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Int J Syst Evol Microbiol 53 (2003), 1595-1599; DOI  10.1099/ijs.0.02593-0
© 2003 International Union of Microbiological Societies

Nocardia puris sp. nov.

A. F. Yassin1, B. Sträubler2, P. Schumann2 and K. P. Schaal1

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


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A bacterial isolate (IMMIB R-145T) from a human abscess was subjected to a polyphasic taxonomic study. Chemotaxonomic investigations revealed the isolate to have cell wall chemotype IV and mycolic acids consistent with characteristics of the genus Nocardia. Comparative 16S rRNA gene sequencing showed that the isolate constituted a distinct subline within the genus Nocardia, displaying greater than 1·7 % sequence divergence with established species. However, a DNA–DNA hybridization study demonstrated unambiguously that the isolate was genealogically distinct from closely related species, namely, Nocardia abscessus, Nocardia cyriacigeorgica and Nocardia farcinica, with which it showed high levels of 16S rDNA sequence similarity (97·8, 97·9 and 98·3 %, respectively). Based on phenotypic and phylogenetic data, it is proposed that this isolate be classified as a new species of the genus Nocardia, for which the name Nocardia puris (type strain IMMIB R-145T=DSM 44599T=NRRL B-24204T) is proposed.


The GenBank accession number for the 16S rDNA sequence of Nocardia puris IMMIB R-145T is AJ508748.


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The application of chemotaxonomic methods (Collins et al., 1977Go; Kroppenstedt, 1985Go; Lechevalier, 1976Go; Lechevalier et al., 1977Go; Minnikin et al., 1980Go; Schleifer & Kandler, 1972Go), in combination with a phylogenetic approach based on 16S rRNA gene sequence analyses (Chun & Goodfellow, 1995Go; Ruimy et al., 1994Go; Rainey et al., 1995Go; Stackebrandt & Goodfellow, 1991Go; Stackebrandt et al., 1997Go; Stackebrandt & Goebel, 1994Go; Stackebrandt & Woese, 1981Go), has resulted in a much improved taxonomy of the genus Nocardia (Goodfellow et al., 1999Go). The improved classification provides a sound framework for the recognition of additional species and for resolving the taxonomy of isolates which were collectively assigned to the Nocardia asteroides complex. Thus far, Nocardia abscessus (Yassin et al., 2000bGo) and Nocardia cyriacigeorgica (Yassin et al., 2001Go) equated to some strains originally classified as Nocardia asteroides subgroup IIIA by Schaal & Reutersberg (1978)Go. The genus Nocardia, at the time of writing, encompasses 30 validly described species, which form a distinct phylogenetic line within the suborder Corynebacteriniae (Stackebrandt et al., 1997Go) that constitutes a home for the mycolic-acid-containing genera of the order Actinomycetales. This study describes a novel Nocardia species isolated from a human abscess. Based on phylogenetic and phenotypic data, it is proposed that this species (strain IMMIB R-145T) be classified as Nocardia puris.

Strain IMMIB R-145T was cultured on Brain–Heart 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, 1966Go, 1967Go; Gordon & Mihm, 1957Go) as well as tests to determine carbon source utilization according to Yassin et al. (1995)Go. The isomeric form of the diaminopimelic acid was determined by the methods of Becker et al. (1964)Go and whole-cell sugars were determined by the method of Lechevalier (1968)Go. Lipids were extracted using acid methanolysis and mycolic acids were detected with TLC as described by Minnikin et al. (1980)Go; pyrolysis gas chromatography of the mycolates was performed according to Yassin et al. (1993a)Go. Non-hydroxylated fatty acids were purified, identified and quantified by gas chromatography as described by Yassin (1988)Go. Menaquinones were extracted, purified and identified according to Collins et al. (1977)Go. Phospholipids were extracted, purified and identified as described previously (Yassin et al., 1993cGo).

DNA was isolated and purified as described previously (Yassin et al., 2000aGo). DNA–DNA hybridization studies were carried out by using the thermal renaturation method (Yassin et al., 1993bGo). 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., 1996Go). 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, 1996Go) 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, 1969Go), neighbour-joining (Saitou & Nei, 1987Go) and maximum-likelihood (Felsenstein, 1981Go) algorithms. An evolutionary distance matrix was calculated using the corrections of Jukes & Cantor (1969)Go. 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, 1996Go).

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 acid–alcohol-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 1Go.


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Table 1. Differential physiological characteristics of strain IMMIB R-145T and other significant validly described Nocardia species

Strain: 1, IMMIB R-145T; 2, N. veterana DSM 44445T; 3, N. africana SD769T; 4, N. ignorata DSM 44496T; 5, N. salmonicida JCM 4826T; 6, N. cyriacigeorgica DSM 44484T; 7, N. abscessus DSM 44432T; 8, N. paucivorans DSM 44386T; 9, N. asteroides ATCC 19247T; 10, N. nova ATCC 33726T; 11, N. brasiliensis DSM 43758T; 12, N. farcinica DSM 43665T; 13, N. otitidiscaviarum DSM 43242T; 14, N. vaccinii DSM 43285T; 15, N. transvalensis NCTC 2392T; 16, N. beijingensis JCM 10666T (data from Wang et al., 2001)Go. -, Negative; +, positive; ND, not determined; W, weakly utilized after 3 weeks incubation; d, different, some strains are positive and some are negative.

 
Chemotaxonomically, strain IMMIB R-145T contained chemical markers which support its assignment to the genus Nocardia. The cell wall contains meso-diaminopimelic acid as well as arabinose and galactose (i.e. wall chemotype IV sensu Lechevalier & Lechevalier, 1970Go). One-dimensional TLC of whole-cell acid methanolysates of strain IMMIB R-145T revealed the presence of two lipid spots on the chromatogram: the lower one corresponded to mycolic acids as identified by its RF value (0·47) and the higher one corresponded to the non-hydroxylated fatty acids. Pyrolysis gas chromatography of the purified mycolic acid methyl esters from strain IMMIB R-145T released fatty acid methyl esters of C14 : 0 (4·4 % of total cleavage products), C16 : 0 (61·5 %), C17 : 0 (3·6 %) and C18 : 0 (30·6 %) as pyrolysis cleavage products. Gas chromatographic analyses of the non-hydroxylated fatty acid methyl esters revealed the presence of tetradecanoate (0·9 % of total fatty acids), pentadecanoate (0·6 %), cis-hexadecenoate (3·1 %), hexadecanoate (32·7 %), heptadecanoate (2·40 %), octadecenoate (10·0 %), octadecanoate (14·0 %), tuberculostearic acid (10-methyl octadecanoate, 20·4 %), nonadecanoate (0·2 %), eicosenoate (6·0 %), eicosanoate (4·7 %), heneicosenoate (0·4 %), heneicosanoate (0·3 %), docosenoate (3·0 %) and docosanoate (2·1 %) as the major cellular fatty acid methyl esters. Polar lipid analysis showed that strain IMMIB R-145T contains phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and diphosphatidylglycerol as the characteristic phospholipids (i.e. phospholipid type PII sensu Lechevalier et al., 1977Go). Mass spectral analysis of the respiratory quinones showed that strain IMMIB R-145T possesses hexahydrogenated menaquinones with eight isoprene units in which the two terminal isoprene moieties are cyclized. The main component corresponds to MK-8(H6) and the minor component corresponds to 2,3-epoxy-MK-8(H6). These chemotaxonomic similarities to the validly described species of the genus Nocardia are supported by the high levels of 16S rRNA gene sequence similarity observed between isolate IMMIB R-145T and members of the genus Nocardia (>95 %).

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., 1978Go)] 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., 1997Go) 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 (95·5–98·3 %) 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. 1Go. 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, 1994Go). In view of the high levels of 16S rDNA sequence similarity between strain IMMIB R-145T and some Nocardia species, chromosomal DNA–DNA 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 DNA–DNA 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)Go and confirm the separation of strain IMMIB R-145T from its nearest phylogenetic neighbours.



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Fig. 1. Unrooted phylogenetic tree showing the position of strain IMMIB R-145T within the radiation of species of the genus Nocardia. The tree, constructed using the neighbour-joining method, was based on a comparison of sequences that were at least 90 % complete (with regard to E. coli sequence). Bar, 5·0 % sequence divergence.

 
The genus Nocardia contains a number of species for which numerous distinctive characters have been described that fully justify their classification in separate species but that exhibit only limited 16S rDNA divergence. For instance, the 16S rDNA of N. beijingensis is 97·6 and 97·5 % similar to that of N. brasiliensis and N. farcinica, respectively, though the distinction between N. beijingensis and the two species has been convincingly illustrated by different characters and did not require the determination of DNA hybridization values (Wang et al., 2001Go). Similarly, Nocardia vaccinii and Nocardia africana share 98·5–98·7 % 16S rDNA sequence similarity (Hamid et al., 2001Go). More critical examples are Nocardia veterana and N. africana, the 16S rDNA of which are 99·3 % similar, whereas the total labelled genomic DNA of the two species exhibits only 28·8 % homology. Similar situations were found for Nocardia brevicatena and Nocardia paucivorans, which have a 16S rDNA similarity value of 99·6 % but 61·9 % DNA–DNA relatedness (Yassin et al., 2000aGo), and for Nocardia carnea and Nocardia flavorosea, which have a 16S rRNA similarity value of 99·2 % but 5·0 % DNA–DNA relatedness (Chun et al., 1998Go). The 97 % limit is thus not always fulfilled in the genus Nocardia and additional distinctive characteristics must be determined to allow the definition of a new species. Given the 2·4–2·5 % sequence divergence values of strain IMMIB R-145T and its closest relatives N. transvalensis, N. beijingensis and N. brasiliensis on the one hand and the biochemical tests presented in Table 1Go to discriminate strain IMMIB R-145T from the last three species on the other hand, we feel that it is reasonable to define a new species of the genus Nocardia. The chemical (and morphological) data clearly indicate that strain IMMIB R-145T belongs to the genus Nocardia, and the 16S rDNA sequencing, DNA–DNA pairing and biochemical results indicate that it forms a new species when compared with the type strains of validly described species of the genus Nocardia. Thus, on the basis of the results of the reported polyphasic taxonomic study, we consider that strain IMMIB R-145T merits classification as a new species of the genus Nocardia, for which the name Nocardia puris is proposed.

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 acid–alcohol-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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Since this work was submitted for publication, two more species of Nocardia have been described, Nocardia cerradoensis (Albuquerque de Barros et al., 2003Go) and Nocardia caishijiensis (Zhang et al., 2003Go).


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H. Yamamura, M. Hayakawa, Y. Nakagawa, T. Tamura, T. Kohno, F. Komatsu, and Y. Iimura
Nocardia takedensis sp. nov., isolated from moat sediment and scumming activated sludge
Int J Syst Evol Microbiol, January 1, 2005; 55(1): 433 - 436.
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Int. J. Syst. Evol. Microbiol.Home page
A. Kageyama, K. Yazawa, A. Mukai, M. Kinoshita, N. Takata, K. Nishimura, R. M. Kroppenstedt, and Y. Mikami
Nocardia shimofusensis sp. nov., isolated from soil, and Nocardia higoensis sp. nov., isolated from a patient with lung nocardiosis in Japan
Int J Syst Evol Microbiol, November 1, 2004; 54(6): 1927 - 1931.
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Int. J. Syst. Evol. Microbiol.Home page
J. Zhang, Z. Liu, and M. Goodfellow
Nocardia xishanensis sp. nov., a novel actinomycete isolated from soil
Int J Syst Evol Microbiol, November 1, 2004; 54(6): 2301 - 2305.
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Int. J. Syst. Evol. Microbiol.Home page
L. Wang, Y. Zhang, Y. Huang, L. A. Maldonado, Z. Liu, and M. Goodfellow
Nocardia pigrifrangens sp. nov., a novel actinomycete isolated from a contaminated agar plate
Int J Syst Evol Microbiol, September 1, 2004; 54(5): 1683 - 1686.
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J. Clin. Microbiol.Home page
J. M. Brown, K. N. Pham, M. M. McNeil, and B. A. Lasker
Rapid Identification of Nocardia farcinica Clinical Isolates by a PCR Assay Targeting a 314-Base-Pair Species-Specific DNA Fragment
J. Clin. Microbiol., August 1, 2004; 42(8): 3655 - 3660.
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Int. J. Syst. Evol. Microbiol.Home page
P. Kampfer, S. Buczolits, U. Jackel, I. Grun-Wollny, and H.-J. Busse
Nocardia tenerifensis sp. nov.
Int J Syst Evol Microbiol, March 1, 2004; 54(2): 381 - 383.
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Int. J. Syst. Evol. Microbiol.Home page
D. Saintpierre-Bonaccio, L. A. Maldonado, H. Amir, R. Pineau, and M. Goodfellow
Nocardia neocaledoniensis sp. nov., a novel actinomycete isolated from a New-Caledonian brown hypermagnesian ultramafic soil
Int J Syst Evol Microbiol, March 1, 2004; 54(2): 599 - 603.
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