ANALYSIS OF THE INTESTINAL MUCOSAL MICROBIOTA BY REAL-TIME PCR IN BROILER CHICKENS FED DIETS BASED ON CORN OR SORGHUM Raquel Lunedo 1 ; Marcos Macari 1 ; Luiz Roberto Furlan 2 ; Miguel Frederico Fernandez- Alarcon 1 . 1 Department of Animal Physiology and Morphology, FCAV – UNESP, Jaboticabal – SP, Brazil. 2 Aquaculture Center – CAUNESP, FCAV – UNESP, Jaboticabal – SP, Brazil. ABSTRACT The understanding of gut microbiota is increasing rapidly, since the involvement of microorganisms in diseases, and also in the bacteria resistance to antibiotics, is relevant to human health. The use of culture based methods is limited because the number of strain tested may not reflect the real effect of external factors on the whole microbial community. Thus, the DNA/RNA-based molecular techniques have been used. The aim of this study was to establish a profile of the main bacterial groups present in the mucosa of the small intestine segments of broilers fed diets based on corn or sorghum, using real-time PCR. The absolute quantification assay was performed with 16S rDNA specific primers for the phylogenetic groups: Family Enterobacteriaceae, Genus Enterococcus spp. and Lactobacillus group, and with an universal primer to estimate the total number of bacterial copies. Samples of intestinal mucosa were collected at 7, 21 and 42 days of age. Along the rearing period, the group Enterobacteriaceae remains in small quantities, Enterococcus spp was seen only at 7-days of age, and Lactobacillus become majority from the first week until the end of rearing period. The use of sorghum determined: a high number bacterial copies in the duodenum and jejunum, and Lactobacillus in the duodenum at all ages; Enterococcus spp at 7 days and Enterobacteriaceae at 42 days of age. KEYWORDS: 16S rDNA, microbiota, mucosal, real-time PCR INTRODUCTION Sorghum (Sorghum bicolor L. Moench) is a major substitute for maize in diets for monogastric animals, especially by it cost and availability. Sorghum and maize have similar nutritional value, but some intrinsic characteristics of sorghum grain can affect the digestive process as a whole, modifying mucosa mechanisms, nutrients digestibility and bacterial community present in the digestive tract of the animal. Studies related intestinal mucosa changes with consumption of sorghum. However, the action of this grain in the intestinal microbiota is not well understood. The microbiota present in the broiler gastrointestinal tract acts in symbiosis with the host, regulating absorptive efficiency, residence time of the bolus in the tract, utilization of some nutrients, intestinal maturation, antagonism against pathogens, gut integrity, immunity modulation and serving as sources of vitamins and energy (AMIT- ROMACH et al., 2004; OVIEDO-RONDÓN, 2009). The colonizer sub-ecosystem, comprising mucosa microorganisms, has an inherent capability to modify the functional structure of the mucosa by modifying the villus height and crypt depth and therefore the digestive and absorptive processes.