Defaunation, the removal of protozoa from the rumen was used to investigate the effects of protozoa on rumen bacteria. Twelve Sindhi x Yellow cattle were allowcated into a two by two factorial design (absence or presence of protozoa; cottonseed cake or concentrate supplement). The basal rougahe diet was based on natural grass and rice straw. The animals were adapted for 21 days with the experimental diets before being dosed with soybean oil, a defaunation agent, at 6 ml/kg live weight. Rumen fluid was collected at day 5, 30,60 and 90 post defaunation. Conventional counting of protozoa was performed. In additon, genomic DNA  rumen microorganisms was extracted to further used in real-time PCR quantification of cellulolytic bacteria.

 Protozoa numbers significantly reduced at 5 days after oil drench and gradually recovered until day 90. Relative fold changes of Ruminococcus albus and Ruminococcus flavefaciens were significanly higher in defaunated cattle at both protein source supplements but the number of Fibrobacter succinogenes was lower (0.84-0.39 fold) in defaunated cattle under concentrate supplementation. Moreover, defaunation did not show significant effects on the abundance of methanogens, with an exception of increasing fold change at day 5 in defaunated cattle.

 It is concluded that partial defaunation using soybean oil was beneficial regarding to an increasing numbers of R. albus and R. flavefaciens but the advantagous evidence on methanogens abundance was not achieved.