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Schistosomiasis is a tropical disease that poses a significant risk to hundreds of millions of people, yet often goes unnoticed. While praziquantel, a widely used anti-schistosome drug, has a low cost and a high cure rate, it has several drawbacks. These include ineffectiveness against schistosome larvae, reduced efficacy in young children, and emerging drug resistance. Discovering new and active anti-schistosome small molecules is therefore critical, but this process presents the challenge of low accuracy in computer-aided methods. To address this issue, we proposed GNN-DDAS, a novel deep learning framework based on graph neural networks (GNN), designed for drug discovery to identify active anti-schistosome (DDAS) small molecules. Initially, a multi-layer perceptron was used to derive sequence features from various representations of small molecule SMILES. Next, GNN was employed to extract structural features from molecular graphs. Finally, the extracted sequence and structural features were then concatenated and fed into a fully connected network to predict active anti-schistosome small molecules. Experimental results showed that GNN-DDAS exhibited superior performance compared to the benchmark methods on both benchmark and real-world application datasets. Additionally, the use of GNNExplainer model allowed us to analyze the key substructure features of small molecules, providing insight into the effectiveness of GNN-DDAS. Overall, GNN-DDAS provided a promising solution for discovering new and active anti-schistosome small molecules., (© 2024 Wiley Periodicals LLC.)

Background: Accurately identifying drug-target affinity (DTA) plays a pivotal role in drug screening, design, and repurposing in pharmaceutical industry. It not only reduces the time, labor, and economic costs associated with biological experiments but also expedites drug development process. However, achieving the desired level of computational accuracy for DTA identification methods remains a significant challenge., Results: We proposed a novel multi-view-based graph deep model known as MvGraphDTA for DTA prediction. MvGraphDTA employed a graph convolutional network (GCN) to extract the structural features from original graphs of drugs and targets, respectively. It went a step further by constructing line graphs with edges as vertices based on original graphs of drugs and targets. GCN was also used to extract the relationship features within their line graphs. To enhance the complementarity between the extracted features from original graphs and line graphs, MvGraphDTA fused the extracted multi-view features of drugs and targets, respectively. Finally, these fused features were concatenated and passed through a fully connected (FC) network to predict DTA., Conclusions: During the experiments, we performed data augmentation on all the training sets used. Experimental results showed that MvGraphDTA outperformed the competitive state-of-the-art methods on benchmark datasets for DTA prediction. Additionally, we evaluated the universality and generalization performance of MvGraphDTA on additional datasets. Experimental outcomes revealed that MvGraphDTA exhibited good universality and generalization capability, making it a reliable tool for drug-target interaction prediction., (© 2024. The Author(s).)

Identifying the catalytic regioselectivity of enzymes remains a challenge. Compared to experimental trial-and-error approaches, computational methods like molecular dynamics simulations provide valuable insights into enzyme characteristics. However, the massive data generated by these simulations hinder the extraction of knowledge about enzyme catalytic mechanisms without adequate modeling techniques. Here, we propose a computational framework utilizing graph-based active learning from molecular dynamics to identify the regioselectivity of ginsenoside hydrolases (GHs), which selectively catalyze C6 or C20 positions to obtain rare deglycosylated bioactive compounds from Panax plants. Experimental results reveal that the dynamic-aware graph model can excellently distinguish GH regioselectivity with accuracy as high as 96-98% even when different enzyme-substrate systems exhibit similar dynamic behaviors. The active learning strategy equips our model to work robustly while reducing the reliance on dynamic data, indicating its capacity to mine sufficient knowledge from short multi-replica simulations. Moreover, the model's interpretability identified crucial residues and features associated with regioselectivity. Our findings contribute to the understanding of GH catalytic mechanisms and provide direct assistance for rational design to improve regioselectivity. We presented a general computational framework for modeling enzyme catalytic specificity from simulation data, paving the way for further integration of experimental and computational approaches in enzyme optimization and design.

Most proteins exert their functions by interacting with other proteins, making the identification of protein-protein interactions (PPI) crucial for understanding biological activities, pathological mechanisms, and clinical therapies. Developing effective and reliable computational methods for predicting PPI can significantly reduce the time-consuming and labor-intensive associated traditional biological experiments. However, accurately identifying the specific categories of protein-protein interactions and improving the prediction accuracy of the computational methods remain dual challenges. To tackle these challenges, we proposed a novel graph neural network method called GNNGL-PPI for multi-category prediction of PPI based on global graphs and local subgraphs. GNNGL-PPI consisted of two main components: using Graph Isomorphism Network (GIN) to extract global graph features from PPI network graph, and employing GIN As Kernel (GIN-AK) to extract local subgraph features from the subgraphs of protein vertices. Additionally, considering the imbalanced distribution of samples in each category within the benchmark datasets, we introduced an Asymmetric Loss (ASL) function to further enhance the predictive performance of the method. Through evaluations on six benchmark test sets formed by three different dataset partitioning algorithms (Random, BFS, DFS), GNNGL-PPI outperformed the state-of-the-art multi-category prediction methods of PPI, as measured by the comprehensive performance evaluation metric F1-measure. Furthermore, interpretability analysis confirmed the effectiveness of GNNGL-PPI as a reliable multi-category prediction method for predicting protein-protein interactions., (© 2024. The Author(s).)

Background: Accurately identifying drug-target interaction (DTI), affinity (DTA), and binding sites (DTS) is crucial for drug screening, repositioning, and design, as well as for understanding the functions of target. Although there are a few online platforms based on deep learning for drug-target interaction, affinity, and binding sites identification, there is currently no integrated online platforms for all three aspects., Results: Our solution, the novel integrated online platform Drug-Online, has been developed to facilitate drug screening, target identification, and understanding the functions of target in a progressive manner of "interaction-affinity-binding sites". Drug-Online platform consists of three parts: the first part uses the drug-target interaction identification method MGraphDTA, based on graph neural networks (GNN) and convolutional neural networks (CNN), to identify whether there is a drug-target interaction. If an interaction is identified, the second part employs the drug-target affinity identification method MMDTA, also based on GNN and CNN, to calculate the strength of drug-target interaction, i.e., affinity. Finally, the third part identifies drug-target binding sites, i.e., pockets. The method pt-lm-gnn used in this part is also based on GNN., Conclusions: Drug-Online is a reliable online platform that integrates drug-target interaction, affinity, and binding sites identification. It is freely available via the Internet at http://39.106.7.26:8000/Drug-Online/ ., (© 2024. The Author(s).)

The prediction of the drug-target affinity (DTA) plays an important role in evaluating molecular druggability. Although deep learning-based models for DTA prediction have been extensively attempted, there are rare reports on multimodal models that leverage various fusion strategies to exploit heterogeneous information from multiple different modalities of drugs and targets. In this study, we proposed a multimodal deep model named MMDTA, which integrated the heterogeneous information from various modalities of drugs and targets using a hybrid fusion strategy to enhance DTA prediction. To achieve this, MMDTA first employed convolutional neural networks (CNNs) and graph convolutional networks (GCNs) to extract diverse heterogeneous information from the sequences and structures of drugs and targets. It then utilized a hybrid fusion strategy to combine and complement the extracted heterogeneous information, resulting in the fused modal information for predicting drug-target affinity through the fully connected (FC) layers. Experimental results demonstrated that MMDTA outperformed the competitive state-of-the-art deep learning models on the widely used benchmark data sets, particularly with a significantly improved key evaluation metric, Root Mean Square Error (RMSE). Furthermore, MMDTA exhibited excellent generalization and practical application performance on multiple different data sets. These findings highlighted MMDTA's accuracy and reliability in predicting the drug-target binding affinity. For researchers interested in the source data and code, they are accessible at http://github.com/dldxzx/MMDTA.

Accurate calculation of drug-target affinity (DTA) is crucial for various applications in the pharmaceutical industry, including drug screening, design, and repurposing. However, traditional machine learning methods for calculating DTA often lack accuracy, posing a significant challenge in accurately predicting DTA. Fortunately, deep learning has emerged as a promising approach in computational biology, leading to the development of various deep learning-based methods for DTA prediction. To support researchers in developing novel and highly precision methods, we have provided a comprehensive review of recent advances in predicting DTA using deep learning. We firstly conducted a statistical analysis of commonly used public datasets, providing essential information and introducing the used fields of these datasets. We further explored the common representations of sequences and structures of drugs and targets. These analyses served as the foundation for constructing DTA prediction methods based on deep learning. Next, we focused on explaining how deep learning models, such as Convolutional Neural Networks (CNNs), Recurrent Neural Networks (RNNs), Transformer, and Graph Neural Networks (GNNs), were effectively employed in specific DTA prediction methods. We highlighted the unique advantages and applications of these models in the context of DTA prediction. Finally, we conducted a performance analysis of multiple state-of-the-art methods for predicting DTA based on deep learning. The comprehensive review aimed to help researchers understand the shortcomings and advantages of existing methods, and further develop high-precision DTA prediction tool to promote the development of drug discovery., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Zeng, Li, Lv, Wen and Li.)

A Gram stain-positive, rod-shaped, and subterminal endospore-forming bacterium, designated strain YIM B01967 T , was isolated from a forest soil sample collected in Ailaoshan National Nature Reserve, Yuxi City, Xinpin county, Yunnan province, China. Strain YIM B01967 T showed the highest 16S rRNA gene sequence similarity with Viridibacillus arvi (99.1%) and Viridibacillus arenosi (98.9%). Based on the phylogenetic and 16S rRNA gene sequence results, strain YIM B01967 T was affiliated to the genus Viridibacillus. The growth of YIM B01967 T was observed at 15-35 °C (optimum, 28 °C), pH 7.0-9.0 (optimum, pH 7.5) and in the presence of 0-2% (w/v) NaCl (optimum in 2% NaCl). The cell wall sugars include ribose, glucose, arabinose, galactose, and mannose. The quinone system consisted of the major compound MK-8 and moderate amounts of MK-7. The major fatty acids (> 10%) included iso-C 15:0 , anteiso-C 15:0 , C 16:1 ω10c. The major polar lipids profile included DPG, PME. The cell wall peptidoglycan was most likely of the type A4α with an L-Lys-D-Asp interpeptide bridge. The genomic DNA G + C content of strain YIM B01967 T was 36.3 mol%. The ANI and digital DNA-DNA hybridization (dDDH) values between strain YIM B01967 T and Viridibacillus arvi DSM 16317  T , Viridibacillus arenosi DSM 16319  T were 61.0% and 32.1%, 60.0% and 33.1% based on the draft genome sequence. The results support the conclusion that strain YIM B01967 T represents a novel species of the genus Viridibacillus, for which the name Viridibacillus soli sp. nov., is proposed. The type strain is YIM B01967 T (= KCTC 43249  T  = CGMCC 1.18436  T )., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

A Gram-stain-positive, coccus-shaped, facultatively anaerobic, non-motile bacterial strain, designated YIM S02567 T , was isolated from a forest soil sample collected from Gejiu City, Yunnan Province, southwest PR China. Growth was observed at 10-45 °C, at pH 6.0-9.5, in the presence of up to 4.0% (w/v) NaCl on R2A medium. The results of 16S rRNA gene sequence similarity analysis showed that strain YIM S02567 T was most closely related to the type strain of Brevilactibacter sinopodophylli (95.4%) and Propioniciclava tarda (94.7%), and phylogenetic analysis based on genome data showed that strain YIM S02567 T should be assigned to the genus Propioniciclava. The cell-wall diamino acid was meso-diaminopimelic acid. The major cellular fatty acids were identified as anteiso-C 15:0 and C 16:0 , and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and two unidentified glycolipids. The predominant menaquinone was MK-9(H 4 ). The genomic DNA G + C content was 71.2 mol%. Based on the polyphasic taxonomic evidence, strain YIM S02567 T is assigned to a novel member of the genus Propioniciclava, for which the name Propioniciclava soli sp. nov., (type strain YIM S02567 T  = CCTCC AB 2020128 T  = CGMCC 1.18504 T  = KCTC 49478 T ) is proposed. Furthermore, we propose the reclassification of Brevilactibacter as Propioniciclava gen. nov., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Laggera pterodonta, known in China as 'Choulingdan' for its stimulous odor, has long been used as traditional herbal medicine. The essential oil of L. pterodonta, which exhibits various pharmacological activities, is a rich resource of monoterpenes and sesquiterpenes. To date, however, the terpene synthases responsible for their production remain unknown. In present study, a new terpene synthase gene (LpNES1) was identified from L. pterodonta, transcript level of which was significantly upregulated in response to methyl jasmonate treatment. Recombinant LpNES1 could synthesize (E)-nerolidol and minor β-farnesene from farnesyl diphosphate and linalool from geranyl diphosphate in vitro. Whereas, only sesquiterpenes including (E)-nerolidol and minor β-farnesene were released when LpNES1 was reconstituted in yeast, even coexpressed with a geranyl diphosphate synthase (ERG20 WW ). Combined with subcellular localization experiment, the result indicated that the cytosol-targeted LpNES1 was responsible for (E)-nerolidol biosynthesis exclusively in L. pterodonta. Additionally, the expression level of LpNES1 gene was more prominent in floral buds than that in other tissues. LpNES1 characterized in present study not only lays the molecular foundation for sesquiterpene biosynthesis of L. pterodonta, but provides a key element for further biosynthesis of bioactive compound in microbes.

A novel Gram-stain positive, oval-shaped, and non-flagellated bacterium, designated YIM S02566 T , was isolated from alpine soil in Shadui Towns, Ganzi County, Ganzi Tibetan Autonomous Prefecture, Sichuan Province, PR China. Growth occurred at 23-35 °C (optimum, 30 °C) in the presence of 0.5-4% (w/v) NaCl (optimum, 1%) and at pH 7.0-8.0 (optimum, pH 7.0). The phylogenetic analysis based on 16S rRNA gene sequence revealed that strain YIM S02566 T was most closely related to the genus Aestuariimicrobium, with Aestuariimicrobium kwangyangense R27 T and Aestuariimicrobium soli D6 T as its closest relative (sequence similarities were 96.3% and 95.4%, respectively). YIM S02566 T contained LL-diaminopimelic acid in the cell wall. MK-9(H4) was the predominant menaquinone. The major fatty acid patterns were anteiso-C 15:0 (60.0%). The major polar lipid was DPG. The genome size of strain YIM S02566 T was 3.1 Mb, comprising 3078 predicted genes with a DNA G + C content of 69.0 mol%. Based on these genotypic, chemotaxonomic and phenotypic evidences, strain YIM S02566 T was identified as a novel species in the genus Aestuariimicrobium, for which the name Aestuariimicrobium ganziense sp. nov. is proposed. The type strain is YIM S02566 T (= CGMCC 1.18751 T = KCTC 49,477 T).

Moutai Jiuqu is a famous aromatic raw material of Maotai flavor liquor in China. It is brewed at high temperature and contains many kinds of bacteria, molds, and yeasts. There are many useful glycoside hydrolases in these microfloras, from which efficient glycoside hydrolases can be screened for biotransformation of natural saponins. In this study, an α-L-arabinofuranosidase gene (CaAraf51, 1524 bp, 507 amino acid, 55.07 kDa, and pI = 4.8) was cloned from Cellulosimicrobium aquatile Lyp51, which was isolated from the Maotai Jiuqu. The CaAraf51 was heterogeneously expressed in E. coli BL21 (DE3) and purified by N-terminal His-tag with the Ni 2+ -affinity column chromatography. The results show that purified CaAraf51 has a 6.8-fold purification factor and specific activity of 15 U/mg. Under optimal conditions (pH 5.0, temperature 40 °C), kinetic parameters K m of CaAraf51 for pNPαAraf and Rc were 1.1 and 0.57 mM, the V max were 25 and 6.25 μmol/min/mg, respectively. 90% of 0.87 mg Rc substrate can be transformed by 9.6 U purified CaAraf51 in 1 mL reaction system under suitable conditions (30 °C, pH 7.5 phosphate buffer, 1 h). In addition, we also tested the effects of metal ions and chemical agents on the activity of CaAraf51. According to systematically studied its function and enzymatic properties, CaAraf51 has excellent value and potential of biotransformation Rc into Rd.

Forskolin is a complex labdane plant diterpenoid, which has been used in the treatment of a variety of diseases based on its activity as an activator of adenosine monophosphate(cAMP) cyclase. Natural forskolin exists only in the cork layer of the root of Coleus forskohlii. Due to the complexity of the extraction and chemical synthesis processes, the yield and purity of forskolin cannot meet commercial requirements. In recent years, with the rapid development of synthetic biology and the analysis and interpretation of many diterpene biosynthetic pathways, a new approach has been provided for the green production of forskolin. In this paper, the structure, activity, biosynthetic pathway and the heterologous biosynthesis of forskolin were reviewed. The problems and solutions in the heterologous biosynthesis of forskolin were also discussed and summarized, which will provide references for the construction of high-yielding forskolin engineering strains.

Diosgenin is a spiroketal steroidal natural product extracted from plants and used as the single most important precursor for the world steroid hormone industry. The sporadic occurrences of diosgenin in distantly related plants imply possible independent biosynthetic origins. The characteristic 5,6-spiroketal moiety in diosgenin is reminiscent of the spiroketal moiety present in anthelmintic avermectins isolated from actinomycete bacteria. How plants gained the ability to biosynthesize spiroketal natural products is unknown. Here, we report the diosgenin-biosynthetic pathways in himalayan paris (Paris polyphylla), a monocot medicinal plant with hemostatic and antibacterial properties, and fenugreek (Trigonella foenum-graecum), an eudicot culinary herb plant commonly used as a galactagogue. Both plants have independently recruited pairs of cytochromes P450 that catalyze oxidative 5,6-spiroketalization of cholesterol to produce diosgenin, with evolutionary progenitors traced to conserved phytohormone metabolism. This study paves the way for engineering the production of diosgenin and derived analogs in heterologous hosts.

A new pregnane steroid, named aspergillon A ( 1 ), together with two known compounds, (22 E ,24 R )-ergosta-5,7,22-trien-3 β -ol ( 2 ) and (22 E , 24 R )-ergosta-4,6,8(14),22-tetraen-3-one ( 3 ) were isolated from cultures of the tin mine tailings-associated fungus Aspergillus versicolor . The new structure and absolute configuration were determined with the help of extensive spectroscopic analyses and quantum chemical calculations of the electronic circular dichroism (ECD) spectra.

A new cyclohexenone, named phomaligol D (1), together with two known compounds, kojic acid (2) and phomaligol A (3) were isolated from the tin mine tailings-derived fungus Aspergillus flavus YIM DT 10012. Their structures were elucidated by detailed analysis of spectroscopic data.

Stachartone A (1), a novel phenylspirodrimane dimer, was isolated from cultures of the tin mine tailings-associated fungus Stachybotrys chartarum. Its structure was elucidated by means of spectroscopic methods. At the same time, compound (1) was tested for its cytotoxicity against five human cancer cell lines.

A new phenylspirodrimane dimer, named stachartarin A (1), was isolated from cultures of the tin mine tailings-associated fungus Stachybotrys chartarum. Its structures were elucidated by means of spectroscopic methods. At the same time, the compound was tested for its cytotoxicity against HL-60, SMMC-7721, A-549, MCF-7, and SW480 cells., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Two new diketopiperazines, named diphenylalazine C (1) and epicoccin U (2), together with six known compounds (3-8) were isolated from the EtOAc extract of the fermentation broth of the tin mine tailings-derived fungus Schizophyllum commune YIM DT 10058. Their structures were elucidated by detailed analysis of spectroscopic data and comparison with related known compounds. Compounds 1 and 2 exhibited weak antibacterial and cytotoxic activities.

Non-alcoholic fatty liver disease (NAFLD) is a common liver disease, which has no standard treatment available. Panax notoginseng saponines (PNS) have recently been reported to protect liver against hepatocyte injury induced by ethanol or high fat diet (HFD) in rats. Compound K and ginsenoside Rh1 are the main metabolites of PNS. In this study, we evaluated the effects of CK and Rh1 on NAFLD. Rats fed HFD showed significant elevations in liver function markers, lipids, glucose tolerance, and insulin resistance. Treatment with CK or Rh1 either alone or in combination dramatically ameliorated the liver function impairment induced by HFD. Histologically, CK and Rh1 significantly reversed HFD-induced hepatocyte injury and liver fibrosis. In vitro experiments demonstrated that treatment with CK or Rh1 alone or in combination markedly induced cell apoptosis, and inhibited cell proliferation and activation in HSC-T6 cells. Additionally, CK and Rh1, either alone or in combination, also repressed the expression of fibrotic factors TIMP-1, PC-I, and PC-III. Taken together, our results demonstrate that CK and Rh1 have positive effects on NAFLD via the anti-fibrotic and hepatoprotective activity.

One new quinolinone, 7-hydroxy-3-methoxyviridicatin (1), along with eight known compounds (2-9) was isolated from the fungus Myrothecium verrucaria, which was collected from lake water of Chenghai, Yunnan Province, China. Their structures were elucidated by detailed analysis of spectroscopic data and comparison with related known compounds. Compounds 1 and 2 exhibited weak antibacterial activity. To the best of our knowledge, this is the first report on quinolinones (1-4) as the secondary metabolites of M. verrucaria.

Background: Geranium wilfordii is one of the major species used as Herba Geranii (lao-guan-cao) in China, it is commonly used solely or in polyherbal formulations for treatment of joint pain resulted from rheumatoid arthritis (RA) and gout. This herb is used to validate a target-based drug screening platform called Herbochip® and evaluate anti-inflammatory effects of Geranium wilfordii ethanolic extract (GWE) using tumor necrosis factor-alpha (TNF-α) as a drug target together with subsequent in vitro and in vivo assays., Methods: A microarray-based drug screening platform was constructed by arraying HPLC fractions of herbal extracts onto a surface-activated polystyrene slide (Herbochip®). Using TNF-α as a molecular probe, fractions of 82 selected herbal extracts, including GWE, were then screened to identify plant extracts containing TNF-α-binding agents. Cytotoxicity of GWE and modulatory effects of GWE on TNF-α expression were evaluated by cell-based assays using TNF-α sensitive murine fibrosarcoma L929 cells as an in vitro model., Results: The in vivo anti-inflammatory effects of GWE were further assessed by animal models including carrageenan-induced hind paw edema in rats and xylene-induced ear edema in mice, in comparison with aspirin. The hybridization data obtained by Herbochip® analysis showed unambiguous signals which confirmed TNF-α binding activity in 46 herbal extracts including GWE. In L929 cells GWE showed significant inhibitory effect on TNF-α expression with negligible cytotoxicity. GWE also significantly inhibited formation of carrageenan-induced hind paw edema and xylene-induced ear edema in animal models, indicating that it indeed possessed anti-inflammatory activity., Conclusion: We have thus validated effectiveness of the Herbochip® drug screening platform using TNF-α as a molecular target. Subsequent experiments on GWE lead us to conclude that the anti-RA activity of GWE can be attributed to inhibitory effect of GWE on the key inflammatory factor, TNF-α. Our results contribute towards validation of the traditional use of GWE in the treatment of RA and other inflammatory joint disorders.

While much is known about the microbial diversity in some hypersaline environments, little is known about those of salt mine tunnel soils. The objective of this study was to conduct a comprehensive phylogenetic comparison of the archaeal and bacterial communities present in Yipinglang salt mine (YPL) and Qiaohou salt mine (QH) tunnels differing in salinity and salt composition using 16S rRNA gene clone libraries. Two hundred twenty-eight sequences for QH and 182 sequences for YPL were analyzed by amplified ribosomal DNA-restriction analysis. Libraries revealed 44 bacterial and 57 archaeal different operational taxonomic units belonging to at least 8 bacterial and 3 archaeal divisions, but not all divisions were observed in both salt mines. The bacterial community affiliated with the Bacteroidetes was the most abundant (60% of clones) in QH, while the community in YPL was dominated by δ-Proteobacteria (45% of clones). All archaeal clones from QH were affiliated with Halobacteriaceae. In contrast, in the YPL library, 49% of clones belonged to Halobacteriaceae, 31% of clones related to unclassified archaea, and 21% of clones belonged to Crenarchaeota. Bioinformatic analysis and comparisons showed that the clone libraries were significantly different between two salt mines., (© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

A facultatively anaerobic, Gram-staining-negative, pale red-pigmented, non-motile, rod-shaped, moderately halophilic bacterium, designated strain YIM J14(T), was isolated from a sediment sample from a salt mine in Yunnan, south-western China. Growth occurred at NaCl concentrations of between 2 % and 15 % (w/v) and optimally with 5-9 % NaCl. The optimum temperature and pH for growth of the strain were 28 °C and pH 7.5. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 1ω9c/10-methyl-C16 : 0. The polar lipid profile was composed predominantly of diphosphatidylglycerol, phosphatidylcholine and one unknown phospholipid. Minor amounts of other lipids were also detectable. The genomic DNA G+C content was 47.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons indicated that strain YIM J14(T) was related to Gracilimonas tropica in the phylum Bacteroidetes. The level of 16S rRNA gene sequence similarity between strain YIM J14(T) and Gracilimonas tropica CL-CB462(T) was 96.9 %. A DNA-DNA hybridization experiment between strain YIM J14(T) and Gracilimonas tropica indicated levels of relatedness of 28 %. Chemotaxonomic data supported the placement of strain YIM J14(T) in the genus Gracilimonas. DNA-DNA hybridization and biochemical and physiological characterization allowed strain YIM J14(T) to be differentiated from Gracilimonas tropica. It is therefore considered to represent a novel species of the genus Gracilimonas, for which the name Gracilimonas mengyeensis sp. nov. is proposed. The type strain YIM J14(T) ( = ACCC 10717(T) = DSM 21985(T)).

Two rod-shaped, non-motile bacteria were isolated from two separate salt mines in Yunnan, south-western China. These strains, designated YIM D15(T) and YIM J21(T), were Gram-negative and moderately halophilic. The two strains required 6-10 % NaCl (w/v; optimal) for growth. The DNA G+C contents of strains YIM D15(T) and YIM J21(T) were 49.0 mol% and 48.4 mol%, respectively. The predominant isoprenoid quinone was MK-7. The polar lipid profiles of strains YIM D15(T) and YIM J21(T) were composed predominantly of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, three unknown polar lipids and one glycolipid. Minor amounts of other lipids were also detectable. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 1ω9c/10 methyl-C16 : 0 and C16 : 1ω7c/C16 : 1ω6c. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the two isolates formed a distinct clade with the genus Fodinibius (in the phylum Bacteroidetes) and were related to the species Fodinibius salinus, with sequence similarities of 91.9-92.4 %. Analyses of 16S rRNA gene sequences revealed that strains YIM D15(T) and YIM J21(T) were related to each other (97.3 % sequence similarity). The DNA-DNA hybridization relatedness between the two isolates was 34 %. On the basis of the phylogenetic analysis, DNA-DNA hybridization relatedness, phenotypic and chemotaxonomic characteristics, strains YIM D15(T) and YIM J21(T) should be classified as members of a novel genus and as two novel species, for which the names Aliifodinibius roseus gen. nov., sp. nov. (type strain YIM D15(T) = ACCC 10715(T) = KCTC 23442(T)) and Aliifodinibius sediminis sp. nov. (type strain YIM J21(T) = ACCC 10714(T) = DSM 21194(T)) are proposed.

Griseusins F (1) and G (2), two 2a-hydro-8a-(2-oxopropyl)-substituted spiro-naphthoquinones with a previously undescribed C23 polyketide skeleton, were isolated from a Yunnan tin mine tailings-derived alkalophilic actinomycete, Nocardiopsis sp. YIM DT266. Their complete structure assignments with the absolute stereochemistry were elucidated by spectroscopic data, X-ray crystal diffraction, calculation of optical rotation, and CD spectroscopic analysis. Compounds 1 and 2 exhibited strong cytotoxicity (IC50 0.37-0.82 μM) and antibacterial activity (MIC 0.80-1.65 μg/mL) against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA) in vitro.

A Gram-negative, facultatively anaerobic, short rod-shaped, heterotrophic bacterium, designated strain YIM D21(T), was isolated from a salt mine in Yunnan province, south-west China. Strain YIM D21(T) formed cream-yellow colonies, was non-motile and moderately halophilic, and tolerated NaCl concentrations of 1-15% (w/v), with optimum growth at 5-10 % (w/v). Growth occurred at 15-42 °C (optimum 28 °C) and at pH 6.5-8.5 (optimum 7.5-8.0). The respiratory quinone was ubiquinone-10 (Q-10). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, three unidentified phospholipids, one unidentified aminolipid and two unidentified lipids. The major fatty acids were C(18:1)ω7c and cyclo C(19:0)ω8c and the DNA G+C content was 67.7 mol%. Phylogenetic analyses revealed that strain YIM D21(T) belongs to the genus Roseivivax. 16S rRNA gene sequence similarities of YIM D21(T) were 95.7, 95.0 and 94.8% with the type strains of Roseivivax halodurans, Roseivivax lentus and Roseivivax halotolerans, respectively. Physiological and biochemical tests allowed phenotypic differentiation of strain YIM D21(T) from closely related species with validly published names. We therefore propose that this isolate represents a novel species, Roseivivax sediminis sp. nov.; the type strain is YIM D21(T) ( = KCTC 23444(T) = ACCC 10710(T)).

A novel, moderately halophilic, rod-shaped bacterium, designated strain YIM D17(T), was isolated from a sample of sediment from a salt mine in Yunnan, south-western China. The taxonomy of strain YIM D17(T) was investigated using a polyphasic approach. Strain YIM D17(T) was Gram-stain-negative, strictly aerobic and non-motile and formed pink colonies on marine agar. Optimal growth occurred at 37 °C, pH 7.5-8.0 and in the presence of 10-15 % (w/v) NaCl. The major menaquinone was MK-7. The polar lipid profile was composed predominantly of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, one phospholipid, one glycolipid and one aminolipid. Minor amounts of other lipids were also detectable. The predominant cellular fatty acids were iso-C(17 : 1)ω9c/10-methyl-C(16 : 0) (24.0 %), iso-C(15 : 0) (23.6 %) and C(16 : 1)ω7c/C(16 : 1)ω6c (13.8 %). The DNA G+C content was 43.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the isolate formed a distinct clade with the genera Gracilimonas and Balneola (both in the phylum Bacteroidetes) and was related to the species Gracilimonas tropica, Balneola vulgaris and Balneola alkaliphila, with sequence similarities of 85.6 %, 83.0 % and 82.8 % to the respective type strains. On the basis of its phenotypic, chemotaxonomic and phylogenetic features, strain YIM D17(T) represents a novel species of a new genus, for which the name Fodinibius salinus gen. nov., sp. nov. is proposed. The type strain is YIM D17(T) ( = ACCC 10716(T) = DSM 21935(T)).

Phenazinolins A-E (1-5), which possess a carbon skeleton unique to diphenazines (the azabicyclo[3.3.1]nonadienol moiety in 1-3 and the oxabicyclo[3.3.1]nonadienol moiety in 4 and 5), were isolated from tin mine tailings-derived Streptomyces diastaticus YIM DT26, with 1-3 exhibited appreciable cytotoxicity and antibiotic effects.

A novel alkaliphilic, halotolerant, rod-shaped bacterium, designated strain YIM CH208(T), was isolated from a soda lake in Yunnan, south-west China. The taxonomy of strain YIM CH208(T) was investigated by a polyphasic approach. Strain YIM CH208(T) was Gram-negative, strictly aerobic and non-motile and formed red colonies. Optimal growth conditions were 28°C, pH8.5 and 0.5-2.5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the isolate formed a distinct line within a clade containing the genus Echinicola in the phylum Bacteroidetes and was related to the species Echinicola pacifica and Rhodonellum psychrophilum, with sequence similarity of 91.7 and 91.6 % to the respective type strains. The DNA G+C content was 45.1 mol%. The major respiratory quinone was menaquinone-7 (MK-7). The predominant cellular fatty acids were iso-C(17 : 1)ω9c (19.9 %), C(15 : 0) 3-OH (12.1 %), iso-C(17 : 0) 3-OH (11.3 %), summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c; 10.7 %) and C(17 : 1)ω6c (8.7 %). On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain YIM CH208(T) represents a novel species of a new genus, for which the name Litoribacter ruber gen. nov., sp. nov. is proposed. The type strain of Litoribacter ruber is YIM CH208(T) (=ACCC 05414(T) =KCTC 22899(T)).

A Gram-negative, rod-shaped, facultatively anaerobic, halotolerant bacterial strain, designated YIM YD3(T), was isolated from a salt mine in Yunnan, south-west China. The taxonomy of strain YIM YD3(T) was investigated by a polyphasic approach. Strain YIM YD3(T) was motile, formed pink colonies and was positive for catalase and oxidase activities. Q-10 was the predominant respiratory ubiquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine and two unknown phospholipids. The major fatty acids (>10 % of total fatty acids) were C(18 : 1)omega7c, C(18 : 1)omega9c, C(16 : 0) and C(19 : 0) cyclo omega8c. The DNA G+C content was 71.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the isolate formed a distinct line within a clade containing the genera Balneimonas, Bosea, Chelatococcus and Microvirga in the order Rhizobiales, with highest levels of 16S RNA gene sequence similarity to the type strain of Balneimonas flocculans (93.5 %). On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain YIM YD3(T) represents a novel species in a new genus, for which the name Salinarimonas rosea gen. nov., sp. nov. is proposed, with strain YIM YD3(T) (=KCTC 22346(T)=CCTCC AA208038(T)) as the type strain.

A Gram-positive-staining, aerobic, catalase- and oxidase-positive, irregular short rod-shaped actinobacterium, designated strain YIM C003T, was isolated from a salt mine in Yunnan, PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM C003T was most closely related to strains of the genera Knoellia (94.2-96.0% similarity), Oryzihumus (95.6%), Terrabacter (94.9-95.4%), Janibacter (94.9-95.4%), Kribbia (95.0%), Lapillicoccus (95.0%) and Phycicoccus (94.2-95.0%) of the family Intrasporangiaceae and that it formed an independent monophyletic lineage with three strains of Oryzihumus leptocrescens. The DNA G+C content of strain YIM C003T was 72.0 mol%. The diagnostic cell-wall diamino acid was meso-diaminopimelic acid. The predominant menaquinone was MK-8(H4). Mycolic acids were not detected. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and two unknown phospholipids. The major cellular fatty acids were C18:1omega9c and C16:0. These chemotaxonomic properties, together with data from phylogenetic analysis, enabled the novel isolate to be differentiated from all other members of the family. A novel species in a new genus, Fodinibacter luteus gen. nov., sp. nov., is proposed, with strain YIM C003T (=DSM 21208T=CCTCC AA 208036T) as the type strain of Fodinibacter luteus.

A Gram-positive, moderately halophilic, alkalitolerant, strictly aerobic, oxidase- and catalase-positive, rod-shaped bacterium, strain YIM kkny3T, was isolated from a sediment sample collected from a salt lake in the Qaidam Basin of north-west China. Cells were motile by means of peritrichous flagella and formed ellipsoidal endospores lying in subterminal swollen sporangia. Growth occurred with 1-20% (w/v) total salts (optimum, 5-10%) and at pH 6.0-10.5 (optimum, pH 7.5-8.0) and 10-55 degrees C (optimum, 35-40 degrees C). It was unable to grow with NaCl as the only salt. meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The strain contained menaquinone 7 (MK-7) as the predominant respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as polar lipids. The major cellular fatty acids were anteiso-C15:0 and anteiso-C17:0. The DNA G+C content was 40.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM kkny3T belonged to the genus Virgibacillus, and was most closely related to the type strains of Virgibacillus olivae (97.1% similarity), Virgibacillus marismortui (97.0%) and Virgibacillus kekensis (96.8%). Levels of DNA-DNA relatedness between strain YIM kkny3T and the type strains of V. olivae, V. marismortui and V. kekensis were 12.4, 10.6 and 15.7%, respectively. The combination of phylogenetic analysis, genotypic data, phenotypic characteristics and chemotaxonomic differences indicated that strain YIM kkny3T represents a novel species of the genus Virgibacillus, for which the name Virgibacillus sediminis sp. nov. is proposed. The type strain is YIM kkny3T (=CCTCC AA 207023T=DSM 19797T=KCTC 13193T).

Two aerobic bacterial strains, YIM B024(T) and YIM B025, were isolated from a salt mine in Yunnan, south-west China. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. The novel strains grew at 15-37 degrees C, pH 6.5-9.0 and 0.25-20 % (w/v) NaCl; optimum growth was observed at 28-30 degrees C, pH 7.0-8.5 and 1.5-10 % NaCl. Oxidase, catalase and nitrate-reducing activities were detected. The two strains were closely related to each other with a 16S rRNA gene sequence similarity of 100 %. DNA-DNA hybridization experiments revealed high relatedness values (90+/-0.4 %) between strains YIM B024(T) and YIM B025, which suggested that these two new strains constituted a single species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates formed a loose cluster with members of the genus Roseivivax in the Roseobacter clade, but were clearly separated from this genus. The levels of 16S rRNA gene sequence similarity between the two isolates and members of the genus Roseivivax ranged from 92.4 to 93.9 %. The major polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and four unknown phospholipids. The major cellular fatty acids were C(18 : 1)omega7c, C(16 : 0), C(18 : 1)omega9c, 11-methyl C(18 : 1)omega7c and C(19 : 0) cyclo omega8c. The sole respiratory quinone was Q-10 and the genomic DNA G+C content was 63.0-64.1 mol%. The distinct phylogenetic position and a combination of phenotypic and chemotaxonomic characteristics supported the proposal of the new isolates as representing a novel species in a new genus, for which the name Sediminimonas qiaohouensis gen. nov., sp. nov. is proposed. The type strain of the type species is YIM B024(T) (=KCTC 22349(T)=CCTCC AA 208033(T)).

A novel Gram-negative, non-sporulating, moderately halophilic, facultatively alkaliphilic, catalase- and oxidase-positive, obligately aerobic bacterium, strain YIM-Y25(T), was isolated from a subterranean brine sample collected from a salt mine in Yunnan, south-west China. Cells were spirilla, motile by monopolar flagella, with meso-diaminopimelic acid in the cell-wall peptidoglycan. Growth occurred with 1-15 % (w/v) NaCl (optimum 5 %), at pH 6.0-10.0 (optimum pH 8.0) and at 15-50 degrees C (optimum 35-40 degrees C). Ubiquinone Q-8 was the predominant respiratory quinone. Polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylamine and an unidentified phospholipid. The major cellular fatty acids were C(18 : 1)omega7c, iso-C(16 : 0), C(16 : 0) and C(16 : 1). The genomic DNA G+C content was 58.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM-Y25(T) was most closely related to the type strain of the sole recognized species of the genus Saccharospirillum, Saccharospirillum impatiens EL-105(T) (sequence similarity 97.0 %), and these two strains formed a robust lineage in the phylogenetic tree. The level of DNA-DNA relatedness between them was 12.6 %. The combination of phylogenetic analysis, phenotypic differences, chemotaxonomic properties and DNA-DNA hybridization data supported the view that this strain represents a novel species of the genus Saccharospirillum, for which the name Saccharospirillum salsuginis sp. nov. is proposed, with YIM-Y25(T) (=CCTCC AA 207033(T) =KCTC 22169(T)) as the type strain.

A novel Gram-positive-staining, catalase- and oxidase-positive, non-motile, non-spore-forming coccus, designated YIM-Y21(T), was isolated from a salt mine in Yunnan, south-west China. The strain was moderately halophilic, facultatively alkaliphilic and obligately aerobic. Colonies were white. Growth occurred with 1.0-30.0 % NaCl (optimum, 10.0 % NaCl), at pH 6.0-10.0 (optimum, pH 8.5) and at 5-40 degrees C (optimum, 25 degrees C). The major amino acid constituents of the cell wall were glycine and lysine. The major cellular fatty acids were anteiso-C(15 : 0), anteiso-C(17 : 0) and iso-C(15 : 0). MK-6 was the predominant respiratory quinone, with MK-7 present in minor amounts. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and an unidentified phospholipid. The DNA G+C content was 46.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain YIM-Y21(T) was most closely related to the type strains of the nine recognized species of the genus Salinicoccus. The sequence similarities between the isolate and the type strains of members of this genus were in the range of 90.6-93.8 %, which indicated that strain YIM-Y21(T) is a representative of a novel species within the genus Salinicoccus. Together with the phenotypic characteristics and chemotaxonomic differences, these results support the proposal of a novel species of the genus Salinicoccus, Salinicoccus albus sp. nov., with YIM-Y21(T) (=CCTCC AA 207024(T) =DSM 19776(T) =KCTC 13192(T)) as the type strain.

An unprecedented new natural product named nocarsin A (1), 5H-4a,6,7a-triazacyclopenta[cd]indene-5,7(6H)-dione (1), together with seven known compounds lumichrome (2), cyclo (L-Leu-L-Tyr) (3), cyclo (L-Ala-L-Ile) (4), cyclo (L-Ala-L-Leu) (5), cyclo (L-Val-L-Ala) (6), 5-methyluracil (7) and uracil (8), was isolated from Nocardia alba sp.nov (YIM 30243(T)), which was isolated from a soil sample collected from Yunnan Province, P. R. China. NMR techniques including COSY, HSQC, ROESY, and HMBC were used to elucidate the structures of these compounds. We report the unambiguous assignments of the (1)H and (13)C NMR spectra of the new compound nocarsin A (1)., (Copyright (c) 2009 John Wiley & Sons, Ltd.)

A Gram-positive, moderately halophilic, endospore-forming, catalase- and oxidase-positive, obligately aerobic bacterium, designated strain YIM-C158T, was isolated from sediment of a salt lake in the Qaidam Basin, north-west China. Cells were motile with peritrichous flagella and rod-shaped, with meso-diaminopimelic acid in the cell-wall peptidoglycan. Strain YIM-C158T grew in the presence of 1-20 % (w/v) NaCl and pH 6.0-10.0, with optimum growth at 5 % (w/v) NaCl and pH 8.0. The strain grew at 4-50 degrees C, with optimum growth at 37 degrees C. The major cellular fatty acids were anteiso-C(15 : 0), iso-C(14 : 0), C(16 : 0), anteiso-C(17 : 0), iso-C(16 : 0), C(16 : 1)omega7c alcohol and C(16 : 1)omega11c. Strain YIM-C158T contained menaquinone MK-7 as the sole respiratory quinone and phosphatidylmethylethanolamine and phosphatidylcholine as the polar lipids. The genomic DNA G+C content was 39.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM-C158T was most closely related to Paraliobacillus ryukyuensis DSM 15140T (96.8 % similarity), and the two strains formed a distinct branch in the phylogenetic tree. The level of DNA-DNA relatedness between the two strains was 15.6 %. The combination of phylogenetic analysis, phenotypic characteristics, chemotaxonomic differences and DNA-DNA hybridization data supported the view that strain YIM-C158T represents a novel species of the genus Paraliobacillus, for which the name Paraliobacillus quinghaiensis sp. nov. is proposed. The type strain is YIM-C158T (=DSM 17857T=CGMCC 1.6333T).

A novel Gram-negative, slightly halophilic, catalase- and oxidase-positive, obligately aerobic bacterium, strain YIM-C248(T), was isolated from a sediment sample collected from a salt-lake in the Qaidam Basin in Qinghai, north-west China. Cells were non-sporulating short rods, occurring singly or as doublets, motile with peritrichous flagella. Growth occurred with 1-15% (w/v) NaCl [optimum 2-4% (w/v) NaCl], at pH 6.0-10.0 (optimum pH 7.5) and at 4-35 degrees C (optimum 25-30 degrees C). The major cellular fatty acids were C(18:1) omega 7c, C(12:0) 3-OH, cyclo C(19:0) omega 8c, C(16:0) and C(16:1). The predominant respiratory quinone was Q-9 and the genomic DNA G + C content was 58.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM-C248(T) should be assigned to the genus Halomonas. The sequence similarities between the isolate and the type strains of members of the genus Halomonas were in the range of 92.5-97.5%. The combination of phylogenetic analysis, DNA-DNA hybridization data, phenotypic characteristics and chemotaxonomic differences supported the view that strain YIM-C248(T) represents a new species of the genus Halomonas, for which the name Halomonas sediminis sp. nov. is proposed, with YIM-C248(T) (=CCTCC AA 207031 = KCTC 22167) as the type strain.

Gilvocarcin-type polyketide glycosides represent some of the most powerful antitumor therapeutics. Bioactivity-guided fractionation of a culture extract of Streptomyces polyformus sp. nov. (YIM 33176) yielded the known gilvocarcin V (2) and a novel related compound, polycarcin V (1). Structure elucidation by NMR and chemical derivatization revealed that the congener (1) features a C-glycosidically linked alpha-L-rhamnopyranosyl moiety in lieu of the D-fucofuranose. The concomitant production of two distinct furanosyl and pyranosyl C-glycosides that share the same aglycone is unprecedented in bacteria. A conversion of both isoforms via a quinone methide intermediate can be ruled out, thus pointing to two individual C-glycosylation pathways. Cytotoxicity profiling of polycarcin V in a panel of 37 tumor cell lines indicated significant antitumoral activity with a pronounced selectivity for non-small-cell lung cancer, breast cancer and melanoma cells. As the antiproliferative fingerprint is identical to that of actinomycin D, the known DNA interaction of gilvocarcins was established as a general principle of antitumorigenic activity.

A Gram-positive, moderately halophilic, moderately thermophilic, endospore-forming, catalase- and oxidase-positive, obligately aerobic bacterium, strain YIM-C55.5(T), was isolated from saline soil in the Qaidam Basin, north-west China. Cells were slender rods, motile by means of peritrichous flagella. Filamentous forms were present throughout the growth cycle. Strain YIM-C55.5(T) was able to grow in the presence of 7-30 % (w/v) NaCl and at pH 6.0-9.0, with optimum growth at 15 % (w/v) NaCl and pH 7.0. It was able to grow at 28-60 degrees C, with optimum growth at 45-50 degrees C. meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The major cellular fatty acids were iso-C(15 : 0), C(16 : 0), anteiso-C(15 : 0), anteiso-C(17 : 0) and C(18 : 0). Strain YIM-C55.5(T) possessed menaquinone 7 (MK-7) as the predominant respiratory quinone and diphosphatidylglycerol and phosphatidylglycerol as polar lipids. The genomic DNA G+C content was 42.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM-C55.5(T) belonged to the family Bacillaceae and was related most closely to members of the genus Gracilibacillus, but with low levels of similarity to the type strains of recognized species of the genus (Gracilibacillus orientalis XH-63(T), 95.1 %; Gracilibacillus boraciitolerans T-16X(T), 94.0 %; Gracilibacillus dipsosauri DD1(T), 93.7 %; Gracilibacillus halotolerans NN(T), 93.5 %). Together with phenotypic data, these results suggest that strain YIM-C55.5(T) represents a novel species of the genus Gracilibacillus, for which the name Gracilibacillus halophilus sp. nov. is proposed. The type strain is YIM-C55.5(T) (=DSM 17856(T) =CGMCC 1.6303(T)).

A motile, Gram-positive, slightly halophilic, endospore-forming, catalase- and oxidase-positive, obligately aerobic, slender rod-shaped bacterium, strain YIM-C229T was isolated from the sediment of a salt lake in the Qaidam Basin, north-west China. Filamentous forms were present throughout the growth cycle. Strain YIM-C229T grew in the presence of 0.5-8% NaCl and at pH 6.0-8.5, with optimum growth at 1-3% NaCl and pH 7.0-7.5. It grew at 4-45 degrees C, with optimum growth at 37 degrees C. The major cellular fatty acids were anteiso-C15:0, C16:0, iso-C15:0, C16:1 omega11c and anteiso-C(17:0). The predominant respiratory quinone was MK-7, and diphosphatidylglycerol and phosphatidylglycerol were the polar lipids, with meso-diaminopimelic acid occurring in the cell-wall peptidoglycan. The genomic DNA G+C content was 40.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM-C229T was closely related to the type strains of the four recognized species of the genus Gracilibacillus: G. halotolerans NN T (sequence similarity 95.5%), G. dipsosauri DD1T (96.1%), G. orientalis XH-63T (96.8%) and G. boraciitolerans T-16X(T) (99.1%). The DNA-DNA relatedness between strain YIM-C229(T) and G. boraciitolerans DSM 17256(T) was 30.8%. The combination of phylogenetic analysis, phenotypic characteristics, chemotaxonomic differences and DNA-DNA hybridization data supported the view that this strain represented a novel species of the genus Gracilibacillus, for which the name Gracilibacillus quinghaiensis sp. nov. is proposed, with YIM-C229T (=DSM 17858T=CGMCC 1.6304T) as the type strain.

A Gram-positive, moderately halophilic, motile, strictly aerobic, endospore-forming, oxidase- and catalase-positive, rod-shaped bacterium, strain YIM kkny16(T), was isolated from a saline mud sample collected from the Keke salt lake in the Qaidam Basin, north-west China. This isolate grew in the presence of 0-25 % (w/v) NaCl and at pH 6.0-10.0 and 10-50 degrees C; optimum growth was observed with 10 % (w/v) NaCl and at pH 7.0 and 37 degrees C. Strain YIM kkny16(T) had meso-diaminopimelic acid as the diagnostic diamino acid, MK-7 as the predominant respiratory quinone, with a significant amount of MK-6, and anteiso-C(15 : 0), iso-C(14 : 0) and C(16 : 1)omega7c alcohol as major fatty acids. Major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C content was 41.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain YIM kkny16(T) was a member of the genus Virgibacillus, exhibiting sequence similarities of 94.9-97.3 % to the type strains of recognized Virgibacillus species. Strain YIM kkny16(T) could be differentiated from recognized Virgibacillus species based on phenotypic characteristics, chemotaxonomic differences, phylogenetic analysis and DNA-DNA hybridization data. On the basis of evidence from this polyphasic study, strain YIM kkny16(T) is considered to represent a novel species of the genus Virgibacillus, for which the name Virgibacillus kekensis sp. nov. is proposed. The type strain is YIM kkny16(T) (=DSM 17056(T)=CGMCC 1.6298(T)).

A novel pale-yellow-pigmented, moderately halophilic, facultatively alkaliphilic, non-motile, non-spore-forming, catalase- and oxidase-positive, obligately aerobic Gram-positive coccus, strain YIM-C678T was isolated from a saline soil sample collected from a hypersaline habitat in the Qaidam basin, northwest China. The organism grew at 4-37 degrees C and pH 6.0-11.0, with optimum growth at 25 degrees C and pH 8.0. Strain YIM-C678T grew optimally in the presence of 10-12% (w/v) NaCl and growth was observed in 1-25% (w/v) NaCl. The cell wall murein type was L: -Lys-Gly5. Major cellular fatty acids were anteiso-C15:0, iso-C15:0, iso-C16:0 and C16:0. Menaquinone 6 (MK-6) was the major respiratory quinone. The DNA G + C content was 46.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain YIM-C678T belonged to the family Staphylococcaceae and was most closely related to the eight described species of the genus Salinicoccus with sequence similarities from 92.2 (S. luteus YIM 70202T) to 97.5% (S. kunmingensis YIM Y15T). The DNA-DNA relatedness between strain YIM-C678T and S. kunmingensis YIM Y15T was 35.4%. Chemotaxonomic data and 16S rRNA gene sequence analysis supported the affiliation of strain YIM-C678T with the genus Salinicoccus. The combination of phylogenetic analysis, phenotypic characteristics, chemotaxonomic differences and DNA-DNA hybridization data supported the view that the bacterium represents a novel species of the genus Salinicoccus, for which the name Salinicoccus salitudinis sp. nov. is proposed, with YIM-C678T (=DSM 17846 = CGMCC 1.6299) as the type strain.

A previously unknown Gram-positive, obligately aerobic actinomycete, YIM 28A4(T), was isolated from a sample of saline soil collected from the Qaidam Basin in Qinghai Province, north-west China, and was investigated using a polyphasic taxonomic approach. The strain grew well on most of the media tested, producing white to pale-yellow substrate mycelium, white aerial mycelium and straight to flexuous hyphae. The substrate mycelium was well developed and fragmented with age; the aerial mycelium produced long, straight spore chains. The spore chains were composed of non-motile, smooth-surfaced, rod-shaped spores. No diffusible pigments were produced on any of the media tested. The strain grew in the presence of 0-10 % (w/v) NaCl and at pH 6.0-8.0, with optimum growth occurring at 3 % (w/v) NaCl and pH 7.0. It grew at 10-37 degrees C, the optimum growth temperature being 28 degrees C. Whole-cell hydrolysates of strain YIM 28A4(T) contained meso-diaminopimelic acid and no diagnostic sugars. The predominant phospholipids were phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol. The predominant menaquinones were MK-10, MK-10(H(2)), MK-11 and MK-11(H(2)). The major cellular fatty acids were iso-C(16 : 0), anteiso-C(15 : 0) and anteiso-C(17 : 0). The DNA G+C content was 67.1 mol%. The morphological and chemotaxonomic characteristics of the isolate matched those described for Nocardiopsis species. A phylogenetic analysis based on 16S rRNA gene sequence comparisons confirmed that strain YIM 28A4(T) was a member of the genus Nocardiopsis and most closely related to the type strains Nocardiopsis aegyptia DSM 44442(T) and Nocardiopsis halotolerans DSM 44410(T), showing 98.1 and 97.8 % 16S rRNA gene sequence similarity, respectively. Strain YIM 28A4(T) can be differentiated from these type strains by using phenotypic, phylogenetic and DNA-DNA hybridization data. On the basis of the polyphasic evidence, strain YIM 28A4(T) represents a novel species of the genus Nocardiopsis, for which the name Nocardiopsis quinghaiensis sp. nov. is proposed. The type strain is YIM 28A4(T) (=DSM 44739(T) =CGMCC 4.3494(T)).

A new pyranonaphthoquinone antibiotic, griseusin D (1) was isolated from the cultural fluid of the alkaphilic Nocardiopsis sp. The structure was determined as 5'-one-4-hydroxy-12-methoxygriseusin by spectroscopic methods, comparison with reported data and single-crystal X-ray analysis. 1 displayed strong cytotoxicity against human leukemia cells (HL60) and modest cytotoxicity against human lung adenocarcinoma cell lines (AGZY) with IC(50) values of 0.23 and 19.6 microg/ml, respectively. It also exhibited weak antifungal activity against Alternaria alternate with MIC of 140 microg/ml.

A novel yellow-pigmented, non-motile, non-sporulating, catalase- and oxidase-positive, obligately aerobic, moderately halophilic, facultatively alkaliphilic Gram-positive coccus, strain YIM Y15(T), was isolated from a brine sample from a salt mine in Yunnan, south-west China. Strain YIM Y15(T) grew in the presence of 0.5-25 % (w/v) NaCl and at pH 6.0-10.0, with optimum growth at 8-10 % (w/v) NaCl and pH 8.0. It grew at 4-45 degrees C, with optimum growth at 37.0 degrees C. The major cellular fatty acids were anteiso-C(15 : 0) and iso-C(15 : 0). Menaquinone 6 (MK-6) was the major respiratory quinone. The cell wall contained Lys and Gly. The DNA G+C content was 46.2 mol%. Phylogenetic analyses based on 16S rRNA gene sequence comparisons revealed that strain YIM Y15(T) was a member of the genus Salinicoccus, with low 16S rRNA gene sequence similarity to the type strains of the five described species of the genus, Salinicoccus alkaliphilus JCM 11311(T) (sequence similarity 96.0 %), Salinicoccus roseus DSM 5351(T) (94.9 %), Salinicoccus jeotgali KCTC 13030(T) (94.8 %), Salinicoccus salsiraiae LMG 22840(T) (94.8 %) and Salinicoccus hispanicus DSM 5352(T) (94.7 %). Together with the phenotypic differences, these results supported the proposal of a novel species of the genus Salinicoccus, Salinicoccus kunmingensis sp. nov., with YIM Y15(T) (=DSM 17847(T) =CGMCC 1.6302(T)) as the type strain.

The prokaryotic microbial diversity of the ancient salt deposits in the Kunming Salt Mine, PR China was investigated using PCR-DGGE and rRNA approaches. Total community DNA was extracted and purified by a direct method, which yielded amplified DNA of high molecular weight for samples. A variable region of 16S rRNA gene was then amplified by PCR with bacterial and archaeal primers and analyzed by denaturing gradient gel electrophoresis (DGGE). Twenty-seven major bands were detected in the bacterial DGGE profile of the sample, but only one band of pure culture strains of bacteria isolated from the Kunming Salt Mine matched with one band of sample. No band of pure culture strains of archaea isolated from the Kunming Salt Mine matched with 18 major bands of sample. The results indicated that most of microbes in this environment are likely uncultivable. Clones on the plate were not the predominant species in the community. Two 16S rRNA gene clone libraries (bacteria and archaea) were also constructed, and 36 and 20 clones were selected for amplified ribosomal DNA restriction analysis (ARDRA). ARDRA with enzymes Afa I, Hha I, Hae III revealed 10 bacterial operational taxonomic units (OTUs), with three most abundant OTUs accounting for 38.9%, 25.0%, 16.7% of all the bacterial 16S rDNA clones, respectively. The remaining 7 OTUs presented at low levels, were represented by a single clone. Eight archaeal OTUs were obtained but no predominant OTUs. Some clones were sequenced and each sequence was compared with all nucleotide sequences in GenBank database. Examination of 16S rDNA clones showed that the ancient salt deposits in the Kunming Salt Mine contained a phylogenetically diverse population of organisms from the Bacteria domain with members of three major lineages represented: alpha-proteobacteria, gamma-Proteobacteria and Actinobacteria, especially Pseudomonas. Surprisingly, we recovered a variety of sequence closely related to Actinobacteria which was not found in other salt deposits. All of archaeal clones are from Halorubrum, Haloterrigena and uncultured archaea. The results of DGGE and clone library profiling analysis both indicated that microbial community of the Kunming Salt Mine had higher diversity. In this initial survey, our polyphasic approaches demonstrated that novel and uncultured microbes thrive in the ancient salt deposits of the Kunming Salt Mine. Molecular analysis of the microbial diversity in salt deposits provides foundation for better application of microbial resources.

In order to understand the diversity of culturable bacteria, 44 bacteria strains inhabiting brines and salt crystals in the Kunming Salt Mine, P. R. China were isolated and cultured. Results showed that the numbers of the bacteria isolated from salt crystals (3.1 x 10(3) - 3.7 x 10(6) CFU/g) were higher than those from brines (1.3 - 6.3 x 10(3) CFU/L). A neighbor-joining tree of the partial 16S rDNA sequences (about 600bp of 5'-end) showed that 44 strains were phylogenetically clustered into 4 major groups and 44 distinct lineages or species (the similarities of 16S rDNA sequences <97%): 24 strains of Firmicutes (54.6%), 2 strains of alpha-Proteobacteria (4.6%), 4 strains of gamma-Proteobacteria (9.1%) and 14 strains of Actinobacteria (31.7%). Strains of the genus Bacillus (26.1% and 59.9%) were the most predominant microorganisms among brines and salt crystals. Additionally, seven potential novel species were found, based on the similarities of 16S rDNA sequences to those of previously published species, and seven strains with bioactivities against pathogenic microorganisms were isolated. The conclusion is that there are a number of novel species and bioactive strains, as well as great diversity in Kunming Salt Mine.