The numbers of ARISA peaks for the different treatments were similar to those previously reported in sheep using the
same methodology (Ramos et al., 2009a; Saro et al., 2012, 2014). Neither the Shannon index nor the number of peaks were
affected by the processing method, which indicates a similar diversity and number of identified operational taxonomic
units (OTUs) in all inocula. However, bacterial structure was different among individual animals and processing methods,
as indicated by the ARISA-profile dendrogram (Fig. 1). For three of the four sheep, SQ and FL samples clustered together
and showed more than 85% similarity, indicating that SQ and FL inocula shared many OTUs. The lower similarity of STO
samples to SQ and FL samples would indicate the presence of different OTUs in this inoculum, which may suggest that
stomaching the ruminal contents detached specific bacteria from the solid phase; however, there were only three peaks
exclusive to the STO method. The cluster pattern observed in the dendrogram of ARISA profiles indicates that sheep had
the largest effect on bacterial communities, as previously reported by others in the rumen of sheep fed different diets (Saro
et al., 2012, 2014; Mateos et al., 2015)