Bioactive Streptomycetes from Isolation to Applications: A Tasmanian Potato Farm Example.

The genus Streptomyces constitutes approximately 50% of all soil actinomycetes, playing a significant role in the soil microbial community through vital functions including nutrient cycling, production of bioactive metabolites, disease-suppression and plant growth promotion. Streptomyces produce many bioactive compounds and are prime targets for industrial and biotechnological applications. In addition to their agrobiological roles, some Streptomyces spp. can, however, be phytopathogenic, examples include, common scab of potato that causes economic losses worldwide. Currently used chemical control measures can have detrimental effect to environmental and human health as a result alternative methods to chemical disease control are being investigated. One alternative is the use of streptomycete specific phages to remove this pathogenic bacterium before it can cause the disease on potatoes. However, due to co-existence of non-common scab-causing species belonging to the genus Streptomyces, phage treatment is likely to affect a wide range of non-target streptomycete species including the beneficial ones in the soil. Therefore, before such treatment starts the host range of the phages within the targeted family of bacteria should be determined. In a study conducted using soil samples from a Tasmanian potato farm, streptomycetes were isolated and tested against streptomycete-specific phages. Their antifungal activity was also determined using multiple assays against selected phytopathogens. The four strongest antifungal activity-displaying isolates were further tested for their persistent antifungal activity using wheat and Fusarium solani in a pot trial. A second pot trial was also conducted to evaluate whether the beneficial streptomycetes were affected by streptophage treatment and whether their removal via the phage battery would cause opportunistic fungal infections to plants in soil. The streptomycetes prevented the reduction in wheat shoot weight caused by F. solani indicating their disease suppressive effect. However, when phages were added into the pots, the growth of wheat was detrimentally impacted. This finding might suggest that the reduced presence of antifungal streptomycetes via phage-induced lysis might encourage opportunistic fungal infections in plants.

Amnibacterium flavum sp. nov., a novel endophytic actinobacterium isolated from bark of Nerium indicum Mill.

A Gram-stain-positive, aerobic, short-rod-shaped, non-spore-forming actinobacterial strain, designated M8JJ-5T, was isolated from a surface-sterilized bark of Neriumindicum Mill. collected from Guizhou, China, and investigated by a polyphasic approach to determine its taxonomic position. Strain M8JJ-5T grew optimally without NaCl at 28 °C and at pH 7.0-8.0. Substrate mycelia and aerial mycelia were not formed, and no diffusible pigments were observed on the media tested. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain M8JJ-5T was most closely related to the type strains of genus Amnibacterium, and shared highest 16S rRNA gene sequence similarity of 97.29 % to Amnibacterium kyonggiense KSL51201-037T. The DNA G+C content of strain M8JJ-5T was 68.6 mol%. The cell-wall peptidoglycan contained l-2,4-diaminobutyric acid and MK-12, MK-11 were the major menaquinones. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid, an unidentified phospholipid and an unidentified lipid, while the major fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. On the basis of phylogenetic, chemotaxonomic and phenotypic data, strain M8JJ-5T can be characterized to represent a novel species of the genus Amnibacterium, for which the name Amnibacteriumflavum sp. nov. is proposed. The type strain is M8JJ-5T (=KCTC 49089T=CGMCC 1.16390T).

Nocardioides houyundeii sp. nov., isolated from Tibetan antelope faeces.

In the present study, we describe two novel Gram-stain-positive, irregular rod-shaped bacterial strains, 78T and 601, that had been isolated from the faeces of Tibetan antelopes at the Hoh Xil Nature Reserve, Qinghai-Tibet Plateau, China. The cells were aerobic, oxidase-negative and catalase-positive. When cultured on brain-heart infusion agar supplemented with 5 % sheep blood, colonies were cream in colour, circular, smooth and convex. Phylogenetic analysis based on the full-length 16S rRNA sequences revealed that type strain 78T and strain 601 belong to the genus Nocardioides, sharing the highest similarity to Nocardioides solisilvae JCM 31492T (98.3 %), Nocardioides gilvus XZ17T (97.4 %) and Nocardioides daejeonensis JCM 16922T (97.4 %). The average nucleotide identity values between the two novel strains and the three closely related type strains of the genus Nocardioides were lower than the 95-96 % threshold. The DNA G+C content of strains 78T and 601 were 71.2 and 71.3 mol% respectively. MK-8 (H4) was the predominant respiratory quinone and ll-2,6-diaminopimelic acid was the diagnostic diamino acid in its cell-wall peptidoglycan. Its polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unidentified phospholipid and an unidentified lipid. The main whole-cell sugars were rhamnose, xylose and galactose and the major fatty acids (>10 %) were C17 : 1ω8c, iso-C16 : 0 and C18 : 1ω9c. These data supported the affiliation of strains 78T and 601 to genus Nocardioides. Based on evidence collected from the phenotypic, genotypic and phylogenetic analyses, we propose a novel species named Nocardioideshouyundeii sp. nov. The type strain is 78T (=CGMCC 4.7461T=DSM 106424T).

Actinomadura hankyongense sp. nov. Isolated From Soil of Ginseng Cultivating Field.

A Gram-positive, rod-shaped, non-spore-forming, and aerobic bacterium (Gsoil 556T) was isolated from soil of a ginseng field and subjected to its taxonomic position. Based on 16S rRNA gene sequence similarity, strain Gsoil 556T was shown to belong to the genus Actinomadura of the family Thermomonosporaceae and was closely related to A. montaniterrae CYP1-1BT (99.3%), A. nitritigenes DSM 44137T (98.7%), and A. rudentiformis HMC1T (98.5%), while it showed less than 98.4% sequence similarity to the other species of this genus. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that it is most closely related to A. rudentiformis HMC1T and A. nitritigenes DSM 44137T. The DNA G+C content was 73.1 mol%. The peptidoglycan was meso-diaminopimelic acid and the whole-cell sugar contained fucose, galactose, glucose, mannose, and ribose. The predominant menaquinone (KK) was MK-9(H8) [55%] and MK-9(H6) [45%]. The major cellular fatty acids were C14:0, C16:0, C18:1 ω9c and summed feature 3 (C16:1 ω6c/C16:1 ω7c). All these data supported the affiliation of strain Gsoil 556T to the genus Actinomadura. The DNA-DNA hybridization between strain Gsoil 556T and its phylogenetically closest relatives were less than 40%. Furthermore, the results of physiological and biochemical tests enabled strain Gsoil 556T to be differentiated genotypically and phenotypically from currently known Actinomadura species. Therefore, strain Gsoil 556T represents a novel species of the genus Actinomadura, for which the name Actinomadura hankyongense sp. nov. is proposed. The type strain Gsoil 556T (=KACC 19438T=LMG 30327T).

Seasonal dynamics of the bacterioplankton community in a large, shallow, highly dynamic freshwater lake.

The spatiotemporal shifts of the bacterioplankton community can mirror their transition of functional traits in an aquatic ecosystem. However, the spatiotemporal variation of the bacterioplankton community composition structure (BCCS) within a large, shallow, highly dynamic freshwater lake is still poorly understood. Here, we examined the seasonal and spatial variability of the BCCs within Poyang Lake by sequencing the 16S rRNA gene amplicon to explore how hydrological changes affect the BCCs. Principal coordinate analysis showed that the BCCs varied significantly among four sampling seasons, but not spatially. The seasonal changes of the BCCs were mainly attributed to the differences between autumn and spring-winter. Higher α diversity indices were observed in autumn. Redundancy analysis indicated that the BCCs co-variated with water level, pH, temperature, total phosphorus, ammoniacal nitrogen, electrical conductivity, total nitrogen, and turbidity. Among them, water level was the key determinant separating autumn BCCs from the BCCs in other seasons. A significantly lower relative abundance of Burkholderiales (betI and betVII) and a higher relative abundance of Actinomycetales (acI, acTH1, and acTH2) were found in autumn than in other seasons. Overall, our results suggest that water level changes associated with pH, temperature, and nutrient status shaped the seasonal patterns of the BCCs within Poyang Lake.

Glycomyces paridis sp. nov., isolated from the medicinal plant Paris polyphylla.

Three actinomycete strains originating from the surface-sterilized roots of Paris polyphylla were characterized by using a polyphasic approach. Phylogenetic analyses based on the 16S rRNA gene sequence showed that they formed a deep, monophyletic branch in the genus Glycomyces, and were most closely related to the type strains of the species Glycomyces harbinensis and Glycomycesscopariae. Morphological and chemotaxonomic data supported the affiliation of strains CPCC 204357T, CPCC 204354 and CPCC 204355 to the genus Glycomyces. The results of physiological and biochemical tests allowed phenotypic differentiation of strains CPCC 204357T, CPCC 204354 and CPCC 204355 from their closest phylogenetic related species in the genus Glycomyces. Low levels of DNA-DNA relatedness with its closest type strains of G. harbinensis and G. scopariaeindicated that strain CPCC 204357T represent a novel species, for which the name Glycomyces paridis sp. nov. is proposed, with CPCC 204357T (=DSM 102295T=KCTC 39745T) as the type strain.

Aeromicrobium panacisoli sp. nov. Isolated from Soil of Ginseng Cultivating Field.

A Gram-positive, rod-shaped, non-spore-forming, and aerobic bacterium (Gsoil 137T) was isolated from soil of a ginseng field of Pocheon province in South Korea and subjected to a polyphasic approach in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 137T was shown to belong to the family Nocardioidaceae and was closely related to Aeromicrobium ginsengisoli Gsoil 098T (96.7%), Aeromicrobium panaciterrae (96.7%), and Aeromicrobium halocynthiae JCM 15749T (96.6%). Being phylogenetic, it was most closely related to Aeromicrobium halocynthiae JCM 15749T. The G+C content of the genomic DNA was 70.3 mol%. The diagnostic diamino acid of the cell wall peptidoglycan was LL-diaminopimelic acid. The predominant menaquinone was menaquinone MK-8 (H4) and MK-7 (H4) was a minor compound. The major cellular fatty acids were C14:0, C16:0, C18:1 ω9c and summed feature 4 (C16:1 ω7c/C15:0 iso 2-OH). All these data supported the affiliation of strain Gsoil 137T to the genus Aeromicrobium. The results of physiological and biochemical tests enabled strain Gsoil 137T to be differentiated genotypically and phenotypically from currently known Aeromicrobium species. Therefore, strain Gsoil 137T represents a novel species of the genus Aeromicrobium, for which the name Aeromicrobium panacisoli sp. nov. is proposed. The type strain is Gsoil 137T (= KCTC 19130T = DSM 17940T = CCUG 52475T).

The microbiology and treatment of human mastitis.

Mastitis, which is generally described as an inflammation of breast tissue, is a common and debilitating disease which frequently results in the cessation of exclusive breastfeeding and affects up to 33% of lactating women. The condition is a primary cause of decreased milk production and results in organoleptic and nutritional alterations in milk quality. Recent studies employing culture-independent techniques, including metagenomic sequencing, have revealed a loss of bacterial diversity in the microbiome of mastitic milk samples compared to healthy milk samples. In those infected, the pathogens Staphylococcus aureus, Staphylococcus epidermidis and members of corynebacteria have been identified as the predominant etiological agents in acute, subacute and granulomatous mastitis, respectively. The increased incidence of antibiotic resistance in the causative species is also a key cause of concern for treatment of the disease, thus leading to the need to develop novel therapies. In this respect, probiotics and bacteriocins have revealed potential as alternative treatments.

Allobranchiibius huperziae gen. nov., sp. nov., a member of Dermacoccaceae isolated from the root of a medicinal plant Huperzia serrata (Thunb.).

A Gram-stain-positive, non-spore-forming actinobacterial strain, designated CPCC 204077T, was isolated from the surface-sterilized root of a medicinal plant Huperzia serrata (Thunb.) collected from Sichuan Province, south-west China. The peptidoglycan type of strain CPCC 204077T was detected as A4α with an l-Lys-l-Ser-d-Asp interpeptide bridge. Galactose, glucose, rhamnose and ribose were the sugar compositions in the whole-cell hydrolysates. MK-8(H4) was the only menaquinone. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, one unidentified phospholipid and one unidentified glycolipid. The major fatty acid was iso-C16 : 0. The genomic DNA G+C content was 71.0 mol%. The phylogenetic tree based on 16S rRNA gene sequences showed that strain CPCC 204077T stood for a distinct lineage within the family Dermacoccaceaealongside the genera Branchiibius, Demetria and Barrientosiimonas, with the highest 16S rRNA gene sequence similarities to Branchiibius hedensis Mer 29717T (95.0 %), Calidifontibacter indicus PC IW02T (95.0 %), Barrientosiimonas humi 39T (94.9 %) and Demetria terragena HKI 0089T (94.7 %), and less than 94.7 % sequence similarities to all other species. Signature nucleotides in the 16S rRNA sequence showed that the strain contained the Dermacoccaceaefamily-specific 16S rRNA signature nucleotides and a genus-specific diagnostic nucleotide signature pattern. Combining the genotypic and phenotypic analyses, we propose that strain CPCC 204077T represents a novel species of a new genus in the family Dermacoccaceae with the name Allobranchiibius huperziae gen. nov., sp. nov. Strain CPCC 204077T (=NBRC 110719T=DSM 29531T) is the type strain of the type species.

Prauserella oleivorans sp. nov., a halophilic and thermotolerant crude-oil-degrading actinobacterium isolated from an oil-contaminated mud pit.

A crude-oil-degrading, Gram-stain-positive actinobacterial strain, RIPIT, was isolated from a soil sample collected from an oil-contaminated mud pit in Khangiran oil and gas field, in the north-east of Iran. RIPIT was strictly aerobic, catalase- and oxidase-positive. The strain grew with 0-12.5 % (w/v) NaCl (optimum 3-5 %), at 25-55 °C (optimum 45 °C) and at pH 6.0-9.5 (optimum pH 7.0). The results of 16S rRNA gene sequence comparative analysis indicated that RIPIT represents a member of the genus Prauserella, with high phylogenetic similarity to Prauserella coralliicola SCSIO 11529T (97.5 %), Prauserella endophytica SP28S-3T (97.5 %) and Prauserella marina MS498T (97.2 %). DNA-DNA relatedness values between the novel strain and P. coralliicola DSM 45821T, P. endophytica DSM 46655T and P. marina DSM 45268T were 28 , 19 and 23 %, respectively. The cell wall peptidoglycan of RIPIT contained meso-diaminopimelic acid as the diamino acid and the whole-cell sugars are galactose and arabinose. The polar lipids pattern contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and two unknown phospholipids. Its cellular fatty acids pattern consisted of C17 : 1ω6c, iso-C16 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), and the major respiratory quinone was MK-9(H4). The G+C content of the genomic DNA was 69 mol%. On the basis of polyphasic taxonomic data we propose that RIPIT represents a novel species of the genus Prauserella, for which the name Prauserella oleivorans sp. nov. is proposed. The type strain of Prauserellaoleivorans is RIPIT (=IBRC-M 10906T=LMG 28389T).

Nocardioides litoris sp. nov., isolated from the Taean seashore.

A novel Gram-stain-positive, irregularly rod-shaped actinomycete, designated strain 002-2T, was isolated from sand beach sediment collected from the Taean seashore, Republic of Korea. Cells were aerobic, oxidase-negative and catalase-positive. Colonies of cells were bright yellow, circular, smooth and convex. The diagnostic diamino acid in the cell wall was ll-diaminopimelic acid. The predominant menaquinone was MK-8(H4). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unknown phospholipid and two unknown amino phospholipids. The major fatty acids were iso-C16 : 0 and C17 : 1ω8c. The DNA G+C content was 68.8 mol%. 16S rRNA gene sequence analysis revealed that strain 002-2T belongs to the family Nocardioidaceae and formed a cluster with Nocardioides rubroscoriae Sco-A25T (98.1 % sequence similarity) and Nocardioides plantarum NCIMB 12834T (97.6 %). On the basis of the phenotypic and phylogenetic data, strain 002-2T (=KCTC 39838T=DSM 103718T) is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides litoris sp. nov. is proposed.

Draft genome analysis of Dietzia sp. 111N12-1, isolated from the South China Sea with bioremediation activity

Abstract Dietzia sp. 111N12-1, isolated from the seawater of South China Sea, shows strong petroleum hydrocarbons degradation activity. Here, we report the draft sequence of approximately 3.7-Mbp genome of this strain. To the best of our knowledge, this is the first genome sequence of Dietzia strain isolated from the sea. The genome sequence may provide fundamental molecular information on elucidating the metabolic pathway of hydrocarbons degradation in this strain.

Draft genome analysis of Dietzia sp. 111N12-1, isolated from the South China Sea with bioremediation activity.

Dietzia sp. 111N12-1, isolated from the seawater of South China Sea, shows strong petroleum hydrocarbons degradation activity. Here, we report the draft sequence of approximately 3.7-Mbp genome of this strain. To the best of our knowledge, this is the first genome sequence of Dietzia strain isolated from the sea. The genome sequence may provide fundamental molecular information on elucidating the metabolic pathway of hydrocarbons degradation in this strain.

Polysaccharide Degradation Capability of Actinomycetales Soil Isolates from a Semiarid Grassland of the Colorado Plateau.

Among the bacteria, members of the order Actinomycetales are considered quintessential degraders of complex polysaccharides in soils. However, studies examining complex polysaccharide degradation by Actinomycetales (other than Streptomyces spp.) in soils are limited. Here, we examine the lignocellulolytic and chitinolytic potential of 112 Actinomycetales strains, encompassing 13 families, isolated from a semiarid grassland of the Colorado Plateau in Utah. Members of the Streptomycetaceae, Pseudonocardiaceae, Micromonosporaceae, and Promicromonosporaceae families exhibited robust activity against carboxymethyl cellulose, xylan, chitin, and pectin substrates (except for low/no pectinase activity by the Micromonosporaceae). When incubated in a hydrated mixture of blended Stipa and Hilaria grass biomass over a 5-week period, Streptomyces and Saccharothrix (a member of the Pseudonocardiaceae) isolates produced high levels of extracellular enzyme activity, such as endo- and exocellulase, glucosidase, endo- and exoxylosidase, and arabinofuranosidase. These characteristics make them well suited to degrade the cellulose and hemicellulose components of grass cell walls. On the basis of the polysaccharide degradation profiles of the isolates, relative abundance of Actinomycetales sequences in 16S rRNA gene surveys of Colorado Plateau soils, and analysis of genes coding for polysaccharide-degrading enzymes among 237 Actinomycetales genomes in the CAZy database and 5 genomes from our isolates, we posit that Streptomyces spp. and select members of the Pseudonocardiaceae and Micromonosporaceae likely play an important role in the degradation of hemicellulose, cellulose, and chitin substances in dryland soils.IMPORTANCE Shifts in the relative abundance of Actinomycetales taxa have been observed in soil microbial community surveys during large, manipulated climate change field studies. However, our limited understanding of the ecophysiology of diverse Actinomycetales taxa in soil systems undermines attempts to determine the underlying causes of the population shifts or their impact on carbon cycling in soil. This study combines a systematic analysis of the polysaccharide degradation potential of a diverse collection of Actinomycetales isolates from surface soils of a semiarid grassland with analysis of genomes from five of these isolates and publicly available Actinomycetales genomes for genes encoding polysaccharide-active enzymes. The results address an important gap in knowledge of Actinomycetales ecophysiology-identification of key taxa capable of facilitating lignocellulose degradation in dryland soils. Information from this study will benefit future metagenomic studies related to carbon cycling in dryland soils by providing a baseline linkage of Actinomycetales phylogeny with lignocellulolytic functional potential.

Actinophytocola xanthii sp. nov., an actinomycete isolated from rhizosphere soil of the plant Xanthium sibiricum.

A novel actinomycete strain, 11-183T, was isolated from the rhizosphere soil of Xanthium sibiricum, which was collected in Tangshan, Hebei, China. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain 11-183T formed a clade within the genus Actinophytocola, with a maximum similarity of 98.44 % to Actinophytocola xinjiangensis QAIII60T, followed by 97.76 % similarity to Actinophytocola sediminis YIM M13705T. The average nucleotide identity and digital DNA-DNA hybridization values differed by 79.24 and 23.4 %, respectively, between strain 11-183T and Actinophytocolaxinjiangensis QAIII60T. Strain 11-183T grew well on N-Z-amine agar, and it produced a scant, white aerial mycelium. The isolate formed pale yellow to brown-black colonies and a dense, non-fragmented, branched substrate mycelium, and produced aerial hyphae on which nodular spore chains formed. Growth was observed at salinities ranging from 0 to 2 %, at pH values ranging from pH 6.5 to 8.0 and at temperatures ranging from 15 to 37 °C. The cell-wall amino acids included meso-diaminopimelic acid. Whole cell hydrolysates contained galactose and glucose. The principal fatty acids were iso-C16 : 0, iso-C16 : 1 H and C17 : 1ω6c. Diphosphatidylglycerol, phosphatidylmonomethylethanolamine and phosphatidylethanolamine were the diagnostic phospholipids. The isoprenoid quinones included MK-9(H4) and MK-10(H4). The G+C content of the genomic DNA was 71.7 mol%. Based on the genotypic and phenotypic data, we conclude that strain 11-183T belongs to a novel species of the genus Actinophytocola. The name proposed for the novel species is Actinophytocola xanthii sp. nov., with the type strain 11-183T (=KCTC 39690T= MCCC 1K02062T).

Microbacterium rhizosphaerae sp. nov., isolated from a Ginseng field, South Korea.

A novel Gram-stain positive, aerobic, short rod-shaped, non-motile bacterium, designated strain CHO1T, was isolated from rhizosphere soil from a ginseng agriculture field. Strain CHO1T was observed to form yellow colonies on R2A agar medium. The cell wall peptidoglycan was found to contain alanine, glycine, glutamic acid, D-ornithine and serine. The cell wall sugars were identified as galactose, mannose, rhamnose and ribose. Strain CHO1T was found to contain MK-11, MK-12, MK-13 as the predominant menaquinones and anteiso-C15:0, iso-C16:0, and anteiso-C17:0 as the major fatty acids. Diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid, an unidentified phospholipid and three unidentified glycolipids were found to be present in strain CHO1T. Based on 16S rRNA gene sequence analysis, strain CHO1T was found to be closely related to Microbacterium mangrovi DSM 28240T (97.81 % similarity), Microbacterium immunditiarum JCM 14034T (97.45 %), Microbacterium oryzae JCM 16837T (97.33 %) and Microbacterium ulmi KCTC 19363T (97.10 %) and to other species of the genus Microbacterium. The DNA G+C content of CHO1T was determined to be 70.1 mol %. The DNA-DNA hybridization values of CHO1T with M. mangrovi DSM 28240T, M. immunditiarum JCM 14034T, M. oryzae JCM 16837T and M. ulmi KCTC 19363T were 46.7 ± 2, 32.4 ± 2, 32.0 ± 2 and 29.2 ± 2 %, respectively. On the basis of genotypic, phenotypic and phylogenetic properties, it is concluded that strain CHO1T represents a novel species within the genus Microbacterium, for which the name Microbacterium rhizosphaerae sp. nov. is proposed. The type strain of M. rhizosphaerae is CHO1T (= KEMB 7306-513T = JCM 31396T).

Phycicoccus ginsengisoli sp. nov., isolated from cultivated ginseng soil.

Ginseng-cultivated soil is an excellent habitat for soil-borne bacteria to proliferate. A novel strain, DCY87T, was isolated from ginseng-cultivated soil in Gochang County, Republic of Korea, and subsequently characterized by polyphasic approach. Cells were rod shaped, non-motile, aerobic, Gram-reaction-positive, oxidase-negative and catalase-positive. 16S rRNA gene sequence analysis showed that strain DCY87T shared the highest similarity to 'Phycicoccus ochangensis' L1b-b9 (98.7 %). Closely phylogenetic relatives of strain DCY87T were identified: Phycicoccus ginsenosidimutans BXN5-13T (97.9 %), Phycicoccus soli THG-a14T (97.8 %), Phycicoccus bigeumensis MSL-03T (97.3 %), Phycicoccus cremeus V2M29T (97.3 %), Phycicoccus aerophilus 5516T-20T (97.3 %), Phycicoccus dokdonensis DS-8T (97.3 %) and Phycicoccus jejuensis KSW2-15T (97.1 %). The major polar lipids were classified as phosphatidylinositol and diphosphatidylglycerol. The major cellular fatty acids were composed of iso-C15 : 0, anteiso-C15:0, C17 : 0 and C17 : 1ω8c. The menaquinone was resolved as MK-8(H4). Strain DCY87T contained meso-diaminopimelic acid as diamino acid in the cell-wall peptidoglycan and glucose, xylose and rhamnose in the whole-cell sugar. The genomic DNA G+C content was calculated to be 72.7 mol%. DNA-DNA hybridization value between strain DCY87T and 'P. ochangensis' L1b-b9 was estimated to be 50 %. However, DNA-DNA hybridization value obtained between strain DCY87T and P. ginsenosidimutans BXN5-13T, P. soli THG-a14T and P. bigeumensis MSL-03T was well below 17 %. In general, polyphasic taxonomy demonstrated that DCY87T strain represented a novel species within the genus Phycicoccus. Accordingly, we propose the name Phycicoccus ginsengisoli sp. nov. The type strain is DCY87T (=KCTC 39635T=JCM 31016T).

Inhibitory Effect of Three Diketopiperazines from Marine-Derived Bacteria on HMGB1-Induced Septic Responses in Vitro and in Vivo.

The nucleosomal protein high-mobility group box-1 (HMGB1), which has recently been established as a late mediator of lethal systemic inflammation, has a relatively wide therapeutic window for pharmacological interventions. Compounds produced by marine-derived microbes have been widely investigated for their potential use as bioactive natural products. Cyclic dipeptides, which are also known as diketopiperazines, are molecules that are frequently found in marine-derived microorganisms. While their pharmacological potential has been well established, their biological activities against septic responses have not yet been reported. Here, three diketopiperazines (1-3) isolated from two strains of marine-derived bacteria were investigated for their potential activities against HMGB1-mediated septic responses. The data showed that 1-3 effectively inhibited the lipopolysaccharide (LPS)-induced release of HMGB1 and suppressed the HMGB1-mediated septic responses, including hyperpermeability, leukocyte adhesion and migration, and cell adhesion molecule expression. In addition, 1-3 inhibited the HMGB1-mediated production of tumor necrosis factor-[Formula: see text] (TNF-[Formula: see text] and interleukin (IL)-6 and the activation of nuclear factor-[Formula: see text]B (NF-[Formula: see text]B) and extracellular signal-regulated kinase (ERK) 1 and ERK2. Collectively, these results indicated that 1-3 might act as potential therapeutic agents for various severe vascular inflammatory diseases through the inhibition of the HMGB1 signaling pathway.

Microbacterium aureliae sp. nov., a novel actinobacterium isolated from Aurelia aurita, the moon jellyfish.

The taxonomic position of a lemon-yellow-pigmented actinobacterium, strain JF-6T, isolated from Aurelia aurita, the moon jellyfish, collected from the Bay of Bengal coast, Kanyakumari, India, was determined using a polyphasic approach. The strain had phenotypic and chemotaxonomic properties that were consistent with its classification in the genus Microbacterium. Alignment of the 16S rRNA gene sequence of strain JF-6T with sequences from Microbacterium arthrosphaerae CC-VM-YT, Microbacterium yannicii G72T, Microbacterium trichothecenolyticum IFO 15077T, Microbacterium flavescens DSM 20643T, Microbacterium insulae DS-66T, Microbacterium resistens DMMZ 1710T and Microbacterium thalassium IFO 16060T revealed similarities of 98.95, 98.76, 98.43, 98.41, 98.41, 98.26 and 98.22 %, respectively. However, the levels of DNA-DNA relatedness with its closest phylogenetic neighbours confirmed that it represents a novel species within the genus. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and an unknown glycolipid. The major menaquinones detected for strain JF-6T were MK-13 and MK-12. The diamino acid in the cell-wall peptidoglycan was ornithine and the peptidoglycan was type B2ß (Glu/Hyg-Gly-d-Orn). The DNA G+C content was 69.4 mol%. Based on these differences, strain JF-6T (=MTCC 11843T=JCM 30060T=KCTC 39828T) should be classified as the type strain of a novel species of Microbacterium, for which the name Microbacterium aureliae sp. nov. is proposed.

16S-gyrB-rpoB multilocus sequence analysis for species identification in the genus Microbispora.

The genus Microbispora has been considered difficult to define taxonomically. While 16S rRNA gene analysis is required to determine phylogenetic relationships among species in this genus, most 16S rRNA gene-based phylogenetic tree topologies are not reliable. The genus Microbispora currently contains eight species along with six reclassified species (Microbispora chromogenes, Microbispora diastatica, Microbispora parva, Microbispora indica, Microbispora karnatakensis, Microbispora rosea) and Microbispora rosea subsp. aerata, a taxon composed of three further reclassified species (Microbispora aerata, Microbispora thermodiastatica, and Microbispora thermorosea). 16S rRNA, 23S rRNA, gyrB, and rpoB gene sequences were obtained for the type strains of Microbispora species, and eleven endophytic isolates from a Brazilian medicinal plant, Vochysia divergens. Using the concatenated sequence, most Microbispora type strains could be distinguished with high probability support. Based on these analyses, we propose that five of the species reclassified within the subspecies of M. rosea (M. chromogenes, M. karnatakensis, M. parva, M. aerata and M. thermorosea) are distinct from M. rosea and so should be retained as distinct species. The concatenated 16S-gyrB-rpoB gene phylogenic tree had significant probability support and topology. We propose the use of concatenated 16S-gyrB-rpoB gene sequences to determine phylogenetic relationships within the genus Microbispora. We also suggest that strains sharing >98.1 % 16S-gyrB-rpoB gene sequences similarity be defined as a single species, based on results from this analysis. Seven of the strains isolated from V. divergens were not related to any previously described Microbispora species.