Given the shorter digestive tract and faster digesta transit in poultry than in mammalian animals, the average whole tract transit time in poultry tract is less than 3.5 h. Gut microbiota communities in small intestine (duodenum, jejunum and ileum) are less abundant than cecum. The advent of high-throughput DNA sequencing technologies has allowed an integrative approach to identify the bacteria communities residing within or on their host organism.
This study showed that Firmicutes is the dominant phylumand Lactobacillus was the predominant bacterial genus identified in the intestinal ileumin all broiler breeds and all treatment groups. This result is consistent with previous studies that showed Lactobacillus as the principal microorganism in the gastrointestinal tract of uninfected conventional
broilers. Because Firmicute is fat loving gram positive bacteria, this result suggests interrelationship of this bacteria and genetic selection for fast growing characteristics
of these broilers by the industry. In addition, we observed that the relative changes in the proportion of intestinal lactobacilli, as well as the total number of OTUs, differed between the broiler breeds.When comparing the control and NE treatment groups, both parameters correlated with breed susceptibility or resistance to experimental NE. Thus, the more NE susceptible Cobb breed had a decreased number of OTUs and an increased fraction of Lactobacillus, while the more NE resistant Hubbard and Ross chickens had the opposite pattern, i.e. an increase in OTUs and decreased fraction of Lactobacillus. This relationship, however,was not seen when comparing the NE and NE+XT treatment groups, where OTUs were increased in Cobb and Ross but decreased in
Hubbard, and Lactobacillus was increased in Cobb and Hubbard, but decreased in Ross.