No abstract

Four hundred and seventy-five strains, which included 394 type cultures of Streptomyces and representatives of 14 other actinomycete genera, were studied. Overall similarities of these strains for 139 unit characters were determined by the SSM and SJ coefficients and clustering by the UPGMA algorithm. Test error and overlap between the phena defined were within acceptable limits. Cluster-groups were defined by the SSM coefficient at the 70.1% similarity (S) level and by the SJ coefficient at the 50% S-level. Clusters were distinguished at the 77.5% SSM and 63% SJ S-levels. Groupings obtained with the two coefficients were generally similar, but there were some changes in the definition and membership of cluster-groups and clusters. The phenetic data obtained, together with those from previous diverse studies, indicated that the genera Actinopycnidium, Actinosporangium, Chainia, Elytrosporangium, Kitasatoa and Microellobosporia should be reduced to synonyms of Streptomyces, while Intrasporangium, Nocardioides and Streptoverticillium remained as distinct genera in the family Streptomycetaceae. Nocardiopsis dassonvillei also showed strong phenetic affinity to Streptomyces, despite its chemotaxonomic differences. Actinomadura sensu stricto was phenetically distinguishable from Streptomyces and 'Nocardia' mediterranea was recognized as a taxon distinct from both these genera and from Nocardia sensu stricto. Most of the Streptomyces type cultures fell into one large cluster-group. At the 77.5% SSM S-level, they were recovered in 19 major and 40 minor clusters, with 18 strains recovered as single member clusters. The status of the latter as species was therefore confirmed. Most of the minor clusters, consisting of two to five strains, can also be regarded as species. The major clusters varied in size (from 6 to 71 strains) and in there homogeneity. Therefore, it is suggested that they be regarded as species-groups until further information is available. The results provide a basis for the reduction of the large number of Streptomyces species which have been described. They also demonstrate that the previous use of a limited number of subjectively chosen characters to define species-groups or species has resulted in artificial classifications.

A numerical taxonomic classification study was carried out on 177 strains representing the ' rhodochrous ' complex and the genera Gordona, Mycobacterium and Nocardia. The strains were examined for 92 unit characters and the data were analysed by computer. Three clusters were defined at the 75 to 80 % similarity level. The first was a heterogeneous cluster corresponding to the ' rhodochrous' taxon whereas the other two contained Mycobacterium and Nocardia strains respectively. The good correlation between the numerical analysis and chemotaxonomic, serological and genetical data collected from previous studies provides sufficient evidence for raising the ' rhodochrous ' taxon to generic status. We consider the generic name Rhodococcus Zopf to have priority over Proactinomyces

The character state data obtained for clusters defined at the 77.5% SSM similarity level in the phenetic numerical classification described by Williams et al. (1983) were used to construct a probabilistic identification matrix. The 23 phena included were the major clusters (19 Streptomyces, 2 Streptoverticillium and 'Nocardia' mediterranea) and one minor cluster (Streptomyces fradiae). The characters most diagnostic for these clusters were selected using Sneath's CHARSEP and DIACHAR programs. The resulting matrix consisted of 41 characters x 23 phena. Identification scores, determined by Sneath's MATIDEN program were used to evaluate the matrix. Theoretical assessment was achieved by determination of the cluster overlap (OVERMAT), the identification scores for the Hypothetical Medium Organism of each cluster (MOSTTYP), and the scores for randomly selected cluster representatives using the classification data of Williams et al. (1983). The matrix was evaluated practically by the independent re-determination of the characters for the same cluster representatives, which also provided a measure of test error. Finally it was used to identify unknown isolates from a range of habitats. The results showed that the matrix was theoretically sound. Test error was within acceptable limits and did not distort identifications. Of the unknown isolates, 80% were clearly identified with a cluster. It is suggested that the matrix could form the basis for a more objective identification and grouping of the large number of Streptomyces species which have been described.

The menaquinones of 141 actinomycetes representing the genera Caseobacter, Mycobacterium, Nocardia, Rhodococcus and some related taxa lacking mycolic acids were examined by mass spectrometry. The mycolic acid-containing strains were assigned to four groups on the basis of the predominant isoprenologue detected: Rhodococcus coprophilus, R. equi, R. erythropolis, R. globerulus, R. rhodnii, R. rhodochrous and R. ruber contained dihydrogenated menaquinones with eight isoprene units; Nocardia asteroides, N. brasiliensis, N. carnea, N. otitidis-caviarum and N. transvalensis contained tetrahydrogenated menaquinones with eight isoprene units; Caseobacter polymorphus, R. bronchialis, R. rubropertinctus and R. terrae and representatives of twenty-one approved species of Mycobacterium contained dihydrogenated menaquinones with nine isoprene units; a single strain of 'Mycobacterium album', contained unsaturated menaquinones with nine isoprene units. Actinomycetes containing meso-diaminopimelic acid, arabinose and galactose in the wall peptidoglycan but lacking mycolic acids were recovered in two groups: tetrahydrogenated menaquinones with eight isoprene units were the main components from 'Nocardia' autotrophica and Pseudonocardia thermophila whereas Saccharopolyspora hirsuta and Pseudonocardia spp. contained tetrahydrogenated menaquinones with nine isoprene units. Promicromonospora citrea and 'skin coryneforms' with LL-diaminopimelic acid and glycine in the wall peptidoglycan also contained tetrahydrogenated menaquinones with nine isoprene units as the major isoprenologue. In contrast, representatives of the genera Kitasatoa, Microellobosporia, Streptomyces and Streptoverticillium were characterized by the presence of complex mixtures of tetra-, hexa- and octa-hydrogenated menaquinones with nine isoprene units. The menaquinone data correlate well with other developments in actinomycete systematics and confirm earlier suggestions that menaquinone analyses are of value in both the classification and identification of actinomycetes. Indeed, the data suggest that minimal descriptions of wall chemotype IV taxa should ideally include information on menaquinone composition.

Various approaches that have been used in the development of a system of classification for the genus Rhodococcus are discussed. The application of chemotaxonomic, molecular systematic and numerical phenetic methods have greatly contributed to improvements in the systematics of rhodococci and related mycolic-acid containing actinomycetes. The genus currently encompasses twelve validly described species but improved diagnostic methods are needed to distinguish between them. In addition, evidence from 16S ribosomal RNA sequencing suggests that the genus is still heterogeneous.

One hundred and fifty-six Actinomadura strains, marker strains of related taxa, and related isolates from bagasse and fodder were the subject of numerical phenetic analyses using 90 unit characters. The data were examined using the simple matching (SSM), Jaccard (SJ) and pattern (Dp) coefficients and clustering was achieved using both single and average linkage algorithms. Cluster composition was not markedly affected either by the coefficient or clustering algorithms used or by test error, estimated at 4-5 %. Actinomadura dassonvillei, Actinomadura madurae and Streptomyces somaliensis formed good taxospecies, but the separation of Actinomadura pelletieri strains into two clusters by SJ and SSM analysis requires further study. The single representatives of Actinomadura helvata, Actinomadura pusilla, Actinomadura roseoviolacea, Actinomadura spadix and Actinomadura verrucosospora seemed to form new centres of variation while Actinomadura citrea and Actinomadura malachitica showed much similarity with Actinomadura madurae. Most of the isolates from bagasse and fodder were recovered in two well-defined phena, provisionally labelled clusters 'A' and 'B' which showed little similarity to either Actinomadurn or Nocardia strains, The effect of the different coefficients on the aggregation of clusters is discussed.

Rhodococcus equi is a facultative pathogen of foals. Infection causes an often fatal pulmonary pneumonia. The organism has also been isolated from pigs, cattle, humans and the environment. Equine virulence has a high positive correlation with the expression of a 17.4 kD polypeptide of unknown function, VapA, the product of the plasmid-encoded vapA gene. More recently an isogene of vapA, referred to as vapB and encoding an 18.2 kDa polypeptide, has been identified among pig and human isolates. The two genes share > 80% sequence identity, yet their host strains apparently exhibit different pathogenicity profiles (for example by reference to virulence in mouse model system and host specificity). In this study, a polymerase chain reaction (PCR) technique was developed that permits the selective amplification of vapA and vapB. Using this technique the distribution of the two genes among 35 randomly selected isolates of Rhodococcus equi from various animal and environmental sources was determined. Using this technique the genotype of each isolate could be unambiguously assigned as vapA+, vapB+ or vap- (i.e., scoring negative for both vapA and vapB). No isolate scored positive for both vapA and vapB. 100% of equine isolates scored vapA+, confirming the status of vapA as a reliable marker of equine virulence. All three genotypes were found among human isolates; porcine isolates scored either vapB+ or vap- and no vapA+ isolates were present in this sample. Rigorous statistical analysis using the Fisher Exact test confirmed that the high frequency of vapA+ among equine isolates is significant; however the sample size was too small to draw statistically significant conclusions regarding the distribution of genotypes among within other animal groups.