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Volume 54, Issue 6

Dissection of phylogenetic relationships among 19 rapidly growing species by 16S rRNA, , , and gene sequencing Free

Abstract

The current classification of non-pigmented and late-pigmenting rapidly growing mycobacteria (RGM) capable of producing disease in humans and animals consists primarily of three groups, the group, the – group and the group. Since 1995, eight emerging species have been tentatively assigned to these groups on the basis of their phenotypic characters and 16S rRNA gene sequence, resulting in confusing taxonomy. In order to assess further taxonomic relationships among RGM, complete sequences of the 16S rRNA gene (1483–1489 bp), (3486–3495 bp) and (1041–1056 bp) and partial sequences of (420 bp) and (441 bp) were determined in 19 species of RGM. Phylogenetic trees based upon each gene sequence, those based on the combined dataset of the five gene sequences and one based on the combined dataset of the and gene sequences were then compared using the neighbour-joining, maximum-parsimony and maximum-likelihood methods after using the incongruence length difference test. Combined datasets of the five gene sequences comprising nearly 7000 bp and of the + gene sequences comprising nearly 4600 bp distinguished six phylogenetic groups, the – group, the group, the group, the group, the group and the group, respectively comprising four, three, eight, one, one and two species. The two protein-encoding genes and improved meaningfully the bootstrap values at the nodes of the different groups. The species , and formed new groups separated from the –, and groups, respectively. The group was well delineated, in contrast to the and groups. For phylogenetic organizations derived from the and gene sequences, the bootstrap values at the nodes of a few clusters were <70 %. In contrast, phylogenetic organizations obtained from the 16S rRNA, and genes were globally similar to that inferred from combined datasets, indicating that the and genes appeared to be useful tools in addition to the 16S rRNA gene for the investigation of evolutionary relationships among RGM species. Moreover, gene sequence analysis yielded bootstrap values higher than those observed with and 16S rRNA genes. Also, molecular signatures in the and 16S rRNA genes of the group showed that it was a sister group of the – group. In this group, ATCC 49650 was clearly distinguished from ATCC 49649 with regard to analysis of the five gene sequences. This was in agreement with phenotypic and biochemical characteristics and suggested that these strains are representatives of two closely related, albeit distinct species.

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Keyword(s): ILD, incongruence length difference , K2P, Kimura's two-parameter , PRA, PCR-RFLP analysis and RGM, rapidly growing mycobacterium
SGM
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2004-11-01
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Dissection of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S rRNA, hsp65, sodA, recA and rpoB gene sequencing
Int J Syst Evol Microbiol 54, 2095 (2004); https://doi.org/10.1099/ijs.0.63094-0
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