Comparative Metagenomics of Indian Ruminants

Abstract

Cattle, buffalo, goat and sheep are major ruminant livestock species in India, newlineand they serve as a major food source for the human population. The ability of newlineruminants to convert feeds into food is conferred by the resident microflora. The rumen newlinemicrobes are known to perform various metabolic, physiological and immunological newlinefunctions. Therefore, it is important to understand the structure and composition of the newlinemicrobial communities in the rumen to devise successful strategies for livestock newlineimprovement. The main aim of the study was to identify appropriate methodology for newlinerumen microbial DNA isolation and the rumen microbial community structure and newlinecomposition analysis using the partial 16S rRNA gene sequencing using the next newlinegeneration sequencing platform in cattle, buffalo, sheep and goat species. newlineThe rumen metagenomic DNA isolation methods compared revealed challenges newlinein isolating the metagenomic DNA from the whole rumen contents. Among the newlinecompared methods, the ZR Fecal DNA isolation kit isolated metagenomic DNA, newlinealthough the quantity was low, was usable in the PCR reaction. The other methods also newlineyielded the metagenomic DNA, but the presence of contaminants rendered the methods newlineless effective and required additional purification steps. The effect of the methods on newlinethe rumen microbial community composition was also studied using Terminal newlineRestriction Fragment Length Polymorphism (T-TFLP) method. The assessment newlineestablished that the ZR fecal DNA isolation method was found better in terms of newlinemicrobial coverage assessment from the whole rumen liquor pellet. Among the newlinereference databases compared for annotation of the 16S rRNA data, the Silva v132 was newlinefound better as compared to the Greengenes database. newlineThe rumen microbiome of the cattle, buffalo, goat and sheep was distributed newlineover 21 Phyla, 36 Classes, 51 Orders, 70 Families and 137 genera after removal of the newlinelow prevalence OTUs. Out of the 21 phyla detected in the rumen microbiome, 14 phyla newlinehas significantly different distribution across the livestock species. The core newlinemicrobiome at the phylum level revealed less number of phyla in the goat as compared newlineto the cattle, buffalo and sheep. The Firmicutes and Bacteroidetes were the major phyla newlinedetected in the rumen microbiome irrespective of the livestock species. The F/B ratio newlinewas higher for cattle as compared to the other species. Among the 70 families detected, newlineA total of 29 families were part of the core microbiome of all the species. newline newlinexiv newline newlineAt the genus level, Prevotella dominates the ruminal ecosystems in the newlineruminants and was one of the most abundant members of the core microbiome of the newlinerumen in all the species. The comparison between large ruminants (cattle and buffalo; newlineLR) Vs small ruminants (sheep and Goat; SR) revealed out of total 68 differentially newlineabundant genus level features 25 were higher in LR group and 43 were higher in the newlineSR group. However, the core microbiomes are similar in the livestock species newlineindicating the conserved function of the rumen in these species. newlineIn conclusion, The rumen metagenomic diversity does not change at the higher newlinelevels of taxonomy (Phylum, Class and Order), however, differences lies at the lower newlinelevels of taxonomy (Family, Genus and OTU levels) and each livestock species has newlinedifferent abundance at the Genus level and the small ruminants and large ruminants newlinemetagenomes are different at this level. The differences at the lower taxonomic levels newlinecan be used for identifying the functional significance or indicator organisms for newlineassessing the animal s performance. newline