Nocardia salmonicida nom. rev., a fish pathogen

Noviherbaspirillum album sp. nov., an airborne bacteria isolated from an urban area of Beijing, China

A Gram-negative, ellipsoidal to short-rod-shaped, motile bacterium was isolated from Beijing's urban air. The isolate exhibited the closest kinship with Noviherbaspirillum aerium 122213-3T, exhibiting 98.4 % 16S rRNA gene sequence similarity. Phylogenetic analyses based on 16S rRNA gene sequences and genomes showed that it clustered closely with N. aerium 122213-3T, thus forming a distinct phylogenetic lineage within the genus Noviherbaspirillum. The average nucleotide identity and digital DNA-DNA hybridization values between strain I16B-00201T and N. aerium 122213-3T were 84.6 and 29.4 %, respectively. The respiratory ubiquinone was ubiquinone 8. The major fatty acids (>10 %) were summed feature 3 (C16:1ω6c/C16:1ω7c, 43.3 %), summed feature 8 (C18:1ω7c/C18:1ω6c, 15.9 %) and C12:0 (11.0 %). The polyamine profile showed putrescine as the predominant compound. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, unknown lipids and unknown phosphatidylaminolipids. The phenotypic, phylogenetic and chemotaxonomic results consistently supported that strain I16B-00201T represented a novel species of the genus Noviherbaspirillum, for which the name Noviherbaspirillum album sp. nov. is proposed, with I16B-00201T (=CPCC 100848T=KCTC 52095T) designated as the type strain. Its DNA G+C content is 59.4 mol%. Pan-genome analysis indicated that some Noviherbaspirillum species possess diverse nitrogen and aromatic compound metabolism pathways, suggesting their potential value in pollutant treatment.

Pathological variations and immune response in Channa argus infected with pathogenic Nocardia seriolae strain

Nocardia seriolae pathogen causes chronic granulomatous disease, reportedly affecting over 40 species of marine and freshwater cultured fish. Hence, research is required to address and eliminate this significant threat to the aquaculture industry. In this respect, a reliable and reproducible infection model needs to be established to better understand the biology of this pathogen and its interactions with the host during infection, as well as to develop new vaccines or other effective treatment methods. In this study, we examined the pathogenicity of the pathogen and the immune response of snakehead (Channa argus) juvenile to N. seriolae using a range of methods and analyses, including pathogen isolation and identification, histopathology, Kaplan-Meier survival curve analysis, and determination of the median lethal dose (LD50) and cytokine expression. We have preliminarily established a N. seriolae - C. argus model. According to our morphological and phylogenetic analysis data, the isolated strain was identified as N. seriolae and named NSE01. Eighteen days post-infection of healthy juvenile C. argus with N. seriolae NSE01, the mortality rate in all four experimental groups (intraperitoneally injected with 1 × 105 CFU/mL - 1 × 108 CFU/mL of bacterial suspension) (n = 120) was 100 %. The LD50 of N. seriolae NSE01 for juvenile C. argus was determined to be 1.13 × 106 CFU/fish. Infected juvenile C. argus had significant pathological changes, including visceral tissue swelling, hemorrhage, and the presence of numerous nodules of varying sizes in multiple tissues. Further histopathological examination revealed typical systemic granuloma formation. Additionally, following infection with N. seriolae NSE01, the gene expression of important cytokines, such as Toll-like receptor genes TLR2, TLR13, interleukin-1 receptor genes IL1R1, IL1R2, and interferon regulatory factor IRF2 were significantly upregulated in different tissues, indicating their potential involvement in the host immune response and regulation against N. seriolae. In conclusion, juvenile C. argus can serve as a suitable model for N. seriolae infection. The establishment of this animal model will facilitate the study of the pathogenesis of nocardiosis and the development of vaccines.

Biological characteristics and pathogenicity comparison of Nocardia seriolae isolated from Micropterus salmoides and Channa argus

Nocardia seriolae is the primary pathogen causing nocardiosis in various fish species, leads to significant economic losses in the aquaculture industry. In this study, 10 bacterial strains isolated from Micropterus salmoides and Channa argus infected with nocardiosis, were identified as N. seriolae by physiological and biochemical identification, as well as 16S rDNA sequencing. Moreover, the key virulence-related genes such as ESX-1, T7SS-2, T7SS-3, EspG1, sodC, sod2 and ESAT6 were all positive, and showing high homology among different strains. Pathogenicity testing revealed mortality rates ranging from 70 to 100%, accompanied by the presence of white nodules in the viscera of deceased fish. The drug sensitivity test demonstrated that LY21811, the most lethal strain, exhibited high sensitivity to nine types of antibiotics, including azithromycin, doxycycline, florfenicol and compound sulfamethoxazole, yet showed complete resistance to β-lactam antibiotics. Additionally, the tannic acid also demonstrated potent inhibitory effects against LY21811, with a minimum inhibitory concentration of 0.0625 mg/mL. These results showed that N. seriolae originated from M. salmoides and C. argus in Zhejiang Province were highly conserved, demonstrating a high homogeneity in genetic characteristics, pathogenicity and antimicrobial susceptibilities. These results provide a foundation for further research on the pathogenic characteristics and disease prevention of N. seriolae infections.

Induction of attenuated Nocardia seriolae and their use as live vaccine trials against fish nocardiosis

Nocardia seriolae, a Gram-positive facultative intercellular pathogen, has been identified as the causative agent of fish nocardiosis, causing substantial mortality and morbidity of a wide range of fish species. Looking into that fact, the effective vaccine against this pathogen is urgently needed to control the significant losses in aquaculture practices. In order to induct attenuated strains for developing the potential live vaccines, the mutagenic N. seriolae strain S-250 and U-20 were obtained from wild-type strain ZJ0503 through continuous passaging and ultraviolet (UV) irradiation, respectively. Additionally, the biological characteristic, virulence, stability, mediating immune response and supplying protective efficacy to hybrid snakehead of the S-250 and U-20 strains were determined in the present study. The results showed that U-20 strain displayed dramatic changes in morphological characteristic and significant decreased in the virulence to hybrid snakehead, while that of S-250 strain had no obvious different in comparison to ZJ0503 strain. When hybrid snakehead were intraperitoneally injected with ZJ0503, S-250 and U-20 strains at their respective sub-clinical dosage, the non-specific immunity parameters (serum LYZ, POD, ACP, AKP and SOD activities), specific antibody (IgM) titers production and immune-related genes (CC1, CC2, IL-1β, IL-8, TNFα, IFNγ, MHCIα, MHCIIα, CD4, CD8α, TCRα and TCRβ) expression were up-regulated, indicating that they were able to trigger humoral and cell-mediated immune responses. Furthermore, the protective efficacy in hybrid snakehead after vaccination with ZJ0503, S-250 and U-20 strains, in terms of relative percentage survival (RPS), were 28.85%, 56.89% and 89.65% respectively. Taken together, two attenuated N. seriolae strains S-250 and U-20 were obtained successfully and they could elicit strong immune response and supply protective efficacy to hybrid snakehead against N. seriolae, which suggested that these two attenuated strains were the potential candidates for live vaccine development to control fish nocardiosis in aquaculture.

Nocardia rosealba sp. nov., a novel ligninase-producing Actinobacterium isolated from soil

A novel ligninase-producing actinomycete, designated strain NEAU-G4T, was isolated from a soil sample and subjected to a polyphasic taxonomic study to establish its status. According to 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Nocardia , with the highest sequence similarity to Nocardia ignorata DSM 44496T (99.2 %). The whole-cell sugars contained galactose and arabinose. The amino acid of the cell wall was determined to be meso-diaminopimelic acid. The major fatty acids (>10 %) were C16 : 0, C18 : 1  ω9c, C18 : 0 and C16 : 1  ω7c. The predominant menaquinone was identified as MK-8(H6, ω-cycl). The major polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. Strain NEAU-G4T had a draft genome size of 6 405 167 bp, annotated with 5815 protein-coding genes. The DNA G+C content was 67.6 mol%. Phylogenetic analysis using the 16S rRNA gene and whole-genome sequences showed that strain NEAU-G4T formed a stable phyletic line with N. ignorata DSM 44496T. The digital DNA–DNA hybridization and average nucleotide identity values between them were 63.7 % (60.8–66.5 %) and 95.5 %, respectively. Moreover, genomic analysis indicated that strain NEAU-G4T had the potential to degrade lignin and produce bioactive compounds. On the basis of genotypic analysis, physiological data, as well as phenotypic and chemotaxonomic characterizations, it is concluded that the organism be classified as representing a novel species of the genus Nocardia , for which the name Nocardia rosealba sp. nov. is proposed. The type strain is NEAU-G4T (=CCTCC AA 2020038T=DSM 111936T).

Molecular Identification of Nocardia seriolae and Comparative Analysis of Spleen Transcriptomes of Hybrid Snakehead (Channa maculata Female × Channa argus Male) With Nocardiosis Disease

Hybrid snakehead (Channa maculata female × Channa argus male) is a new freshwater aquaculture fish species in southern China. During intensive aquaculture, hybrid snakeheads are often infected by Nocardia seriolae. In this study, hybrid snakehead infected suspiciously by N. seriolae in an artificial breeding pond were examined. Diseased hybrid snakeheads swam slowly without food intake, and the clinical symptoms included skin wound, anal swelling and ascites, and white granulomatous in liver, spleen, and kidney of fish. Through bacterial isolation, 16S rDNA sequencing, fluorescence in situ hybridization (FISH) and artificial infection experiment, the pathogen was identified as N. seriolae. Furthermore, the spleen samples from diseased and healthy male hybrid snakeheads in the same pond were used for RNA-Seq analysis. A total of 3,512 unique transcripts (unigenes) were identified as differentially expressed genes (DEGs), and 1,886 of them were up-regulated in diseased fish. The expression patterns of 20 DEGs were verified by quantitative polymerase chain reaction (qPCR). Several immune-related pathways and many immune-related genes were identified. qPCR results showed that the expression patterns of immune-related genes in the liver and kidney of diseased fish were comparable to that in the spleen. This study provides deep-sequencing data of hybrid snakehead spleen and will help understand the immune response of hybrid snakehead to N. seriolae. It is also helpful for the biomarker screening of fish-borne Nocardia spp. and the breeding of nocardiosis-resistant fish species.

Ornithinimicrobium cerasi sp. nov., isolated from the fruit of Cerasus pseudocerasus and emended description of the genus Ornithinimicrobium

Strain CPCC 203383^T, isolated from the surface-sterilized fruit of Cerasus pseudocerasus (Lindl.) G. Don, was taxonomically characterized based on a polyphasic investigation. It had the highest 16S rRNA gene sequence similarities with Ornithinimicrobium pekingense DSM 21552 (97.2 %) and O. kibberense DSM 17687^T (97.2%). Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain formed a distinct phyletic branch within the genus Ornithinimicrobium and the whole genome sequence data analyses supported that strain CPCC 203383^T was phylogenetically related to the Ornithinimicrobium species. The isolate shared a range of phenotypic patterns reported for members of the genus Ornithinimicrobium, but also had a range of cultural, physiological and biochemical characteristics that separated it from related Ornithinimicrobium species. The menaquinone was MK-8(H₄). The polar lipid profile consisted of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylinositol (PI) and unidentified lipids (ULs). The major fatty acids (>5 %) were iso-C_15 : 0, anteiso-C_15 : 0, iso-C_16:0, 9-methyl C_16 : 0, iso-C_17 : 0 and anteiso-C_17 : 0. The cell wall peptidoglycan contains l-ornithine as diagnostic diamino acid and an interpeptide bridge consisting of _L-Orn←_L-Ala←Gly←_D-Asp. The combined genotypic and phenotypic data indicated that the isolate represents a novel species of the genus Ornithinimicrobium, for which the name Ornithinimicrobium cerasi sp. nov. is proposed, with CPCC 203383^T(=NBRC 113522^T=KCTC 49200^T) as the type strain. The DNA G+C composition is 72.3 mol%. The availability of new data allows for an emended description of the genus Ornithinimicrobium.

Identification of common antigens of three pathogenic Nocardia species and development of DNA vaccine against fish nocardiosis

Fish nocardiosis is a chronic granulomatous bacterial disease and three pathogens have been reported so far, including Nocardia asteroids, N. seriolae and N. salmonicida. However, the absence of antigen markers is a bottleneck for developing effective vaccines against fish nocardiosis. In this study, the antigenicity of whole-cell protein of these three pathogenic Nocardia species were profiled by immunoproteomic analysis and 7 common immunogenic proteins were identified as follows: molecular chaperone DnaK (DnaK), molecular chaperone GroEL (GroEL), 30 S ribosomal protein S1 (RpsA), TerD family protein (TerD), FHA domain-containing protein (FHA), 50 S ribosomal protein L7/L12 (RplL) and PspA/IM30 family protein (PspA). Furthermore, the DNA vaccine encoding FHA gene against fish nocardiosis was developed and its efficacy was investigated in hybrid snakehead. The results suggested that it needed at least 7 d to transport pcDNA-FHA DNA vaccine from injected muscle to head kidney, spleen and liver and stimulate host's immune system for later protection. In addition, non-specific immunity paraments (serum lysozyme (LYZ), peroxidase (POD), acid phosphatase (ACP), alkaline phosphatase (AKP) and superoxide dismutase (SOD) activities), specific antibody (IgM) titers production and immune-related genes (MHCIα, MHCIIα, CD4, CD8α, IL-1β and TNFα) were used to evaluate the immune response induced in pcDNA-FHA vaccinated hybrid snakehead, it proved that all these mentioned immune activities were significantly enhanced after immunization. The results also showed hybrid snakehead vaccinated with pcDNA-FHA had higher survival rate (79.33%) compared with the controls after challenge with N. seriolae, indicating that the pcDNA-FHA DNA vaccine can supply immune protection against N. seriolae infection. Taken together, this study may warrant further development of these common immunogenic proteins as the antigens for vaccine or diagnosis and facilitate the prevention and treatment of fish nocardiosis.

Comparison of protective efficacy between two DNA vaccines encoding DnaK and GroEL against fish nocardiosis

Fish nocardiosis is a chronic granulomatous bacterial disease mainly caused by three pathogenic bacteria, including Nocardia seriolae, N. asteroids and N. salmonicida. Molecular chaperone DnaK and GroEL were identified to be the common antigens of the three pathogenic Nocardia species in our previous studies. To evaluate the immune protective effect of two DNA vaccines encoding DnaK or GroEL against fish nocardiosis, hybrid snakehead were vaccinated and the immune responses induced by these two vaccines were comparatively analyzed. The results suggested it needed at least 7 d to transport DnaK or GroEL gene from injected muscle to head kidney, spleen and liver and stimulate host's immune system for later protection after immunization by DNA vaccines. Additionally, non-specific immunity parameters (serum lysozyme (LYZ), peroxidase (POD), acid phosphatase (ACP), alkaline phosphatase (AKP) and superoxide dismutase (SOD) activities), specific antibody (IgM) production and immune-related genes (MHCIα, MHCIIα, CD4, CD8α, IL-1β and TNFα) were used to evaluate the immune responses induced in vaccinated hybrid snakehead. It proved that all the above-mentioned immune activities were significantly enhanced after immunization with these two DNA vaccines. The protective efficacy of pcDNA-DnaK and pcDNA-GroEL DNA vaccines, in terms of relative percentage survival (RPS), were 53.01% and 80.71% respectively. It demonstrated that these two DNA vaccines could increase the survival rate of hybrid snakehead against fish nocardiosis, albeit with variations in immunoprotective effects. Taken together, these results indicated that both pcDNA-DnaK and pcDNA-GroEL DNA vaccines could boost the innate, humoral and cellular immune response in hybrid snakehead and show highly protective efficacy against fish nocardiosis, suggesting that DnaK and GroEL were promising vaccine candidates. These findings will promote the development of DNA vaccines against fish nocardiosis in aquaculture.

Nocardia mangyaensis sp. nov., a novel actinomycete isolated from crude-oil-contaminated soil

A Gram-stain-positive, aerobic, non-motile and mycolic-acid-containing strain, designated Y48^T, was isolated from soil contaminated by crude oil located in the northern margin of the Qaidam Basin. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Y48^T belongs to the genus Nocardia and is closely related to N. cummidelens DSM 44490^T (99.0 % similarity), N. soli DSM 44488^T (99.0 %), N. lasii 3C-HV12^T (98.9 %), N. salmonicida NBRC 13393^T (98.6 %), N. ignorata NBRC 108230^T (98.6 %) and N. coubleae NBRC 108252^T (98.6 %). The average nucleotide identity and DNA-DNA hybridization values between strain Y48^T and the reference strains were 75.9-84.5 and 27.5-29.0 %, respectively, values that were below the thresholds for species delineation. Chemotaxonomic analysis indicated that the major fatty acids of strain Y48^T were C16 : 0, summed feature 3 (C16 : 1ω6c/C16 : 1ω7c), C18 : 1ω9c and C18 : 0 10-methyl (TBSA). The respiratory quinone was MK-8(H4, ω-cycl). The polar lipid profile was composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, two glycolipids and three unidentified lipids. The cell-wall hydrolysates contained meso-diaminopimelic acid, with ribose, arabinose, glucose and galactose as whole-cell sugars. A combination of 16S rRNA gene sequence analysis, and phenotypic and chemotaxonomic characterizations demonstrated that strain Y48^T represents a novel species of the genus Nocardia, for which the name Nocardia mangyaensis sp. nov. is proposed. The type strain is Y48^T (=JCM 32795^T=CGMCC 4.7494^T).

Transcriptome analysis of immune-related gene expression in hybrid snakehead (Channa maculata ♀ × Channa argus ♂) after challenge with Nocardia seriolae

Hybrid snakehead fish (Channa maculata ♀ × Channa argus ♂), a new species used in freshwater aquaculture in China, is the common host of an epizootic bacterial infection by Nocardia seriolae. However, the information on the functions and mechanisms of hybrid snakehead immune pathways with the N. seriolae infection is limited. Thus, the peripheral blood lymphocytes from hybrid snakehead were used for transcriptome analysis to understand the host immune response after challenge with N. seriolae. A total of 49,839,332 and 50,059,283 raw reads were obtained from the N. seriolae-challenged group (Ns group) and phosphate-buffered saline control group (Ctr group), respectively. The 75.50% and 74.25% reads from the Ns and Ctr groups were matched to reference genomic sequence after cleaning the raw reads, respectively. Additionally, there were 2892 significant differentially expressed genes (DEGs) among the 17,196 expressed genes between the Ns and Ctr groups, including 1387 upregulated and 1505 downregulated genes. All the DEGs were classified into three gene ontology categories, and 2502 DEGs had significant matches, which were allocated to 246 Kyoto Encyclopedia of Genes and Genomes pathways. Immune-related genes were detected from immune system pathways among the top 20 enriched pathways. Moreover, the regulation of several observed effective genes was confirmed by real-time quantitative polymerase chain reaction. Altogether, this study offers deep-sequence data of hybrid snakehead peripheral blood lymphocyte via transcriptome analysis and lays the foundation for further study on the immunogenetics of hybrid snakehead. Moreover, it provides insights into the pathogenic mechanism of N. seriolae, facilitating the prevention and treatment of fish nocardiosis.

Roseomonas globiformis sp. nov., an airborne bacteria isolated from an urban area of Beijing

A novel dark pink pigmented bacterium, designated strain CPCC 100847^T (deposited with strain code 0113-15), was isolated from the urban air of Beijing, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CPCC 100847^T was related to members of the genus Roseomonas and had the highest 16S rRNA gene sequence similarity to Roseomonas aestuarii JC17^T (97.5 %). A low level of DNA-DNA relatedness (18.7 %) with its closest type strain R. aestuarii JC17^T (KCTC 22692^T) proved that strain CPCC 100847^T belonged to a unique genomic species. CPCC 100847^T had many common characteristics of the genus Roseomonas, but also had a range of cultural, physiological and biochemical characteristics that separated it from related Roseomonas species. Cells were Gram-negative, cocci- to oval-shaped, non-motile, non-endospore-forming and strictly aerobic. The respiratory ubiquinone was Q-10. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified aminolipid and an unidentified phospholipid. The major fatty acids (>5 %) were C18 : 1ω7c, anteiso-C15 : 0, C16 : 0, iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The combined genotypic and phenotypic data indicated that the isolate represents a novel species of the genus Roseomonas. The name proposed for this species is Roseomonasglobiformis sp. nov., with CPCC 100847^T (=KCTC 52094^T) as the type strain. The DNA G+C composition is 65.2 mol%.

Genomic characterization of Nocardia seriolae strains isolated from diseased fish

Members of the genus Nocardia are widespread in diverse environments; a wide range of Nocardia species are known to cause nocardiosis in several animals, including cat, dog, fish, and humans. Of the pathogenic Nocardia species, N. seriolae is known to cause disease in cultured fish, resulting in major economic loss. We isolated two N. seriolae strains, CK‐14008 and EM15050, from diseased fish and sequenced their genomes using the PacBio sequencing platform. To identify their genomic features, we compared their genomes with those of other Nocardia species. Phylogenetic analysis showed that N. seriolae shares a common ancestor with a putative human pathogenic Nocardia species. Moreover, N. seriolae strains were phylogenetically divided into four clusters according to host fish families. Through genome comparison, we observed that the putative pathogenic Nocardia strains had additional genes for iron acquisition. Dozens of antibiotic resistance genes were detected in the genomes of N. seriolae strains; most of the antibiotics were involved in the inhibition of the biosynthesis of proteins or cell walls. Our results demonstrated the virulence features and antibiotic resistance of fish pathogenic N. seriolae strains at the genomic level. These results may be useful to develop strategies for the prevention of fish nocardiosis.

Reclassification of Nocardia species based on whole genome sequence and associated phenotypic data

Type strains of 72 validated Nocardia species were phylogenetically analyzed based on the multilocus sequence analysis (MLSA) concatenated atpD-groL1-groL2-recA-rpoA-secY-sodA-ychF. Furthermore, their similarity based on digital DNA-DNA hybridization (dDDH) was calculated. Nocardia soli, Nocardia cummidelens and Nocardia salmonicida, Nocardia nova and Nocardia elegans, Nocardia exalbida and Nocardia gamkensis, and Nocardia coubleae and Nocardia ignorata formed coherent clades, respectively. Moreover, each set showed over 70% relatedness by dDDH and shared common phenotypic characteristics. Therefore, we propose a reclassification of Nocardia soli and Nocardia cummidelens as a later heterotypic synonym of Nocardia salmonicida, Nocardia elegans as a later heterotypic synonym of Nocardia nova, Nocardia gamkensis as a later heterotypic synonym of Nocardia exalbida, and Nocardia coubleae as a later heterotypic synonym of Nocardia ignorata.

Current knowledge of nocardiosis in teleost fish

Nocardia sp. is the causative agent of nocardiosis, a lethal granulomatous disease of the skin, muscle, and various inner tissues affecting various teleost and shellfish. Four species of Nocardia have been isolated from diseased fish and shellfish, namely Nocardia asteroides, Nocardia seriolae, Nocardia salmonicida and Nocardia crassostreae. Therefore, in fish aquaculture, nocardiosis has caused severe economic losses, especially in the Asian region. Considerable research has been performed, since the first report of identified Nocardia sp. in fish, to characterize Nocardia sp. and identify rapid detection techniques, immune response against infection and prophylactic approaches. In this review, the current state of knowledge about nocardiosis in fish has been presented, including the pathogenesis, diagnosis, host immune response and vaccine development.

Nocardiosis from 1888 to 2017

The genus Nocardia is an aerobic bacterium, Gram-positive and catalase positive that is in Nocardiaceae family. This bacterium first described by Edmond Nocard in 1888 and is not in human commensal bacteria. To date, nocardiosis incidence is increasing due to increase population growth rate, increase in patients with immune disorder diseases and immunocompromised patients. We surveyed taxonomic position, isolation methods, phenotypic and molecular identification at the genus and species levels, antibiogram, treatment and epidemiology in the world from 1888 to 2017.

Ornithinimicrobium flavum sp. nov., isolated from the leaf of Paris polyphylla

A Gram-positive bacterium originating from the surface-sterilized leaf of Paris polyphylla var. yunnanensis (Franch.) was characterized by using a polyphasic approach. The isolate formed yellow, smooth, circular colonies on nutrient agar with 0.2 % starch (NSA). Cells were non-motile, non-sporulating, irregular rods or cocci. Strain CPCC 203535^T had the highest 16S rRNA gene sequence similarity to the type strain of Ornithinimicrobium kibberense (96.9 %) and formed the deepest branch in the genus Ornithinimicrobium in the neighbour-joining (NJ) phylogenetic tree based on 16S rRNA gene sequences. The major menaquinones of strain CPCC 203535^T were MK-8(H4), MK-8(H2) and MK-8. The peptidoglycan contained ornithine as the diagnostic diamino acid. The polar lipid profile consisted of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylinositol (PI) and unknown lipid (UL). The major fatty acids iso-C14 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C15 : 0 were consistent with the fatty acid patterns reported for members of the genus Ornithinimicrobium. The DNA G+C composition is 71.4 mol%. The results of physiological and biochemical tests allowed phenotypic differentiation of strain CPCC 203535^T from its closest phylogenetic species in the genus Ornithinimicrobium. Strain CPCC 203535^T represents a novel species of the genus Ornithinimicrobium, for which the name Ornithinimicrobium flavum sp. nov. is proposed, with CPCC 203535^T (=NBRC 109452 ^T=KCTC 29164^T) as the type strain.

Isolation, identification, optimization, and metabolite profiling of Streptomyces sparsus VSM-30

Deep sea sediment samples of Bay of Bengal (Visakhapatnam) have been analyzed for actinomycetes as an elite source to screen for the production of bioactive metabolites. The actinomycetes strain VSM-30 has an exciting bioactivity profile and was isolated during our systemic screening of marine actinomycetes. It was identified as Streptomyces sparsus based on morphological, physiological, biochemical, and molecular approaches. Response surface methodology regression analysis was carried out to fit the experimental data of each response by the second-order polynomial. The results have proven right interaction among process variables at optimized values of incubation time at 12 days, pH at 8, temperature at 30 °C, concentrations of starch at 1%, and tryptone at 1% and the data have been adequately fitted into the second-order polynomial models. Under these conditions, the responses (zones of inhibition) of plant pathogenic fungi Aspergillus niger, Aspergillus flavus, Fusarium oxysporum, Fusarium solani, and Penicillium citrinum were also matched with experimental and predicted results. Chemotypic analysis of ethyl acetate extract of the strain was done using LC-Q-TOF-MS revealed the presence of bioactive compounds including tryptophan dehydrobutyrine diketopiperazine, maculosin, 7-o-demethyl albocycline, albocycline M-2, and 7-o-demethoxy-7-oxo albocycline in a negative ion mode. The ethyl acetate extract of actinobacterium has been subjected to gas chromatography and mass spectroscopy (GC-MS) revealed the presence of diverse compounds such as dotriacontane, tetracosane 11-decyl-, diheptyl phthalate, 1-hexadecanesulfonyl chloride, L-alanyl-L-tryptophan, phthalic acid ethyl pentyl ester, 4-trifluoroacetoxyhexadecane, and 1H-imidazole 4,5-dihydro-2,4-dimethyl. Hence, the ethyl acetate extract of Streptomyces sparsus VSM-30 may have antibacterial, antifungal, and antioxidant activities due to the presence of secondary metabolites in ethyl acetate extract. The study also supports marine sediment samples of Bay of Bengal, a promising marine ecosystem remained to be explored for new bioactive compounds.

Paenibacillus eucommiae sp. nov., isolated from a traditional Chinese medicinal herbal plant, Eucommia ulmoides Oliver

The taxonomic status of a novel bacterium, designated strain CPCC 100226T, isolated from a traditional Chinese medicinal herbal plant, Eucommia ulmoides Oliver, was characterized by using a polyphasic approach. The aerobic isolate formed pale white colonies on tryptic soy agar. Cells were Gram-stain-positive, rod-shaped, motile and endospore-forming. Chemotaxonomic investigations revealed the presence of meso-diaminopimelic acid as the diagnostic diamino acid, MK-7 as the predominant menaquinone, anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and C16 : 0 as the major fatty acids, and the strain had a phospholipid pattern of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and unidentified aminophospholipids. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was closely related to Paenibacillus aestuarii DSM 23861T with 95.1 % similarity. The G+C content of the genomic DNA was 47.9 mol%. On the basis of the genotypic and phenotypic data, the isolate is considered to represent a novel species of the genus Paenibacillus. The name proposed for this taxon is Paenibacillus eucommiae sp. nov. with CPCC 100226T (=DSM 26048T=KCTC 33054T) as the type strain.

Streptomyces cyaneus dermatitis in a dog

BACKGROUND

A nearly 4-year-old neutered male Australian Terrier was referred for a nodular pyogranulomatous mass of the right axilla. It had been poorly responsive to antibiotic therapy.

CASE REPORT

Based on filamentous Gram-positive organisms identified in earlier biopsy material, infection by an Actinomyces sp. was suspected and the dog showed clinical improvement on a trial of potentiated sulfonamides. Recurrence 5 months later prompted euthanasia, with Streptomyces cyaneus being cultured and confirmed by genetic sequencing of part of the 16 s ribosomal RNA gene.

CONCLUSION

Invasive Streptomyces spp. infections are uncommon in humans and animals, and isolations are sometimes considered to be contaminants, but the demonstration of the organism within the lesion in this instance indicates that the isolation of a Streptomyces sp. from veterinary cases should not always be considered as contamination, because this genus is clearly pathogenic.

Nocardia kroppenstedtii sp. nov., an actinomycete isolated from a lung transplant patient with a pulmonary infection

A novel actinomycete, strain N1286T, isolated from a lung transplant patient with a pulmonary infection, was provisionally assigned to the genus Nocardia . The strain had chemotaxonomic and morphological properties typical of members of the genus Nocardia and formed a distinct phyletic line in the Nocardia 16S rRNA gene tree. Isolate N1286T was most closely related to Nocardia farcinica DSM 43665T (99.8 % gene sequence similarity) but could be distinguished from the latter by the low level of DNA–DNA relatedness. These strains were also distinguishable on the basis of a broad range of phenotypic properties. It is concluded that strain N1286T represents a novel species of the genus Nocardia for which the name Nocardia kroppenstedtii sp. nov. is proposed. The type strain is N1286T ( = DSM 45810T = NCTC 13617T).

Functional diversity of Nocardia in metabolism

Bacteria affiliated in the genus Nocardia are aerobic and Gram-positive actinomycetes that are widely found in aquatic and terrestrial habitats. As occasional pathogens, several of them cause infection diseases called 'nocardiosis' affecting lungs, central nervous system, cutaneous tissues and others. In addition, members of the genus Nocardia exhibit an enormous metabolic versatility. On one side, many secondary metabolites have been isolated from members of this genus that exhibit various biological activities such as antimicrobial, antitumor, antioxidative and immunosuppressive activities. On the other side, many species are capable of degrading or converting aliphatic and aromatic toxic hydrocarbons, natural or synthetic polymers, and other widespread environmental pollutants. Because of these valuable properties and the application potential, Nocardia species have attracted much interest in academia and industry in recent years. A solid basis of genetic tools including a set of shuttle vectors and an efficient electroporation method for further genetic and metabolic engineering studies has been established to conduct efficient research. Associated with the increasing data of nocardial genome sequences, the functional diversity of Nocardia will be much faster and better understood.

Combining molecular evolution and environmental genomics to unravel adaptive processes of MHC class IIB diversity in European minnows (Phoxinus phoxinus)

Host-pathogen interactions are a major evolutionary force promoting local adaptation. Genes of the major histocompatibility complex (MHC) represent unique candidates to investigate evolutionary processes driving local adaptation to parasite communities. The present study aimed at identifying the relative roles of neutral and adaptive processes driving the evolution of MHC class IIB (MHCIIB) genes in natural populations of European minnows (Phoxinus phoxinus). To this end, we isolated and genotyped exon 2 of two MHCIIB gene duplicates (DAB1 and DAB3) and 1'665 amplified fragment length polymorphism (AFLP) markers in nine populations, and characterized local bacterial communities by 16S rDNA barcoding using 454 amplicon sequencing. Both MHCIIB loci exhibited signs of historical balancing selection. Whereas genetic differentiation exceeded that of neutral markers at both loci, the populations' genetic diversities were positively correlated with local pathogen diversities only at DAB3. Overall, our results suggest pathogen-mediated local adaptation in European minnows at both MHCIIB loci. While at DAB1 selection appears to favor different alleles among populations, this is only partially the case in DAB3, which appears to be locally adapted to pathogen communities in terms of genetic diversity. These results provide new insights into the importance of host-pathogen interactions in driving local adaptation in the European minnow, and highlight that the importance of adaptive processes driving MHCIIB gene evolution may differ among duplicates within species, presumably as a consequence of alternative selective regimes or different genomic context. Using next-generation sequencing, the present manuscript identifies the relative roles of neutral and adaptive processes driving the evolution of MHC class IIB (MHCIIB) genes in natural populations of a cyprinid fish: the European minnow (Phoxinus phoxinus). We highlight that the relative importance of neutral versus adaptive processes in shaping immune competence may differ between duplicates as a consequence of alternative selective regimes or different genomic contexts.

Williamsia sterculiae sp. nov., isolated from a Chinese medicinal plant

Two actinobacterial strains, CPCC 203464(T) and CPCC 203448, isolated from surface-sterilized stems of medicinal plants were subjected to a polyphasic taxonomic study. These two aerobic organisms formed pale yellow colonies on tryptic soy agar (TSA). Cells were Gram-stain-positive, non-acid-fast, non-motile, rod- or coccoid-like elements. Comparative 16S rRNA gene sequence analysis indicated that strains CPCC 203464(T) and CPCC 203448 were most closely related to the type strains of the species of the genus Williamsia. Chemotaxonomic properties such as containing meso-diaminopimelic acid in the cell wall, arabinose, galactose and ribose being the whole-cell hydrolysate sugars, phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylinositol (PI) as the phospholipids, and C16 : 0, 10-methyl C18 : 0, C18 : 1ω9c, C16 : 1ω7c and/or iso-C15 : 0 2-OH as major fatty acids supported the affiliation of strains CPCC 203464(T) and CPCC 203448 to the genus Williamsia. The DNA-DNA hybridization values in combination with differentiating chemotaxonomic and physiological characteristics strongly suggested that these two isolates should be classified as representatives of a novel species of the genus Williamsia. The name Williamsia sterculiae sp. nov. is proposed, with strain CPCC 203464(T) ( = DSM 45741(T) = KCTC 29118(T)) as the type strain.

Nocardia aciditolerans sp. nov., isolated from a spruce forest soil

Actinomycetes growing on acidified starch-casein agar seeded with suspensions of litter and mineral soil from a spruce forest were provisionally assigned to the genus Nocardia based upon colonial properties. Representative isolates were found to grow optimally at pH 5.5, have chemotaxonomic and morphological features consistent with their assignment to the genus Nocardia and formed two closely related subclades in the Nocardia 16S rRNA gene tree. DNA:DNA relatedness assays showed that representatives of the subclades belong to a single genomic species. The isolates were distantly associated with their nearest phylogenetic neighbour, the type strain of Nocardia kruczakiae, and were distinguished readily from the latter based on phenotypic properties. On the basis of these data it is proposed that the isolates merit recognition as a new species, Nocardia aciditolerans sp. nov. The type strain is isolate CSCA68(T) (=KACC 17155(T) = NCIMB 14829(T) = DSM 45801(T)).

Nocardia goodfellowii sp. nov. and Nocardia thraciensis sp. nov., isolated from soil

The taxonomic position of two soil actinomycetes, strains A2012T and A2019T, isolated from Turkish soils, was determined using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that the strains belonged to the family Nocardiaceae . Strains A2012T and A2019T were most closely related to Nocardia caishijiensis DSM 44831T (98.9 %) and Nocardia mexicana CIP 108295T (98.6 %), respectively; similarity to other type strains of the genus Nocardia ranged from 96.9 to 97.9 %. However, DNA–DNA relatedness and phenotypic data demonstrated that strains A2012T and A2019T could be clearly distinguished from members of the most closely related Nocardia species. It is evident from the genotypic and phenotypic data that the two isolates represent two novel species of the genus Nocardia . It is proposed, therefore, that strains A2012T and A2019T be classified in the genus Nocardia as representatives of Nocardia goodfellowii sp. nov. (type strain A2012T = DSM 45516T = NRRL B-24833T = KCTC 19986T) and Nocardia thraciensis sp. nov. (type strain A2019T = DSM 45517T = NRRL B-24834T = KCTC 19985T), respectively.

Williamsia limnetica sp. nov., isolated from a limnetic lake sediment

An actinomycete, strain L1505(T), was isolated from a limnetic lake sediment and found to have morphological, biochemical, physiological and chemotaxonomic properties consistent with its classification in the genus Williamsia. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain L1505(T) formed a distinct lineage within the genus Williamsia. The isolate belonged to a cluster containing W. muralis MA140/96(T), W. marianensis MT8(T) and W. faeni N1350(T), with which the isolate shared 99.0-98.2 % 16S rRNA gene sequence similarity. Genotypic and phenotypic data also indicated that the isolate was different from known members of the genus Williamsia. On the basis of these data, strain 1505(T) is considered to represent a novel species of the genus Williamsia, for which the name Williamsia limnetica sp. nov. is proposed (type strain L1505(T) = DSM 45521(T) = NRRL B-24829(T) = KCTC 19981(T)).

Taxonomy of bacterial fish pathogens

Bacterial taxonomy has progressed from reliance on highly artificial culture-dependent techniques involving the study of phenotype (including morphological, biochemical and physiological data) to the modern applications of molecular biology, most recently 16S rRNA gene sequencing, which gives an insight into evolutionary pathways (= phylogenetics). The latter is applicable to culture-independent approaches, and has led directly to the recognition of new uncultured bacterial groups, i.e. "Candidatus", which have been associated as the cause of some fish diseases, including rainbow trout summer enteritic syndrome. One immediate benefit is that 16S rRNA gene sequencing has led to increased confidence in the accuracy of names allocated to bacterial pathogens. This is in marked contrast to the previous dominance of phenotyping, and identifications, which have been subsequently challenged in the light of 16S rRNA gene sequencing. To date, there has been some fluidity over the names of bacterial fish pathogens, with some, for example Vibrio anguillarum, being divided into two separate entities (V. anguillarum and V. ordalii). Others have been combined, for example V. carchariae, V. harveyi and V. trachuri as V. harveyi. Confusion may result with some organisms recognized by more than one name; V. anguillarum was reclassified as Beneckea and Listonella, with Vibrio and Listonella persisting in the scientific literature. Notwithstanding, modern methods have permitted real progress in the understanding of the taxonomic relationships of many bacterial fish pathogens.

Nocardiopsis nikkonensis sp. nov., isolated from a compost sample

An actinomycete strain, designated YU1183-22T, was isolated from a compost sample collected in Nikko, Japan. The isolate formed white aerial mycelium with relatively long aerial hyphae showing chains of arthrospores. Strain YU1183-22T grew with 0–10 % (w/v) NaCl, at pH 6–11 and at 10–37 °C (optimum 30 °C). Strain YU1183-22T contained meso-diaminopimelic acid and no diagnostic sugars. The predominant menaquinones were MK-10(H10) and MK-10(H8). The polar lipids were phosphatidylcholine and phosphatidylglycerol. The major cellular fatty acids were iso-C16 : 0, anteiso-C17 : 0 and tuberculostearic acid. The G+C content of the DNA was 72.3 mol%. Chemotaxonomic and morphological characterization clearly demonstrated that strain YU1183-22T belonged to the genus Nocardiopsis. Phylogenetic analysis using 16S rRNA gene sequences showed that the isolate was closely related to Nocardiopsis salina YIM 90010T (98.0 % 16S rRNA gene sequence similarity), Nocardiopsis xinjiangensis YIM 90004T (97.9 %) and Nocardiopsis kunsanensis HA-9T (97.3 %). However, DNA–DNA relatedness as well as physiological and biochemical analyses showed that strain YU1183-22T could be differentiated from its closest phylogenetic relatives. It is proposed that this strain be classified as a representative of a novel species of the genus Nocardiopsis, with the name Nocardiopsis nikkonensis sp. nov. The type strain is YU1183-22T (=NBRC 102170T =KCTC 19666T).

Dietzia timorensis sp. nov., isolated from soil

An actinomycete strain, ID05-A0528(T), was isolated using the SDS-yeast extract pre-treatment method from soil under mahogany (Swietenia mahogani) trees in West Timor, Indonesia, and was examined by using a polyphasic taxonomic approach. Chemotaxonomic and phylogenetic characterizations demonstrated that the novel strain belongs to the genus Dietzia. 16S rRNA gene sequencing studies showed that the strain was related to Dietzia cinnamea (97.2 %). Results of phenotypic and phylogenetic analyses determined that strain ID05-A0528(T) is different from the known species of the genus Dietzia. It is proposed that the isolate should be classified as a representative of a novel species of the genus Dietzia, with the name Dietzia timorensis sp. nov. The type strain is ID05-A0528(T) (=BTCC B-560(T) =NBRC 104184(T)).

Nocardia iowensis sp. nov., an organism rich in biocatalytically important enzymes and nitric oxide synthase

Nocardia strain NRRL 5646, isolated from a garden soil sample in Osceola, Iowa, USA, was initially of interest as an antibiotic producer. It contained biocatalytically important enzymes and represented the first described nitric oxide synthase enzyme system in bacteria. The present polyphasic taxonomic study was undertaken to differentiate strain NRRL 5646(T) from related species of the genus Nocardia. Chemotaxonomic analyses included determinations of the fatty acid methyl ester profile (C(16 : 1)omega6c/C(16 : 1)omega7c, C(16 : 0), C(18 : 1)omega9c and C(18 : 0) 10-methyl as major components), quinone [cyclo MK-8(H(4)) as the major component], polar lipid (diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside as major components) and mycolic acid. These results supported its placement within the genus Nocardia. Biochemical testing and 16S rRNA, 65-kDa heat-shock protein (hsp65) and preprotein translocase (secA1) gene sequence analyses differentiated strain NRRL 5646(T) from recognized Nocardia species. Previous studies have demonstrated that other genetic sequences (carboxylic acid reductase, Nocardia phosphopantetheinyl transferase and GTP cyclohydrolase I) from strain NRRL 5646(T) can also be used to substantiate its uniqueness. The level of 16S rRNA gene sequence similarity between strain NRRL 5646(T) and the type strains of Nocardia tenerifensis and Nocardia brasiliensis was 98.8 %. However, strain NRRL 5646(T) could be clearly distinguished from these Nocardia species based on DNA-DNA hybridization data. Consequently, strain NRRL 5646(T) is considered to represent a novel species of the genus Nocardia, for which the name Nocardia iowensis sp. nov. is proposed. The type strain is NRRL 5646(T) (=UI 122540(T)=NRRL B-24671(T)=DSM 45197(T)).

Nocardia seriolae infection in the three striped tigerfish, Terapon jarbua (Forsskål)

An epizootic in pond cultured three striped tigerfish, Terapon jarbua, in Taiwan was caused by Nocardia seriolae. Diseased fish first showed clinical signs and mortalities in February and March 2003. The cumulative mortality within 2 months was 2.4% (1200 of 50 000) and affected fish were 7 months old with total lengths from 18 to 25 cm. Most affected fish were pale and lethargic with haemorrhages and ulcers on the skin. The most significant gross pathological changes were varying degrees of ascites and enlargement of the spleen, kidney and liver. Obvious white nodules, varying in size, were found in these organs. Bacteria were either coccal or filamentous in appearance, with bead-like forms. Isolates from diseased fish were characterized using the API ZYM (Analytical profile index; Bio Mérieux, France) systems and conventional tests and identified as Nocardia sp. The isolate was designated NS127 and was confirmed as N. seriolae by a polymerase chain reaction assay that gave the expected specific 432 bp amplicon. In addition, its 16S rDNA sequence gave 100% sequence identity with N. seriolae. A partial sequence of the 16S rRNA gene, heat shock protein gene and RNA polymerase gene (rpo B) of NS127 and the type strain of N. seriolae BCRC 13745 formed a monophyletic clade with a high sequence similarity and bootstrap value of 99.9%. White nodules induced in experimental fish were similar to naturally infected cases and N. seriolae was re-isolated on brain heart infusion agar. This is the first report of N. seriolae-infection in three striped tigerfish in aquaculture.

Production, isolation and biological activity of nargenicin from Nocardia sp. CS682

Culture broth of an actinomycete isolate, Nocardia sp. CS682 showed specifically higher antibacterial activity against methicillin resistant Staphylococcus aureus (MRSA). Purified substance from the organism, CS-682, which is active against MRSA and Micrococcus leuteus, is a C(28)H(37)NO(8) (M+H(+), observed: 516.83) and identified as an unusual macrolide antibiotic, nargenicin. The chemical structure of CS-682 was identified by FT-IR, (1)H-NMR, (13)C-NMR, and ((1)H-(1)H and (1)H-(13)H) COSY. The anti-MRSA activity of CS-682 was stronger than that of oxacillin, vancomycin, monensin, erythromycin, and spiramycin. Phylogenetic analysis showed that strain CS682 is closely related to Nocardia tenerifensis DSM 44704(T) (98.7% sequence similarity), followed by N. brasiliensis ATCC 19296(T) (98.4% sequence similarity). The ability of Nocardia sp. CS682 to produce nargenicin was unique.

Nocardia ninae sp. nov., isolated from a bronchial aspirate

A Gram-positive and acid-fast filamentous bacterium (OFN 02.72(T)) was isolated from a bronchial aspirate from a 53-year-old patient. Chemotaxonomic data supported the affiliation of this organism to the genus Nocardia, and the phenotypic characteristics demonstrated that the strain differed from all previously described Nocardia species. Restriction enzyme analysis of the hsp65 gene (encoding the 65 kDa heat-shock protein) and sequencing of the 16S rRNA and hsp65 genes confirmed that this isolate is unique. The most closely related type strains were Nocardia alba YIM 30243(T) (=DSM 44684(T)) and Nocardia jejuensis N3-2(T) (=JCM 13281(T)) (with 16S rRNA gene sequence similarities of 98.3 and 97.2 %, respectively). On the basis of this polyphasic study, strain OFN 02.72(T) represents a novel species within the genus Nocardia, for which the name Nocardia ninae sp. nov. is proposed. The type strain is OFN 02.72(T) (=CIP 108955(T)=DSM 44978(T)).

Nocardia amamiensis sp. nov., isolated from a sugar-cane field in Japan

An actinomycete, strain TT 00-78T, was isolated from soil from a sugar-cane field on Amami Island in Japan, using an SDS/yeast extract pre-treatment method, and the taxonomy was studied using a polyphasic approach. The chemotaxonomic and morphological characterizations clearly demonstrated that the strain belongs to the genus Nocardia. 16S rRNA gene sequencing studies showed that the strain was closely related to the type strains of Nocardia pneumoniae (98.6 %), Nocardia araoensis (98.1 %), Nocardia arthritidis (97.9 %) and Nocardia beijingensis (97.7 %). However, the results of DNA–DNA hybridization and physiological and biochemical tests showed that strain TT 00-78T could be differentiated from its closest phylogenetic relatives both genotypically and phenotypically. Therefore this strain represents a novel species of the genus Nocardia, for which the name Nocardia amamiensis sp. nov. is proposed. The type strain is TT 00-78T (=NBRC 102102T=DSM 45066T=KCTC 19208T).

Nocardia coubleae sp. nov., isolated from oil-contaminated Kuwaiti soil

Two bacterial isolates from Kuwaiti soil contaminated by crude oil were analysed by using a polyphasic taxonomic approach. The isolates, designated OFN N11 and OFN N12T, were shown to have molecular, chemical and morphological properties typical of members of the genus Nocardia. Based on a multigenic approach that included 16S rRNA, hsp65 and sod gene sequencing, these novel isolates formed a monophyletic clade within the genus Nocardia. The closest species was Nocardia ignorata (with 99.4 %, 99.5 %, 98.6 % gene sequence similarity to the 16S rRNA, hsp65 and sod genes, respectively). The novel isolates could be distinguished phenotypically from the type strains of recognized species of the genus Nocardia. The novel isolates were not related to the type strain of N. ignorata in DNA–DNA hybridization experiments (26 % relatedness). On the basis of these genotypic and phenotypic data, the two isolates appear to represent a novel species, for which the name Nocardia coubleae sp. nov. is proposed. The type strain is OFN N12T (=DSM 44960T=CIP 108996T).

Nocardia gamkensis sp. nov

A novel actinomycete, strain CZH20(T), was isolated from a soil sample taken from the banks of the Gamka River in the Swartberg Nature Reserve, Western Cape Province, South Africa. Strain CZH20(T) was identified as a member of the genus Nocardia by a polyphasic approach. Strain CZH20(T) could be differentiated from other members of the genus Nocardia on the basis of physiology and 16S-rRNA gene sequence analysis. It exhibited weak antibiosis against Mycobacterium aurum A+. Organic solvent extracts of the culture filtrate and mycelial mass of CZH20(T) exhibited moderate antibiotic activity against Mycobacterium smegmatis LR222 and Mycobacterium tuberculosis H37Rv. The name Nocardia gamkensis is proposed, with the type strain CZH20(T) (=DSM 44956(T) =NRRL B-24450(T)).

Clinical and laboratory features of the Nocardia spp. based on current molecular taxonomy

The recent explosion of newly described species of Nocardia results from the impact in the last decade of newer molecular technology, including PCR restriction enzyme analysis and 16S rRNA sequencing. These molecular techniques have revolutionized the identification of the nocardiae by providing rapid and accurate identification of recognized nocardiae and, at the same time, revealing new species and a number of yet-to-be-described species. There are currently more than 30 species of nocardiae of human clinical significance, with the majority of isolates being N. nova complex, N. abscessus, N. transvalensis complex, N. farcinica, N. asteroides type VI (N. cyriacigeorgica), and N. brasiliensis. These species cause a wide variety of diseases and have variable drug susceptibilities. Accurate identification often requires referral to a reference laboratory with molecular capabilities, as many newer species are genetically distinct from established species yet have few or no distinguishing phenotypic characteristics. Correct identification is important in deciding the clinical relevance of a species and in the clinical management and treatment of patients with nocardial disease. This review characterizes the currently known pathogenic species of Nocardia, including clinical disease, drug susceptibility, and methods of identification.

Nocardia jejuensis sp. nov., a novel actinomycete isolated from a natural cave on Jeju Island, Republic of Korea

A novel actinomycete, strain N3-2T, was isolated from a natural cave on Jeju Island, Republic of Korea, using a dilution method and was subjected to polyphasic taxonomy. The almost complete 16S rRNA gene sequence was determined by direct sequencing of the purified PCR product and was compared with those of representatives of the genus Nocardia. It was revealed from the phylogenetic analysis that the organism forms a distinct clade between the Nocardia salmonicida cluster and the Nocardia alba branch within the evolutionary radius occupied by the genus Nocardia of the family Nocardiaceae. The organism showed 16S rRNA gene sequence similarity of 97·4 % with its nearest phylogenetic neighbours, namely N. salmonicida and N. alba. The chemotaxonomic properties, such as the principal amino acid of peptidoglycan, predominant menaquinone and polar lipids, supported the classification in the genus Nocardia. The organism was readily differentiated from Nocardia species with validly published names by a broad set of phenotypic properties and its unique phylogenetic position; the name Nocardia jejuensis sp. nov. is proposed, with N3-2T (=JCM 13281T=NRRL B-24430T) as the type strain.

Nocardia elegans sp. nov., a member of the Nocardia vaccinii clade isolated from sputum

Two bacterial isolates from the sputa of a patient with a pulmonary infection were subjected to a polyphasic taxonomic study. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV and mycolic acids consistent with the profile for the genus Nocardia. Comparative 16S rRNA gene sequencing showed that these isolates constitute a distinct subline within the genus Nocardia, displaying 99·6–95·5 % sequence similarities with established species. However, DNA–DNA hybridization studies demonstrated unambiguously that the isolates are genealogically distinct from closely related species, namely Nocardia veterana and Nocardia africana, which show high levels of 16S rRNA sequence similarity (99·2 and 99·6 % sequence similarity, respectively). On the basis of both phenotypic and phylogenetic evidence, it is proposed that these isolates be classified as a novel species of the genus Nocardia, for which the name Nocardia elegans sp. nov. is proposed. The type strain is IMMIB N-402T (=CCUG 50200T=CIP 108553T).

Nocardiosis in large yellow croaker, Larimichthys crocea (Richardson)

An epizootic in seawater-cage reared large yellow croaker, Larimichthys crocea, in China was caused by a Nocardia sp. from August to October 2003. The cumulative mortality rate was 15% and the diseased fish were 16 months old with individual length varying from 25 to 30 cm. Multiple, white nodules, 0.1-0.2 cm in diameter, were scattered on the heart, spleen and kidney. The morphology of isolated bacteria from Lowenstein-Jensen medium and tryptic soy agar was bead-like or long, slender, filamentous rods. Experimental infection indicated that the isolated bacterium was the pathogen responsible for the mortalities. A partial sequence of the 16S rRNA gene of the organism and the type strain of Nocardia seriolae JCM 3360T (Z36925) formed a monophyletic clade with a high sequence similarity of 99.9%. Based on the morphological, physiological, biological properties and the phylogenetic analysis, the pathogenic organism was identified as N. seriolae. This is the first report on N. seriolae-infected large yellow croaker in aquaculture.

Nocardia takedensis sp. nov., isolated from moat sediment and scumming activated sludge

Chemotaxonomic and morphological characterization of two actinomycete strains, MS1-3T and AS4-2, respectively isolated from moat sediment and scumming activated sludge, was carried out. This characterization clearly demonstrated that strains MS1-3T and AS4-2 belong to the genus Nocardia. 16S rRNA gene sequencing studies showed that these isolates are most closely related to Nocardia beijingensis (98.1-98.3 % similarity), Nocardia brasiliensis (97.9-98.0 %) and Nocardia tenerifensis (97.8-97.9 %). However, the results of DNA-DNA hybridizations and physiological and biochemical tests showed that strains MS1-3T and AS4-2 could be differentiated from their closest phylogenetic relatives both genotypically and phenotypically. It is proposed that the two isolates be classified as representatives of a novel species of Nocardia, Nocardia takedensis sp. nov. The type strain is MS1-3T (=NBRC 100417T=DSM 44801T); AS4-2 (=NBRC 100418=DSM 44802) is a reference strain.

Can whole genome analysis refine the taxonomy of the genus Rhodococcus?

The current systematics of the genus Rhodococcus is unclear, partly because many members were originally included before the application of a polyphasic taxonomic approach, central to which is the acquisition of 16S rRNA sequence data. This has resulted in the reclassification and description of many new species. Hence, the literature is replete with new species names that have not been brought together in an organized and easily interpreted form. This taxonomic confusion has been compounded by assigning many xenobiotic degrading isolates with phylogenetic positions but without formal taxonomic descriptions. In order to provide a framework for a taxonomic approach based on multiple genetic loci, a survey was undertaken of the known genome characteristics of members of the genus Rhodococcus including: (i) genetics of cell envelope biosynthesis; (ii) virulence genes; (iii) gene clusters involved in metabolic degradation and industrially relevant pathways; (iv) genetic analysis tools; (v) rapid identification of bacteria including rhodococci with specific gene RFLPs; (vi) genomic organization of rrn operons. Genes encoding virulence factors have been characterized for Rhodococcus equi and Rhodococcus fascians. Based on peptide signature comparisons deduced from gene sequences for cytochrome P-450, mono- and dioxygenases, alkane degradation, nitrile metabolism, proteasomes and desulfurization, phylogenetic relationships can be deduced for Rhodococcus erythropolis, Rhodococcus globerulus, Rhodococcus ruber and a number of undesignated Rhodococcus spp. that may distinguish the genus Rhodococcus into two further genera. The linear genome topologies that exist in some Rhodococcus species may alter a previously proposed model for the analysis of genomic fingerprinting techniques used in bacterial systematics.

Sequence-based identification of aerobic actinomycetes

We investigated the utility of 500-bp 16S rRNA gene sequencing for identifying clinically significant species of aerobic actinomycetes. A total of 28 reference strains and 71 clinical isolates that included members of the genera Streptomyces, Gordonia, and Tsukamurella and 10 taxa of Nocardia were studied. Methods of nonsequencing analyses included growth and biochemical analysis, PCR-restriction enzyme analysis of the 439-bp Telenti fragment of the 65 hsp gene, susceptibility testing, and, for selected isolates, high-performance liquid chromatography. Many of the isolates were included in prior taxonomic studies. Sequencing of Nocardia species revealed that members of the group were generally most closely related to the American Type Culture Collection (ATCC) type strains. However, the sequences of Nocardia transvalensis, N. otitidiscaviarum, and N. nova isolates were highly variable; and it is likely that each of these species contains multiple species. We propose that these three species be designated complexes until they are more taxonomically defined. The sequences of several taxa did not match any recognized species. Among other aerobic actinomycetes, each group most closely resembled the associated reference strain, but with some divergence. The study demonstrates the ability of partial 16S rRNA gene sequencing to identify members of the aerobic actinomycetes, but the study also shows that a high degree of sequence divergence exists within many species and that many taxa within the Nocardia spp. are unnamed at present. A major unresolved issue is the type strain of N. asteroides, as the present one (ATCC 19247), chosen before the availability of molecular analysis, does not represent any of the common taxa associated with clinical nocardiosis.

Nocardia neocaledoniensis sp. nov., a novel actinomycete isolated from a New-Caledonian brown hypermagnesian ultramafic soil

The taxonomic position of an actinomycete isolated from a hypermagnesian ultramafic soil was examined using a polyphasic approach. The strain, designated SBH(R) OA6(T), was shown to have chemical and morphological properties typical of members of the genus Nocardia. The organism was most closely associated with Nocardia asteroides using 16S rRNA gene sequence data. It showed a distinctive set of phenotypic properties that distinguished it from representatives of all species with validly published names classified in the genus Nocardia. The combined genotypic and phenotypic data show that strain SBH(R) OA6(T) (=DSM 44717(T)=NCIMB 13955(T)) merits description as the type strain of a novel Nocardia species, Nocardia neocaledoniensis sp. nov.

Williamsia maris sp. nov., a novel actinomycete isolated from the Sea of Japan

The taxonomic position of a marine actinomycete, strain SJS0289/JS1T, was determined using a polyphasic taxonomic approach. The organism, which had phenotypic properties consistent with its classification in the genusWilliamsia, formed a distinct clade in the 16S rRNA gene tree together with the type strain ofWilliamsia muralis, but was readily distinguished from this species using DNA–DNA relatedness and phenotypic data. The genotypic and phenotypic data show that the organism merits recognition as a new species ofWilliamsia. The name proposed for the new species isWilliamsia maris; the type strain is SJS0289/JS1T(=DSM 44693T=JCM 12070T=KCTC 9945T=NCIMB 13945T).

Nocardia cerradoensis sp. nov., a novel isolate from Cerrado soil in Brazil

An isolate from Cerrado soil, provisionally assigned to the genus Nocardia, was shown to have chemical and morphological properties typical of nocardiae. The strain formed a distinct monophyletic clade in the 16S rDNA tree together with Nocardia africana, Nocardia vaccinii and Nocardia veterana, and showed a unique combination of phenotypic properties that distinguished it from representatives of all recognized species of Nocardia. DNA-DNA relatedness studies indicated that the isolate belongs to a genomic species that is readily distinguished from its nearest neighbours, the type strains of N. africana and N. veterana. The organism is considered to merit species status, and it is proposed that it be designated Nocardia cerradoensis sp. nov., with strain YgT (=CCT 5601T =DSM 44546T) as the type strain.