A batch culture study of the rumen bacterial community and the fermentative digestion of forage in cattle

Environmental pressures of ruminant livestock production could be lessened by improving feed digestion efficiency. As most feed is digested by the rumen microbial community there is interest in its manipulation. Attempts at doing so in vivo have largely been unsuccessful. The aim of this thesis was to determine if, by uncoupling the rumen bacterial community from its host, manipulation would be possible.
Experiments were conducted using an in vitro batch culture fermentation model using cattle rumen fluid as inoculum. Parameters of fermentative digestion were measured, and the bacterial community studied using next generation sequencing methodology, the pipeline for which was tested. The role of epiphytic bacteria and concentration of rumen fluid within the model were also explored.
Rumen fluids differing in their ability to digest dry matter in vitro (IVDMD; Good, Bad) were cross inoculated (1:1 Mix). After 24 hours of fermentation the IVDMD of the Mix (0.29) was intermediate (P<0.001) of the Good (0.34) and Bad (0.20), a result supported by the measured fermentation parameters. However, by the end of the sixth consecutive batch culture (CBC6) there was no difference in IVDMD between rumen fluid treatments, but the overall IVDMD had significantly (P<0.001) improved; compared to the average 24 hr IVDMD of CBC1 that of CBC9 was 69% higher. When this experiment was repeated there was no effect of cross inoculation on IVDMD, but again overall IVDMD significantly improved with each consecutive batch culture. Surprisingly there were no differences in bacterial community composition between the rumen fluids, however, the diversity of the community decreased significantly (P<0.001) with time.
Differences in IVDMD performance in the absence of differences in bacterial community composition would suggest either differences in community function or differences in communities not studied here. The improved performance with time, associated with reduced bacterial diversity, may indicate bacterial activity within the rumen is restrained.