Identification of New Genomospecies in the Mycobacterium terrae Complex

Abstract

Members of the Mycobacterium terrae complex are slow-growing, non-chromogenic acid-fast bacilli found in the natural environment and occasionally in clinical material. These genetically closely-related members are difficult to differentiate by conventional phenotypic and molecular tests. In this paper we describe the use of whole genome data for the identification of four strains genetically similar to Mycobacterium sp. JDM601, a newly identified member of the M. terrae complex. Phylogenetic information from the alignment of genome-wide orthologous genes and single nucleotide polymorphisms show consistent clustering of the four strains together with M. sp. JDM601 into a distinct clade separate from other rapid and slow growing mycobacterial species. More detailed inter-strain comparisons using average nucleotide identity, tetra-nucleotide frequencies and analysis of synteny indicate that our strains are closely related to but not of the same species as M. sp. JDM601. Besides the 16S rRNA signature described previously for the M. terrae complex, five more hypothetical proteins were found that are potentially useful for the rapid identification of mycobacterial species belonging to the M. terrae complex. This paper illustrates the versatile utilization of whole genome data for the delineation of new bacterial species and introduces four new genomospecies to add to current members in the M. terrae complex.

Mycobacterium arupense, Mycobacterium heraklionense, and a Newly Proposed Species, “Mycobacterium virginiense” sp. nov., but Not Mycobacterium nonchromogenicum, as Species of the Mycobacterium terrae Complex Causing Tenosynovitis and Osteomyelitis

“…Upon BLAST analysis of the 16S rRNA gene (full) against the whole-genome shotgun contigs (wgs) database, a 99.9 to 100% match (0 to 1 bp) was achieved with 3 of 4 strains obtained from the trunk washes of captive elephants. These strains were described as new genomospecies within the M. terrae complex (56).…”

Nontuberculous mycobacteria in milk from positive cows in the intradermal comparative cervical tuberculin test: implications for human tuberculosis infections

“…The phylogenetic tree ( Figure 1 ) shows four clusters belonging to nontuberculous mycobacteria grouped in the Mycobacterium terrae complex 23 . A hsp 65 gene dendrogram revealed three subclusters with 76.0% of genetic relatedness, particularly for M. engbaekii and M. arupense cluster, and for M. nonchromogenicum and M. heraklionense cluster (data not show).…”

HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts

“…However, while the capacity to produce distinct viral sequence bins would undoubtedly improve interpretation of holobiont-derived viral metagenomes, a recent investigation into viral metagenome binning confirmed that coverage-based binning methodologies are not appropriate for amplified viral samples (Smits et al, 2015 ). Tetranucleotide frequency binning has been used in several metagenomics analyses to identify discrete microbial bins (Swingley et al, 2012 ; Delmont et al, 2015 ; Moreira et al, 2015 ; Ngeow et al, 2015 ). However, this method requires contigs of at least 5kb for reasonable accuracy (Dick et al, 2009 ).…”