Analysis of Community Structure and Species Richness of Protozoa-Enriched Rumen Metagenome from Indian Surti by Shotgun Sequencing

The present study applies metagenomics to characterize the diversity and relative abundance of protozoa residing in the rumen of Indian Surti buffalo (Bubalus bubalis). To increase protozoa representation in the metagenome, protozoa enrichment was performed by density sedimentation and confirmed by quantitative real time PCR. The highly enriched metagenome sample was subjected to shotgun sequencing by Ion Torrent PGM which resulted in 10,303,375 reads total-ling 1.6 gigabases. The taxonomic profile obtained by comparison with SILVA SSU database showed pre-dominance of the class Litostomatea (99.78%) fol-lowed by Coccidia (0.10%) and Aconoidasida (0.06%). At the genus level Isotricha (48.06%) followed by Polyplastron (9.90%), Dasytricha (9.87%) and Eudiplodinium (7.47%) were predominant. The taxo-nomic assignment based on protein coding regions showed discrepancy with the SSU-based assignments, possibly due to the absence of most eukaryotic ge-nomes in public databases. According to the SEED subsystems annotation database, genes for protein me-tabolism were the most abundant followed by genes for RNA metabolism, regulation and cell signalling. The present study offers a preliminary snapshot of di-versity, functional potential and relative abundance of protozoa within the Indian Surti buffalo rumen and al-so expands our knowledge of these unicellular eukary-otes present in the rumen ecosystem.