Antrihabitans stalactiti gen. nov., sp. nov., a new member of the family Nocardiaceae isolated from a cave.

Two Gram-stain-positive, strictly aerobic, non-spore-forming actinobacterial strains, designated YC2-7T and YC5-17, were isolated from the Yongcheondonggul (larva cave) in Jeju, Republic of Korea and their taxonomic ranks were examined by a polyphasic approach. The 16S rRNA gene tree showed that the novel isolates occupied an independent position separated from recognized genera of the family Nocardiaceae. In the 92 core gene-based phylogenomic analysis, strain YC2-7T was loosely associated with the type strain of Aldersonia kummingensis with 66.2 % average amino acid identity. The 16S rRNA gene sequence simairity between the isolate and members of the family Nocardiaceae was below 96.7 %. The cell-wall peptidoglycan was meso-diaminopimelic acid as a diagnostic diamino acid. Whole-cell sugars consisted of arabinose, galactose and glucose. The predominant menaquinone was MK-8(H4, ω-cycl). The major polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The cellular fatty acids consisted mainly of saturated and unsaturated components with small amounts of tuberculostearic acid. Mycolic acids of 52-58 carbon atoms were present. The DNA G+C content of the genome was 63.8 mol%. On the basis of combination of morphological and chemotaxonomic differences, in addition to phylogenetic distinctness, the novel isolates are considered to constitute members of a novel species of a new genus in the family Nocardiaceae, for which the name Antrihabitans stalactiti gen. nov., sp. nov. is proposed. The type strain is YC2-7T (=KACC 19965T=DSM 108733T).

Mumiamicin: Structure and bioactivity of a new furan fatty acid from Mumia sp. YSP-2-79.

A new antibiotic, designated mumiamicin, was isolated from the cultured broth of the rare actinomycete strain, Mumia sp. YSP-2-79, by Diaion HP-20, silica gel and ODS column chromatography, followed by HPLC purification. The chemical structure of mumiamicin was elucidated as a new furan fatty acid by nuclear magnetic resonance and mass spectrometry. Mumiamicin showed antimicrobial activity and antioxidative activity.

Correlation of the lung microbiota with metabolic profiles in bronchoalveolar lavage fluid in HIV infection.

BACKGROUND: While 16S ribosomal RNA (rRNA) sequencing has been used to characterize the lung's bacterial microbiota in human immunodeficiency virus (HIV)-infected individuals, taxonomic studies provide limited information on bacterial function and impact on the host. Metabolic profiles can provide functional information on host-microbe interactions in the lungs. We investigated the relationship between the respiratory microbiota and metabolic profiles in the bronchoalveolar lavage fluid of HIV-infected and HIV-uninfected outpatients. RESULTS: Targeted sequencing of the 16S rRNA gene was used to analyze the bacterial community structure and liquid chromatography-high-resolution mass spectrometry was used to detect features in bronchoalveolar lavage fluid. Global integration of all metabolic features with microbial species was done using sparse partial least squares regression. Thirty-nine HIV-infected subjects and 20 HIV-uninfected controls without acute respiratory symptoms were enrolled. Twelve mass-to-charge ratio (m/z) features from C18 analysis were significantly different between HIV-infected individuals and controls (false discovery rate (FDR) = 0.2); another 79 features were identified by network analysis. Further metabolite analysis demonstrated that four features were significantly overrepresented in the bronchoalveolar lavage (BAL) fluid of HIV-infected individuals compared to HIV-uninfected, including cystine, two complex carbohydrates, and 3,5-dibromo-L-tyrosine. There were 231 m/z features significantly associated with peripheral blood CD4 cell counts identified using sparse partial least squares regression (sPLS) at a variable importance on projection (VIP) threshold of 2. Twenty-five percent of these 91 m/z features were associated with various microbial species. Bacteria from families Caulobacteraceae, Staphylococcaceae, Nocardioidaceae, and genus Streptococcus were associated with the greatest number of features. Glycerophospholipid and lineolate pathways correlated with these bacteria. CONCLUSIONS: In bronchoalveolar lavage fluid, specific metabolic profiles correlated with bacterial organisms known to play a role in the pathogenesis of pneumonia in HIV-infected individuals. These findings suggest that microbial communities and their interactions with the host may have functional metabolic impact in the lung.

[Recent advance on the genus nocardioides--a review].

The Nocardioides genus was established by Prauser H. in 1976 according to morphological and physiological characteristics, as well as partial chemotaxonomic analyses of 17 nocardio-form actinobacteria isolated from soil, based on which a novel species Nocardioides albus was proposed as the type species. With the development in the technologies of isolation, purification and taxonomy, more and more members of this genus with varied morphological, physiological and biochemical characteristics were increasingly discovered from different sources, while all of them shared the same diagnostic characteristics of the genus. In the past 50 years, some of the members of the genus Nocardioides were ever transferred in or out and then some species description was ever emended. Till date, there were 56 validly described species in this genus. Some members of this genus were used in agriculture and industry. The objective of this review is to summarize the research advances in the genus Nocardioides, such as the changes of the taxonomic position and emendation description of the species as well as the application prospect in industry and agriculture.

Nocardiopsis aegyptia sp. nov., isolated from marine sediment.

An actinomycete, strain SNG49(T), was isolated from marine sediment of Abu Qir Bay, on the western seashore of Alexandria, Egypt. The bacterium was aerobic and Gram-positive. It produced beige to light-yellow aerial mycelium, brown substrate mycelium and straight to flexuous hyphae, but no specific spore chains. 16S rDNA sequence analysis and chemotaxonomic markers were consistent with classification of strain SNG49(T) in the genus Nocardiopsis, i.e. meso-diaminopimelic acid; no diagnostic sugars; phosphatidylcholine, phosphatidylmethylethanolamine, phosphatidylinositol, phosphatidylglycerol and diphosphatidylglycerol as polar lipids; menaquinones of the MK-10 series from MK-10(H(0)) to MK-10(H(8)); and iso/anteiso-branched and 10-methyl-branched fatty acids, the principal fatty acids being anteiso-17 : 0 and tuberculostearic acid. Nocardiopsis lucentensis and Nocardiopsis alba are the phylogenetic neighbours of strain SNG49(T), respectively showing 98.8 and 98.7 % 16S rRNA gene sequence similarity; however, moderate DNA-DNA reassociation values between these two species and strain SNG49(T) (44 and 60 %, respectively) showed that strain SNG49(T) could be clearly separated from them. These data, together with distinct physiological traits, led to the conclusion that this isolate represents a novel species within the genus Nocardiopsis, for which the name Nocardiopsis aegyptia is proposed. The type strain is SNG49(T) (=DSM 44442(T)=NRRL B-24244(T)).

Nocardioides aquiterrae sp. nov., isolated from groundwater in Korea.

A bacterial strain, GW-9T, which was isolated from groundwater in Korea, was subjected to a polyphasic taxonomic study using phenotypic characterization and phylogenetic and genetic methods. Phylogenetic analysis based on 16S rDNA sequences showed that strain GW-9T forms an evolutionary lineage within the radiation enclosing Nocardioides species and, in particular, a coherent cluster with Nocardioides pyridinolyticus. The cell-wall peptidoglycan type of strain GW-9T was based on LL-diaminopimelic acid as the diamino acid, indicating wall chemotype I. The predominant menaquinone was MK-8(H4). Strain GW-9T had a cellular fatty acid profile containing straight-chain, branched, unsaturated and 10-methyl fatty acids. The major fatty acid was iso-C(16:0). The DNA G+C content of strain GW-9T was 73 mol%. The 16S rDNA of strain GW-9T was 99.2% similar to that of the type strain of Nocardioides pyridinolyticus and 94.9-96.0% similar to sequences of the type strains of other Nocardioides species. Differences in phenotypic characteristics and genetic distinctiveness indicate that strain GW-9T is separate from previously described Nocardioides species. Therefore, on the basis of the data presented, a novel species of the genus Nocardioides, Nocardioides aquiterrae sp. nov., is proposed. The type strain is strain GW-9T (=KCCM 41647T=JCM 11813T).

Aeromicrobium marinum sp. nov., an abundant pelagic bacterium isolated from the German Wadden Sea.

An obligately salt-dependent Gram-positive bacterium, designated strain T2(T), was isolated from surface waters of the German Wadden Sea. The organism exhibited optimum growth at salt concentrations similar to that of sea water. On the basis of phenotypic, chemotaxonomic and phylogenetic differences, it is concluded that strain T2(T) (=DSM 15272(T)=LMG 21768(T)) is the first marine species of the genus Aeromicrobium to be identified, for which the name Aeromicrobium marinum is proposed. It is also the first described marine bacterium within the family Nocardioidaceae. Strain T2(T) is a rod-shaped, aerobic, heterotrophic bacterium containing LL-diaminopimelic acid in the peptidoglycan and MK-9(H(4)) as the major menaquinone. The bacterium is characterized by high proportions of the fatty acids palmitic acid, oleic acid, tuberculostearic acid and hydroxypalmitic acid. DNA-DNA hybridization analysis showed the marine bacterium to display 29.1 % relatedness with Aeromicrobium fastidiosum DSM 10552(T) and 44.4 % relatedness with Aeromicrobium erythreum DSM 8599(T). A. marinum was demonstrated to be an abundant member of the pelagic bacterial community in the German Wadden Sea since it represented about 1 % of the total bacterial population as revealed by dot-blot hybridization and most-probable-number counts.

[The 1(2)-dehydrogenation of steroid substrates by Nocardioides simplex VKM Ac-2033D]. / 1(2)-degidrirovanie steroidnykh substratov shtammom Nocardioides simplex BKM Ac-2033D.

The bacterium formerly known as Arthrobacter globiformis 193 has high 1(2)-dehydrogenase activity toward pharmaceutically important steroids, 9(11)-dehydrocortexolone in particular. The complex analysis of the morphostructural, physiological, biochemical, and phylogenetic properties of this bacterium allowed us to reclassify it into Nocardioides simplex (N. simplex VKM Ac-2033D).

Inter- and intraspecific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rDNA sequences.

The 16S rDNAs from 38 strains of the genus Nocardioides, two Aeromicrobium species and Terrabacter tumescens were directly sequenced and then analysed. The mean nucleotide similarity value between the type strains of validly described Nocardioides species was 96.1 +/- 3.0%. The mean nucleotide similarity value between the type strains of validly described Nocardioides species and the two Aeromicrobium species was 93.7 +/- 1.4% T. tumescens was distantly related to the genera Nocardioides and Aeromicrobium. The mean intraspecific nucleotide similarity value of 16S rDNA sequences from Nocardioides albus was 99.5 +/- 0.5%. The mean intraspecific nucleotide similarity of 16S rDNA sequences from Nocardioides simplex was 100%, except for N. simplex strains ATCC 13260, ATCC 19565 and ATCC 19566, which were shown not to be members of the genus Nocardioides. 'Nocardioides flavus' strains IFO 14396T and IFO 14397, and 'Nocardioides fulvus' JCM 3335T showed a 16S rDNA similarity value of 100% with Nocardioides luteus KCTC 9575T and Nocardioides albus JCM 5854. 'N. fulvus' IFO 14399 shared its highest 16S rDNA similarity with Nocardioides sp. ATCC 39419 at 99%. 'N. fulvus' IFO 14399 and Nocardioides sp. ATCC 39419 formed a phylogenetic lineage distinct from the genera Nocardioides and Aeromicrobium. 'Nocardioides thermolilacinus' strains IFO 14335T and IFO 14336 displayed a close relationship to the genus Streptomyces. From 16S rDNA sequence analyses, it is considered that some strains that have been attributed to the genus Nocardioides should be taxonomically re-evaluated.

Reclassification of Nocardioides simplex ATCC 13260, ATCC 19565, and ATCC 19566 as Rhodococcus erythropolis.

Our phylogenetic analysis based on 16S ribosomal DNA (rDNA) sequences and chemotaxonomic analyses showed that Nocardioides simplex ATCC 13260, ATCC 19565, and ATCC 19566 are more closely related to the genus Rhodococcus, especially Rhodococcus erythropolis, than to the genus Nocardioides. N. simplex ATCC 13260 and N. simplex ATCC 19565 and ATCC 19566 exhibited levels of 16S rDNA similarity of 99.4 and 100%, respectively, to R. erythropolis DSM 43066T. Strains ATCC 13260, ATCC 19565, and ATCC 19566 had mesodiaminopimelic acid in their peptidoglycan and MK-8(H2) as their predominant menaquinone. These three strains produced cellular fatty acid patterns similar to those of R. erythropolis strains rather than those of Nocardioides species. Therefore, N. simplex ATCC 13260, ATCC 19565, and ATCC 19566 should be reclassified as strains of R. erythropolis Gray and Thornton 1928.

Helvecardins A and B, novel glycopeptide antibiotics. I. Taxonomy, fermentation, isolation and physico-chemical properties.

A strain of actinomycetes identified as Pseudonocardia compacta subsp. helvetica produced new glycopeptide antibiotics, helvecardins A and B. They were isolated from culture broth mainly by affinity chromatography of D-alanyl-D-alanine and preparative HPLC. The physico-chemical properties of helvecardins A and B showed that they resemble each other. Though helvecardin A was structurally related to beta-avoparcin, it clearly differed in the presence of an O-methyl moiety in its NMR spectrum.

[Actinomadura species as antibiotic producers]. / Vidy roda Actinomadura kak produtsenty antibiotikov.

Screening of antibiotic-producing cultures among Actinomadura showed that definite species mainly produced antibiotics of the same groups. Thus, carminomycins were produced by all the 4 studied strains of A. carminata, maduramycins were produced by 3 strains of A. rubra, prodigiozines were produced by 3 strains of A. madurae and luzopeptines were produced by 6 strains of A. recticatena. Supposedly, new antibiotics with original spectral characteristics were isolated from 2 strains of A. fulvescens. There was a clear-cut relation of the number of the active strains and their antibiotic productivity in definite media to their species. The liquid nutrient media, such as yeast-sucrose, soya-glucose and soya-glucose with cobalt chloride proved to be the most efficient in the primary screening of antibiotic-producing cultures.

Characterization of Nocardia, Rhodococcus and Gordona species by in vitro susceptibility testing.

Representative strains of Gordona, Nocardia and Rhodococcus were tested against 26 antimicrobial agents using the disc diffusion method. A distinct susceptibility profile was noted for most species. Nocardia asteroides, N. brasiliensis, N. otitidiscaviarum, N. transvalensis and N. vaccinii were rarely susceptible to the antibiotics tested; N. brevicatena and N. farcinica varied in their susceptibility depending on the strain tested. Only the antibiotic amikacin was active against all nocardiae. In contrast, the Gordona and Rhodococcus strains showed considerable susceptibility, in particular to the beta-lactam antibiotics. Amoxicillin + clavulanic acid and gentamicin were active against all of the gordonae and rhodococci. The differences in susceptibility patterns may prove useful in characterizing the genera Gordona, Nocardia and Rhodococcus and in separating species within these taxa.

CP-82,996, a novel diglycoside polyether antibiotic related to monensin and produced by Actinomadura sp.

A new polyether antibiotic CP-82,996 (C50H86O16) was isolated by solvent extraction from the fermentation broth of Actinomadura sp. (ATCC 53764). Following purification by silica gel column chromatography and crystallization, the structure of CP-82,996 was determined by a single crystal X-ray analysis. The structure is closely related to monensin, but is unique in that it contains two sugar groups, whereas monensin has none. The 1H and 13C NMR chemical shifts and assignments for CP-82,996 were elucidated, and they were compared with those determined previously for monensin. CP-82,996 is active against certain Gram-positive bacteria, and is a very potent anticoccidial agent. It effectively controlled chicken coccidiosis caused by several Eimeria species at 5-10 ppm in feed, and is 10-20 times more potent than monensin.

Simaomicin (LL-D42067), a novel antibiotic from Actinomadura madurae. I. Taxonomy, fermentation and biological activity.

A new antibacterial antibiotic, designated simaomicin alpha (LL-D42067 alpha) was isolated from the fermentation broth of an actinomycete strain. Based on cultural, physiological, morphological and chemical characteristics, culture LL-D42067 was identified as a new subspecies of Actinomadura madurae. Simaomicin alpha demonstrated potent activity against Gram-positive bacteria and was active in vivo against a variety of Eimeria species causing coccidiosis in chickens.

SF2487, a new polyether antibiotic produced by Actinomadura.

A new antibiotic SF2487 has been isolated from the culture broth of Actinomadura sp. SF2487. The structure of antibiotic SF2487 was determined by spectroscopic analyses of the sodium salt and X-ray diffraction analysis of the silver salt. The antibiotic represents a new member of polyether group antibiotics known as the acyltetronic acid type 4. The antibiotic is weakly active against Gram-positive bacteria and exhibits antiviral activity against influenza virus in vitro.

AT2433-A1, AT2433-A2, AT2433-B1, and AT2433-B2 novel antitumor antibiotic compounds produced by Actinomadura melliaura. Taxonomy, fermentation, isolation and biological properties.

Compounds AT2433-A1 (A1), AT2433-A2 (A2), AT2433-B1 (B1), and AT2433-B2 (B2) were isolated from the cultured broth of Actinomadura melliaura sp. nov. (SCC 1655). Structurally these materials are closely related to rebeccamycin (1), an indolocarbazole antitumor antibiotic. A1, A2, B1, and B2 were active against Staphylococcus aureus A9537, Streptococcus faecalis A20688, Streptococcus faecium (ATCC 9790), Micrococcus lutea (ATCC 9341), Bacillus subtilis (ATCC 6633). A1 and B1 were active against P388 leukemia in mice.

Molecular taxonomic studies on some LL-diaminopimelic acid-containing coryneforms from herbage: description of Nocardioides fastidiosa sp. nov.

Molecular taxonomic studies were performed on two LL-diaminopimelic acid-containing coryneform isolates from herbage. The results indicate that the herbage strains represent a new species of the genus Nocardioides for which the name Nocardioides fastidiosa sp. nov. is proposed. The type strain is NCIB 12713.

The taxonomic status of Rhodococcus equi.

The species Corynebacterium equi was proposed for strains isolated from foals suffering from purulent pneumonia. The taxon has had a confused history and is currently listed under both Corynebacterium and Rhodococcus in the Approved Lists of Bacterial Names. Data from modern taxonomic studies indicate that Corynebacterium equi Magnusson 1923 should be reduced to a synonym of Rhodococcus equi (Magnusson) Goodfellow and Alderson 1980. Rhodococcus equi has repeatedly been shown to be a good species on the basis of chemical, molecular biological, numerical phenetic and serological data. Improved methods are needed to differentiate Rhodococcus equi from closely related species of Rhodococcus.