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Changes in rumen microbial ecology during dietary transition in cattle and sheep: a molecular and metabolic approach

Jones, Fiona (2016) Changes in rumen microbial ecology during dietary transition in cattle and sheep: a molecular and metabolic approach. Masters by Research thesis, Murdoch University.

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Ruminal acidosis is often characterised by decreased ruminal pH below pH 6.0, increased concentrations of ruminal D and L- lactate and volatile fatty acid concentrations in grain fed ruminants, creating an environment for growth of lactic acid producing bacteria such as S. bovis and Lactobacillus spp. and reduction in cellulolytic bacterial populations e.g. F. succinogenes.

This thesis undertook genotypic studies of rumen microbial ecology based on five key bacterial species, Prevotella ruminantium, Fibrobacter succinogenes, Selenomonas ruminantium, Streptococcus bovis, and Lactobacillus spp. using quantitative real time PCR (qRT- PCR) of 16S rRNA genes. This methodology enabled true genetic monitoring of ecological changes rather than traditional phenotypic microbial culture studies. These genetic studies of rumen microbial ecology were aligned with changes in rumen metabolism.

Application of qRT-PCR methodology was validated for complete and consistent extraction of DNA from mixed rumen samples to ensure reliable enumeration of rumen bacteria, and finally development of primers for use in the qRT-PCR assays. The qRT-PCR methods were then used to monitor changes in rumen microbial ecology in cattle managed under commercial conditions in feedlots rather than experimental conditions. The key species were stabilised in the rumen microbial ecology within 7 days of introduction of cattle to feedlots irrespective of feeding hay and grain separately or via total mixed rations. Moreover, metabolic indicators of high production potential coincided with the stable populations of the key rumen bacterial species F. succinogenes, P. ruminicola and S. ruminantium and no evidence of elevated S. bovis populations. Developmental changes in rumen bacterial ecology of steers born during either autumn or winter/spring showed similar trends in bacterial populations when adapting to feedlot rations irrespective of time of calving. However, the rumen protozoal populations were reflective of the time of calving with cattle born in winter/spring maintaining higher protozoal populations throughout the feedlot period. In commercial dairy herds, rumen metabolic end products were consistently correlated with changes in key bacterial populations. Rumen acidosis was observed in sheep fed lupins at 3 times maintenance. Decreased populations of F. succinogenes and increased populations of S. bovis with no decrease in rumen pH were observed in sheep fed high-fat soyabean diets.

Molecular techniques such as qRT-PCR used here as well as newer molecular genetic approaches such as next generation sequencing will allow for more comprehensive interpretation of ecological changes in the rumen leading to improved management and productivity of cattle and sheep especially during dietary transitions.

Publication Type: Thesis (Masters by Research)
Murdoch Affiliation: School of Veterinary and Life Sciences
Supervisor: Costa, Nick
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