Analysis of cow dung microbiota—A metagenomic approach

Abstract

Cow dung is being used from ancient times in agriculture as it has a significant role in plant growth promotion and plant protection. It is also being used in various religious practices as a purifier. Since only a small fraction of the total microbial diversity can be recovered by culturable methods, a culture independent 16S rDNA approach was taken up for more detailed analysis of cow dung microbiota. Total community DNA was extracted from fresh dung of Brown-Swiss breed and bacterial 16S rRNA genes were subsequently amplified, cloned, sequenced and deposited in GenBank. Bacteria belonging to the phyla Bacteroidetes (38.3%), Firmicutes (29.8%), Proteobacteria (21.3%) and Verrucomicrobia (2%) were identified. Bacteroidetes clones included the genera <i style="mso-bidi-font-style:normal">Bacteroides</i>, <i style="mso-bidi-font-style: normal">Alistipes</i> and <i style="mso-bidi-font-style:normal">Paludibacter</i>; while <i style="mso-bidi-font-style:normal">Clostridium</i>, <i style="mso-bidi-font-style:normal">Ruminococcus</i>, <i style="mso-bidi-font-style: normal">Anaerovorax</i> and <i style="mso-bidi-font-style:normal">Bacillus</i> were predominant in Firmicutes. α- and γ-proteobacterial genera included <i style="mso-bidi-font-style:normal">Acinetobacter</i>, <i style="mso-bidi-font-style: normal">Pseudomonas</i>, <i style="mso-bidi-font-style:normal">Rheinheimera</i>, <i style="mso-bidi-font-style:normal">Stenotrophomonas</i> and <i style="mso-bidi-font-style:normal">Rhodobacter</i>. The Verrucomicrobial clone showed high similarity to <i style="mso-bidi-font-style:normal">Akkermansia</i>. Unculturable bacteria constituted 83.3% in the phylum Bacteroidetes and 87.5% in Firmicutes. All clones under phylum Proteobacteria were culturable bacteria. Eight per cent of the clone library represented previously uncharacterized and unidentified bacteria.