In vitro evaluation of effects of gut region and fiber structure on the intestinal dominant bacterial diversity and functional bacterial species

Understanding the intestinal bacteria in ruminants and their population kinetics is essential for their ecological function, as well as their interaction with the host. In this in vitro study, we aimed to determine whether gut region and fiber structure can influence bacterial diversity and functional bacterial population, together with the kinetics of functional bacterial species in the cecal inocula using PCR-DGGE and qPCR. A split plot design was conducted with gut regions (jejunum, ileum, cecum and colon) as main plot, and substrates (neutral detergent fiber (NDF) and cellulose (CEL)) as subplot. Incubation time and gut region affected dominant bacterial diversity. The numbers of total bacteria, cellulolytic bacteria, genus Prevotella and amylolytic bacteria in the hindgut inocula were greater (P < 0.05) than those in the small intestinal inocula. Fiber structure did not significantly influence the dominant bacterial diversity and the numbers of most examined functional bacterial species. The greatest increase rate of cellulolytic bacteria occurred earlier than amylolytic bacteria except for R. albus incubated with NDF. Changes in cellulolytic bacterial populations were not coordinative with alteration of fiber disappearance as well as CMCase and xylanase activities. All these suggest that the hindgut contents have greater potential to digest fiber than small intestinal contents, and cellulolytic bacteria are of significant value at the initial stage of fiber digestion among the fiber digestive microbes in the intestine.