Isolation, Description and Genome Analysis of a Putative Novel Methylobacter Species (‘Ca. Methylobacter coli’) Isolated from the Faeces of a Blackbuck (Indian Antelope)

Abstract

Enteric fermentation of methane by ruminant animals represents a major source of anthropogenic methane. Significantly less information is available on the existence of methanotrophs in the gut of ruminants. Therefore, detailed strain descriptions of methanotrophs isolated from ruminant faeces or gut are rare. We present a first report on the enrichment and isolation of a methanotroph, strain BlB1, from the faeces of an Indian antelope (blackbuck). The 16S rRNA gene sequence of strain BlB1 showed the highest identity (98.40% identity) to Methylobacter marinus A45T and Methylobacter luteus NCIMB 11914T. Strain BlB1 showed coccoidal cells (1.5–2 µm in diameter), which formed chains or aggregates of 3–4 cells of light yellow-coloured colonies on agarose when incubated with methane in the gas phase. The draft genome of BlB1 (JADMKV01) is 4.87 Mbp in size, with a G + C content of 51.3%. The draft genome showed 27.4% digital DNA-DNA hybridization (DDH) and 83.07% average nucleotide identity (ANIb) values with that of its closest phylogenetic neighbour, Methylobacter marinus A45T. Due to the lower values of DDH and ANIb with the nearest species, and <98.7% 16S rRNA gene sequence identity, we propose that strain BlB1 belongs to a novel species of Methylobacter. However, as the culture has to be maintained live and resisted cryopreservation, deposition in culture collections was not possible and hence we propose a Candidatus species name, ‘Ca. Methylobacter coli’ BlB1. ‘Ca. Methylobacter coli’ BlB1 would be the first described methanotroph from ruminants worldwide, with a sequenced draft genome. This strain could be used as a model for studies concerning methane mitigation from ruminants.