Study of rice straw-adherent sheep rumen microbiome diversity: a comparative 16S rDNA and whole metagenome analysis

The rumen is described as one of the most elegant and advanced cellulosic digestion systems in nature. The ruminal microbiome, by attaching and formatting microcolonies on feed particles and releasing the fiber degrading enzymes, decompose lignocellulose compounds and convert them into compounds that are usable for the host animal. The purpose of the present study was identifying and understanding the relationship between the most important bacteria that colonize rice straw during ruminal incubation and also comparing the amplicon and shotgun data generated on incubated rice straw during 24, 48, 72 and 96hrs in three fistulated animals. After bacterial isolation and DNA extraction processes, two sequencing strategies of Illumina Miseq 300PE and Hiseq4000, 100PE were used to sequence the V3-V4 region of 16S ribosomal RNA and the total metagenome. Taxonomic profiling, microbial diversity and species richness were separately prepared for each dataset and comparative analysis was performed. The results indicated that there are synergistic and/or overlapping effects among the members of the identified phyla, and with considering the frequency, it seems that the members of the Firmicutes, Fibrobacters, and Spirochaetes play a critical role in the colonisation process. Our study showed a weak correlation between the two methods, indicating that while taxonomic overlap exists in the phylum and family levels, the methods are different. The most highlighted difference between the two sequencing methods was species-level identification, which the Hiseq method appeared much more robust in terms of genomic coverage and taxonomic profiling algorithm. It was also observed that the selective software for taxonomic profiling could play a vital role and even more differentiation power than the technology utilized for whole metagenome and gene-targeted sequencing.