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1 Institut für Medizinische Mikrobiologie und Immunologie der Universität Bonn, D-53127 Bonn, Germany
2 DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen, Mascheroder Weg 1b, 38124 Braunschweig, Germany
Correspondence
Atteyet F. Yassin
yassin{at}mibi03.meb.uni-bonn.de
| ABSTRACT |
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| MAIN TEXT |
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Strain IMMIB R-145T was cultured on BrainHeart Infusion (BHI) agar to determine its morphological properties. The strain was biochemically characterized by using tests to determine hydrolysis of complex substrates as described previously (Gordon, 1966
, 1967
; Gordon & Mihm, 1957
) as well as tests to determine carbon source utilization according to Yassin et al. (1995)
. The isomeric form of the diaminopimelic acid was determined by the methods of Becker et al. (1964)
and whole-cell sugars were determined by the method of Lechevalier (1968)
. Lipids were extracted using acid methanolysis and mycolic acids were detected with TLC as described by Minnikin et al. (1980)
; pyrolysis gas chromatography of the mycolates was performed according to Yassin et al. (1993a)
. Non-hydroxylated fatty acids were purified, identified and quantified by gas chromatography as described by Yassin (1988)
. Menaquinones were extracted, purified and identified according to Collins et al. (1977)
. Phospholipids were extracted, purified and identified as described previously (Yassin et al., 1993c
).
DNA was isolated and purified as described previously (Yassin et al., 2000a
). DNADNA hybridization studies were carried out by using the thermal renaturation method (Yassin et al., 1993b
). Genomic DNA extraction, PCR-mediated amplification of the 16S rDNA and the purification of PCR products were carried out using procedures described previously (Rainey et al., 1996
). Purified PCR products were sequenced using a Taq DyeDeoxy Terminator Cycle Sequencing Kit (Applied Biosystems) as described in the manufacturer's protocol. An Applied Biosystems 310 DNA Genetic Analyser was used for the electrophoresis of the sequence reaction products. The 16S rDNA sequence of strain IMMIB R-145T as well as those of the validly described species of the genus Nocardia retrieved from the GenBank database were added to the ARB database (Ludwig & Strunk, 1996
) and aligned using the respective tool of the ARB package. The resulting alignment was corrected manually and evolutionary trees were inferred using the maximum-parsimony (Kluge & Farris, 1969
), neighbour-joining (Saitou & Nei, 1987
) and maximum-likelihood (Felsenstein, 1981
) algorithms. An evolutionary distance matrix was calculated using the corrections of Jukes & Cantor (1969)
. The tree topology was evaluated according to the results of the neighbour-joining and maximum-likelihood analyses. The phylogenetic analyses were carried out using the ARB package (Ludwig & Strunk, 1996
).
Strain IMMIB R-145T has morphological properties consistent with its assignment to the genus Nocardia. It is an aerobic organism which forms hyphae that are Gram-positive and slightly acidalcohol-fast. The vegetative hyphae were well developed with irregular branches penetrating the agar and bearing white aerial hyphae. At a late stage of growth, the hyphae fragment into rod-shaped elements characteristic of nocardiae. The physiological properties of strain IMMIB R-145T are given in the species description (see below). Differences in the biochemical characteristics of strain IMMIB R-145T compared to those of some of the validly described species of the genus Nocardia examined in this study can be found in Table 1
.
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To ascertain the phylogenetic position of strain IMMIB R-145T, its almost-complete 16S rRNA gene sequence [1474 nt; 95·6 % of the Escherichia coli sequence (Brosius et al., 1978
)] was determined in this study and subjected to a comparative analysis. The 16S rRNA gene sequence comparison clearly showed that strain IMMIB R-145T is a member of the family Nocardiaceae (Stackebrandt et al., 1997
) and that the determined sequence contains all the signature nucleotides designated for this lineage. The high values for the 16S rRNA gene sequence similarity to other previously described members of the genus Nocardia (95·598·3 %) support the addition of strain IMMIB R-145T to this genus. Significantly lower levels of similarity were shown with other taxa of the order Actinomycetales (data not shown). Highest sequence similarities were shown with Nocardia abscessus (97·8 %), Nocardia cyriacigeorgica (97·9 %) and Nocardia farcinica (98·3 % sequence similarity). A tree, constructed using the neighbour-joining method, depicting the phylogenetic placement of strain IMMIB R-145T within a subset of the genus Nocardia is shown in Fig. 1
. It was evident from the tree that strain IMMIB R-145T represents a distinct subline within the genus Nocardia that is associated with Nocardia beijingensis, Nocardia brasiliensis, N. farcinica and Nocardia transvalensis; the strain displayed sequence similarity values of 97·6, 97·5, 98·3 and 97·6 %, respectively, with these species. These results suggest that strain IMMIB R-145T belongs to a genetically distinct Nocardia species. However, the sequence similarity values are too high to allow the definition of a new species on the basis of 16S rDNA sequence alone, since values below 97 % sequence similarity and/or genomic DNA reassociation values below 70 % are considered relevant for the establishment of new bacterial species (Stackebrandt & Goebel, 1994
). In view of the high levels of 16S rDNA sequence similarity between strain IMMIB R-145T and some Nocardia species, chromosomal DNADNA hybridization studies were performed to establish whether strain IMMIB R-145T represents a distinct species of the genus Nocardia. Strain IMMIB R-145T displayed low levels of DNADNA reassociation with N. abscessus DSM 44432T (20·6 %), N. cyriacigeorgica DSM 44484T (37·6 %) and N. farcinica DSM 43665T (42·3 %), results which are below the cut-off point recommended for the circumscription of bacterial genomic species by Wayne et al. (1987)
and confirm the separation of strain IMMIB R-145T from its nearest phylogenetic neighbours.
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Description of Nocardia puris sp. nov.
Nocardia puris (pu'ris. L. gen. neut. n. puris of corrupt matter, pus, pertaining to the abscess from which the type strain was isolated).
Hyphae are Gram-positive and partially acidalcohol-fast. Vegetative hyphae are well developed with irregular branches penetrating the agar; they also bear white aerial hyphae. At a late stage of growth, the hyphae fragment into rod-shaped elements. Grows between 22 and 45 °C. Contains the salient chemotaxonomic characteristics of nocardiae. Mycolic acids cleaved on pyrolysis to release fatty acids of C14 : 0, C16 : 0, C17 : 0 and C18 : 0, with C16 : 0 as the major cleavage product. Hydrolyses aesculin, testosterone and urea but not adenine, casein, elastin, gelatin, guanine, hypoxanthine, tyrosine or xanthine. Assimilates acetate, citrate, glucose, myo-inositol, maltose, mannitol, sorbitol and sucrose as carbon sources but not adonitol, adipate, isoamyl alcohol, arabinose, 2,3-butanediol, cellobiose, meso-erythritol, galactose, gluconate, m-hydroxybenzoate, p-hydroxybenzoate, lactate, lactose, melezitose, 1,2-propanediol, raffinose, rhamnose, trehalose or xylose. Utilizes alanine but not acetamide, arginine, gelatin, ornithine, proline or serine as simultaneous carbon and nitrogen sources.
The type strain is IMMIB R-145T (=DSM 44599T=NRRL B-24204T). Isolated from a human abscess.
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