Fecal Microbiota Analysis Exploring Taxonomic Diversity of Hindgut Microbial Communities in Kasaragod Dwarf and Holstein Friesian Cattle

Abstract The indigenous cattle are efficient in converting low quality feeds and forage into animal products. Kasaragod Dwarf (K-Dwarf) cattle, a non-descriptive native cattle variety of Kerala, are noted for their unique qualities, like short stature, low feed intake, thermotolerance, greater resistance to diseases and A2 allelic variant milk. This study hypothesizes that K-Dwarf cow relies on their unique hindgut microbes to ferment the low quality feeds into the efficient animal product. To compare and contrast this unique microbiota and their relationship between the host, we performed microbial profiling of the two genetically distinct cattle-type viz., K-Dwarf, and Holstein utilizing 16S rRNA high-throughput sequencing. Principle Coordinate Analysis using weighted and unweighted UniFrac distance matrices showed significantly distinct clustering of K-Dwarf microbial community compared to Holstein, implying the distinct microbial architecture that K-Dwarf harbors. The dissimilarities observed between the two cattle types were further revealed from the signature taxa identified in each cattle type following Random Forest analysis. In addition, the study observed the predominance of feed efficiency associated genera viz., Anaerovibrio, Succinivibrio, Roseburia, Coprococcus, Anaerostipes, Paludibacter, Elusimicrobium, Sutterella, Oribacterium, Coprobacillus, and Ruminobacter in K-Dwarf cattle. The study highlights the abundance of unique and beneficial hindgut microflora found in K-Dwarf, which may attest its importance over exotic cattle breeds viz., Holstein. To our knowledge, this is the first report of K-Dwarf cattle gut microbiome profiling. Further molecular characterization is solicited to better understand the microbial role in the conversion of low-quality feeds into more efficient animal products, a well-defined characteristic of indigenous cattle.