Molecular diversity of protozoa in rumen of Indian buffalo (Bubalus bubalis)

Abstract

Protozoa communities in buffalo rumen were characterized using 18S rRNA gene library prepared from the pooled DNA sample obtained from three adult animals. A total of 172 clones were sequenced, which were grouped into 53 operational taxonomic units (OTUs) based on unique 18S r DNA sequences with 95 % confidence intervals. Phylogenetic analyses showed that 40 OTUs (124 of 172 clones) belonged to uncultured protozoa group, indicating that this group is most dominant component of protozoa resident in rumen of Indian buffalo. 44 clones (12 OTUs) belonged to the class Kinetofragminophorea. Among Kinetofragminophorea, 44 clones fell into two species identified as Dasytricha ruminantium-like clone (27 clones) and Isotricha prostoma-like clone (17 clones). These include 11 single-clone OTUs, so Good's coverage (93.75 %) of 18S rRNA libraries indicated that the sequences identified in the libraries represent the majority of protozoa diversity present in rumen. © 2013 NAAS (National Academy of Agricultural Sciences).