Phylogeny of Rapidly Growing Members of the Genus Mycobacterium

Abstract

The 16s rRNAs from nine rapidly growing Mycobacterium species were partially sequenced by using the dideoxynucleotide-terminated, primer extension method with cDNA generated by reverse transcriptase. The sequences were aligned with 47 16s rRNA or DNA sequences that represented 30 previously described and 5 undescribed species of the genus Mycobacterium, and a dendrogram was constructed by using equally weighted distance values. Our results confirmed the phylogenetic separation of the rapidly and slowly growing mycobacteria and showed that the majority of the slowly growing members of the genus represent the most recently evolved organisms. The 24 strains which represented 21 rapidly growing species constituted several sublines, which were defined by the following taxa: (i) Mycobacterium neoaumm and M. diernhoferi, (ii) M. gudium, (iii) the M. chubuense cluster, (iv) the M. fortuitum cluster, (v) M. kommossense, (vi) M. sphagni, (vii) M. fallax and M. chitae, (viii) M. aurum and M. vaccae, (ix) the M. fravescens cluster, and (x) M. chelonae subsp. abscessus. Our phylogenetic analysis confirmed the validity of the phenotypically defined species mentioned above, but our conclusions disagree with most of the conclusions about intrageneric relationships derived from numerical phenetic analyses.In the early 1980s, using 16s rRNA cataloging methods, workers determined that Mycobacterium phlei, one of the fast-growing Mycobacterium species, is a member of the phylogenetically defined order Actinomycetales (39). Together with other mycolic acid-containing organisms (i.e., members of the genera Rhodococcus and Nocardia), the members of the genus Mycobacterium form one of the several sublines of descent within the radiation of the actinomycetes. Later, the results of reverse transcriptase sequencing of 16s rRNAs from a larger number of strains confirmed the phylogenetic coherency of this subline, which was extended by the inclusion of the genera Corynebacterium (35), Gordona (36), and Tsukamurella (5). Within the genus Mycobacterium, species fall into one of two large groups which by and large correspond to the traditional groups containing the slowly growing and rapidly growing members of the genus (35).With the introduction of even faster analytical methods (i.e., analysis of polymerase chain reaction-mediated DNA stretches [4,28]), the number of actinomycetes analyzed and consequently the knowledge about the natural relationships of these organisms have increased considerably during the last 3 years. From a phylogenetic point of view, the genus Mycobacterium is one of the most thoroughly investigated bacterial taxa. There are 55 or so validly described species in this genus (51), and 45 strains of 34 species have been subjected to either 16s rRNA analysis (31,35,40), 16s rDNA analysis (4, 28), or 23s rDNA analysis (21). The bifurcation within the genus Mycobactenurn has been confirmed, with the majority of the slowly growing strains forming a phylogenetically very shallow (i.e., recent) group. In addition to the phyloge...

Comparison of Mycobacterium 23S rRNA Sequences by High-Temperature Reverse Transcription and PCR

“…Several of these organisms, including M. haemophilum, Mycobacterium shimoidei, and Mycobacterium ulcerans, are considered pathogenic for humans. We compared our results with the comprehensive overview provided by the 16s rRNA phylogenetic tree of the RDP, as well as with the results of specific analyses described previously (13,29,31,36). For the most part, our results corroborate the 16s rRNA tree data, although there are some exceptions.…”

“…2A) and in a subcluster adjacent to Mycobacterium senegalense. This position is very similar to the position determined on the basis of 16s rRNA sequences (29). Although the taxonomic position of this species has not been determined by using other phenetic traits, the results of DNA hybridization studies place it near M. senegalense (34).…”

“…2B are correct, this is the only example of a contradiction with the slow-fast phylogenetic split (31,36). The results of several independent approaches (16s rRNA, 23s rRNA, DNA hybridization) have placed M. farcinogenes with the fast growers, and slow growth appears to be a recently acquired trait (29). It is possible that the loss of rapid growth potential in M. farcinogenes has been acquired independently.…”

“…2B), M. chelonae was placed in the fast-growing species cluster. This change in position probably resulted from the limited sequence examined (29).…”

“…Several important human pathogens, including Mycobacterium tuberculosis and Mycobacterium leprue, are members of the slowly growing group, as are a number of opportunistic pathogens (Table 1) (15). In recent reports workers have described methods for using nucleic acid sequences to identify various specific members of the genus Mycobacterium (4,5,20,21,29,31,37,38). However, not all known members of the genus have been examined; the organisms that have not been examined include some strains which have recently been shown to be problematic in probe-based assays (7,12,14).…”