title: 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.
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Yun Fong
authors.initials: YF
authors.lastname: Ngeow
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Yan Ling
authors.initials: YL
authors.lastname: Wong
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Joon Liang
authors.initials: JL
authors.lastname: Tan
authors.affiliation: Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Kar Wai
authors.initials: KW
authors.lastname: Hong
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Hien Fuh
authors.initials: HF
authors.lastname: Ng
authors.affiliation: Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.
authors.forename: Bee Lee
authors.initials: BL
authors.lastname: Ong
authors.affiliation: Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Kok Gan
authors.initials: KG
authors.lastname: Chan
mesh_terms: D000818:Animals; D001483:Base Sequence; D016680:Genome, Bacterial / Q000235:genetics; D023281:Genomics; D008969:Molecular Sequence Data; D009170:Nontuberculous Mycobacteria / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D010802:Phylogeny; D013045:Species Specificity
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