Genomic insights into Mycobacterium cavoris sp. nov., related to Mycobacterium terrae complex isolated from the oral cavity of a healthy adult.

We report the genome sequence of a novel species of nontuberculous mycobacterium (NTM) belonging to the Mycobacterium terrae complex (MTC). The strain SVM_VP21 was isolated from the mouthwash sample of a healthy human adult residing in Delhi, India. The strain exhibited smooth, cream-coloured colonies on Lowenstein Jensen (LJ) medium after 2 weeks of incubation and could not be identified by Hain's Genotype Mycobacterium CM/AS line probe assay. Whole genome sequencing (WGS) of SVM_VP21 was performed using Illumina NovaSeq 6000 platform for final identification. The whole genome sequence was assembled using Shovill. Gene annotation was performed by Rapid Annotation using Subsystem Technology (RAST) and Prokaryotic Genome Annotation Pipeline (PGAP). The genome of 4,882,418 bp exhibited 67.3% GC content, 59 contigs, 4557 genes and 4502 coding sequences. The genome also encoded four rRNAs, 48 tRNAs, three non-coding RNAs and 177 pseudo genes. BLASTn analysis of the 16S rRNA and hsp65 gene sequences retrieved by WGS showed 100% and 95% identity to M. heraklionense, respectively. AutoMLST showed 93.5% average nucleotide identity of SVM_VP21 to M. virginiense. Digital DNA-DNA Hybridization, finally, identified SVM_VP21 as a novel species of the M. terrae complex. The name Mycobacterium cavoris sp. nov. is proposed for the strain in reference to its isolation from the oral cavity. The data presented here would help in understanding the novel species, which though obtained from a healthy individual in this study, may be a potential pathogen.