the GI tract microflora has been hampered by the lack of practical analytical tools for monitoring of the composition of the total community. Several studies of other animal species and a variety of habitats suggest that only a fraction of the total microbial community is effectively captured by culture-based techniques (2,8,10,14,1...

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