Modeling ruminal microbial ecology: Population adaptation, response to acidosis and introduction of a genetically modified bacterium in a dual flow continuous culture fermenter system

Five experiments were conducted to build a basic framework of ruminal microbial community structure and to evaluate dual flow continuous culture fermenters as a model of ruminal microbial ecology. Relative abundances of microbial populations were determined using rRNA-targeted DNA oligonucleotide probes. Total small subunit (16S and 18S) rRNA (SSU rRNA) extracted from samples was also quantified.;In the rumen, eucarya accounted for 40 to 60% of total SSU rRNA. Fermenters maintained a relative abundance of eucarya at 1 to 3%; decreased eucaryotic abundance in the fermenters was due primarily to loss of ciliated protozoa. Bacterial abundance increased in fermenters (90% of total SSU rRNA) when compared with the rumen (40 to 60% of total SSU rRNA). Fermenters maintained Fibrobacter and archaea relative abundances in amounts similar to those found in the rumen (2 to 3% for Fibrobacter and 2 to 4% for archaea).;Initial inoculation of fermenters resulted in perturbation of the microbial community. The amount of SSU rRNA extracted from inoculum samples was lower than in ruminal samples. The relative abundance of key microbial populations did not differ in inoculum and ruminal samples. The loss of ciliated protozoa occurred rapidly and, after 48 h, none were observed microscopically. Most of the remaining microbial populations monitored, stabilized by 96 h of fermenter operation; longer than the 24 to 48 h required for stabilization of chemical fermentation characteristics. Total amount of SSU rRNA extracted from fermenter samples was similar to that in ruminal samples.;Ruminal acidosis was monitored in animals and fermenters. While results were similar to those reported using cultural and microscopic techniques, use of rRNA-targeted probes gave higher resolution and allowed for evaluation of a number of microbial populations simultaneously. The fermenters were able to model microbial population changes during the initial stages of acidosis. However, Fibrobacter and archaeal populations disappeared, the amount of SSU rRNA extracted from samples decreased and chemical fermentation characteristics were significantly altered in the fermenters. The fermenters and probes successfully determined the persistence and effects of culture inoculation with a genetically engineered bacterium, Bacteroides thetaiotaomicron BTX.