Siderophore-producing Pantoea ferrattrahens sp. nov. isolated from a clinical specimen and Pantoea ferramans sp. nov. isolated from soil at the bottom of a pond.

Two Gram-negative facultative anaerobes were isolated from a sepsis patient with pancreatic cancer (strain PAGU 2156 ) and soil at the bottom of a pond (strain PAGU 2198 ), respectively. These two strains formed haloes around the colonies on chrome azurol S agar plates, indicating the production of siderophores. Two isolates assigned to the genus Pantoea based on the 16S rRNA gene were differentiated from established species by using polymorphic taxonomies.

Optimal selection of learning data for highly accurate QSAR prediction of chemical biodegradability: a machine learning-based approach.

Prior to the manufacture of new chemicals, regulations mandate a thorough review of the chemicals under risk management. This review involves evaluating their effects on the environment and human health. To assess these effects, a review report that conforms to the OECD Test Guidelines must be submitted to the regulatory body.

sp. nov., isolated from estuarine sediment of the Arakawa River.

A Gram-stain-negative, rod-shaped, non-motile and strictly aerobic bacterium, which showed biofilm-forming ability on polystyrene, designated as strain B-399, was isolated from the estuarine sediment of the Arakawa River near Tokyo Bay. It grew at pH 6.0-8.

sp. nov., a novel actinobacterium isolated from gut of larvae of .

A novel actinobacterium strain, designated CFWR-12, was isolated from the larval gut of grown at the National Institute of Agricultural Sciences, Wanju-gun, Republic of Korea, and its taxonomic position was evaluated. Strain CFWR-12 was aerobic, Gram-stain-positive and non-motile. Growth occurred at 10-40 °C, pH 6.

sp. nov., an actinobacterium isolated from clinical specimens in Japan.

Two novel actinobacteria, designated IFM 12276 and IFM 12275, were isolated from clinical specimens in Japan, and their taxonomic positions were investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strains IFM 12276 and IFM 12275 have completely identical 16S rRNA gene sequences and were closely related to members of the genus . The highest 16S rRNA gene sequence similarity was observed to (99.

Physiological and genomic analyses of cobalamin (vitamin B)-auxotrophy of sp. nov., a methionine-auxotrophic chitinolytic bacterium isolated from chitin-treated soil.

A novel bacterium designated 5-21a, isolated from chitin-treated upland soil, exhibits methionine (Met) auxotrophy and chitinolytic activity. A physiological experiment revealed the cobalamin (synonym, vitamin B)(Cbl)-auxotrophic property of strain 5-21a. The newly determined complete genomic sequence indicated that strain 5-21a possesses only the putative gene for Cbl-dependent Met synthase (MetH) and lacks that for the Cbl-independent one (MetE), which implies the requirement of Cbl for Met-synthesis in strain 5-21a.

sp. nov. and sp. nov., isolated from rhizospheres of onion and garlic, respectively.

Three bacterial strains, H21R-40 and H21R-36 from garlic () and H25R-14 from onion (), were isolated from plant rhizospheres sampled in the Republic of Korea. Results of 16S rRNA gene sequence analysis revealed the highest sequence similarity of strain H21R-40 to subsp. CBX151 (97.

sp. nov., an anaerobic bacterium isolated from marine sediment.

A novel bacterium, strain SH18-1, was isolated from marine sediment collected near Sado Island in the Sea of Japan. This strain was strictly anaerobic, Gram-stain-negative, non-spore-forming, rod-shaped, motile, and mesophilic. It grew at 15-40 °C (optimum, 30-35 °C), at a NaCl concentration of 0.

Draft Genome Sequence of the Marine-Derived, Anticancer Compound-Producing Bacterium sp. Strain GMY01.

The marine sp. strain GMY01 was isolated from Indonesian marine sediment. Genome mining analysis revealed that GMY01 has 28 biosynthetic gene clusters, dominated by genes encoding nonribosomal peptide synthetase and polyketide synthase.

Recent Progress of Reclassification of the Genus .

The genus is a representative group of actinomycetes and one of the largest taxa in bacteria, including approximately 700 species with validly published names. Since the classification was mainly based on phenotypic characteristics in old days, many members needed to be reclassified according to recent molecular-based taxonomies. Recent developments of molecular-based analysis methods and availability of whole genome sequences of type strains enables researchers to reclassify these phylogenetically complex members on a large scale.

North-to-South diversity of lipomycetaceous yeasts in soils evaluated with a cultivation-based approach from 11 locations in Japan.

To understand the species distribution, diversity, and density of lipomycetaceous yeasts in soil based on their north-to-south location in Japan, 1146 strains were isolated from soil samples at 11 locations from Hokkaido to Okinawa Prefecture and taxonomically characterized. Lipomycetaceous yeast strains were isolated efficiently from soil by selecting watery mucoid-like colonies on agar plates with nitrogen-depleted medium. Twenty-four (80%) of the 30 known species of the genus were isolated from the soil samples collected in Japan, including species recently proposed.

sp. nov., an aerobic bacteriochlorophyll -containing freshwater bacterium isolated from river epilithic biofilm.

A strictly aerobic bacteriochlorophyll -containing alphaproteobacterium, designated strain S08, was isolated from a biofilm sampled at Tama River in Japan. The non-motile and rod-shaped cells formed pink-beige pigmented colonies on agar plates containing organic compounds and showed absorption maxima at 798 and 866 nm in the near-infrared region, typical for the presence of bacteriochlorophyll . The new bacterial isolate is Gram-negative, oxidase-negative and catalase-positive.

gen. nov., sp. nov., a novel bacterium isolated from the brain of the squid, and reclassification of two species as comb. nov. and comb. nov.

A Gram-stain-positive, non-motile, mesophilic, aerobic, coccus-shaped bacterium, designated strain Y7R2, was isolated from the brain of a squid living in mesopelagic water near Muroto, Kochi, Japan. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain was most closely related to the genus (96.1 % similarity to the type strain of the type species ) and formed a separate distinct cluster in a stable, deep-branching lineage with the type strains of and (98.

Taxonomic Positions and Secondary Metabolite-Biosynthetic Gene Clusters of Akazaoxime- and Levantilide-Producers.

sp. AKA109 is a producer of akazaoxime and A-76356, whereas sp. AKA38 is that of levantilide C.

sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove.

A novel actinobacterium, designated HIs16-36, was isolated from the rhizosphere of a mangrove on Ishigaki Island, Okinawa, Japan, and its taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain HIs16-36 was closely related to the members of the genus . The highest 16S rRNA gene sequence similarity was observed with (98.

Streptomyces pacificus sp. nov., a novel spongiicolazolicin-producing actinomycete isolated from a coastal sediment.

A polyphasic approach was used to determine the taxonomic position of a marine actinomycete, designated isolate CWH03, which we previously reported to produce new linear azole-containing peptides spongiicolazolicins A and B. Strain CWH03 is mesophilic, neutrophilic, and halotolerant streptomycete that forms spiral spore chains on aerial mycelium. Comparative 16S rRNA gene sequencing showed that CWH03 was most closely related to Streptomyces tirandamycinicus HNM0039 (99.

sp. nov., Isolated from Feces of Black Pig ().

An aerobic bacterium, designated as strain KD337-16T, was isolated from the fecal samples of a black pig. It exhibited spherical, non-motile and non−spore-forming, Gram-positive cells. KD337-16T was identified as a member of the genus Micrococcus through 16S rRNA gene sequencing, and its closest relatives were found to be Micrococcus endophyticus YIM 56238T (99.

Biodiversity risk assessment of genetically modified Chaetoceros gracilis for outdoor cultivation.

A genetically modified (GM) strain of the diatom Chaetoceros gracilis expressing the phosphite dehydrogenase gene (ptxD), which is a useful gene both for the biological containment and the avoidance of microbial contamination, was characterized to estimate the risk against the biodiversity by laboratory experiments. GM strain could grow in the medium containing phosphite as a sole source of phosphorus, while its general characteristics such as growth, salt tolerance, heat and dehydration resistance in the normal phosphate-containing medium were equivalent to those of wild type (WT) strain. The increase in potential toxicity of GM strain against plant, crustacean, fish and mammal was also disproved.

Resolution of housekeeping gene sequences used in MLSA for the genus and reclassification of and as heterotypic synonyms of .

Although 16S rRNA gene sequences are conventionally analysed in bacterial systematics, their resolution is not sufficient for species identification. Multilocus sequence analysis (MLSA) is a powerful method for species identification as well as the elucidation of phylogenetic relationships in the genus . Gene sequences of and are generally used in MLSA for species.

Characterization and Demonstration of Mock Communities as Control Reagents for Accurate Human Microbiome Community Measurements.

Standardization and quality assurance of microbiome community analysis by high-throughput DNA sequencing require widely accessible and well-characterized reference materials. Here, we report on newly developed DNA and whole-cell mock communities to serve as control reagents for human gut microbiota measurements by shotgun metagenomics and 16S rRNA gene amplicon sequencing. The mock communities were formulated as near-even blends of up to 20 bacterial species prevalent in the human gut, span a wide range of genomic guanine-cytosine (GC) contents, and include multiple strains with Gram-positive type cell walls.

Taxonomic Positions of a Nyuzenamide-Producer and Its Closely Related Strains.

sp. N11-34 is a producer of bicyclic peptides named nyuzenamides A and B. We elucidated its taxonomic position and surveyed its nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) gene clusters by whole genome analysis.

sp. nov., sp. nov., sp. nov. and sp. nov., isolated from paper mulberry in Taiwan.

Five Gram-stain-positive strains (M1-10, M1-13, M1-21, M2-14 and S1-1) were isolated from paper mulberry () in Taiwan. Cells were rod-shaped, non-motile, non-haemolytic, asporogenous, facultatively anaerobic, heterofermentative, and did not exhibit catalase and oxidase activities. Phylogenetic analysis of the 16S rRNA gene sequences revealed that these novel strains belonged to the genus .

Detection of hepatocarcinogens by combination of liver micronucleus assay and histopathological examination in 2-week or 4-week repeated dose studies.

Background: Currently, revisions to the ICH S1 guidance on rodent carcinogenicity testing are being proposed. Application of this approach would reduce the use of animals in accordance with the 3Rs principles (reduce/refine/replace). The method would also shift resources to focus on more scientific mechanism-based carcinogenicity assessments and promote safe and ethical development of new small molecule pharmaceuticals.

Unsaturated fatty acids and a prenylated tryptophan derivative from a rare actinomycete of the genus .

A genome mining survey combined with metabolome analysis of publicly available strains identified sp. RD010705, a strain belonging to an underexplored genus of rare actinomycetes, as a producer of new metabolites. HPLC-DAD-guided fractionation of its fermentation extracts resulted in the isolation of five new methyl-branched unsaturated fatty acids, (2,4)-2,4-dimethyl-2,4-octadienoic acid (), (2,4)-2,4,7-trimethyl-2,4-octadienoic acid (), ()-(-)-phialomustin B (), (2,4)-7-hydroxy-2,4-dimethyl-2,4-octadienoic acid (), (2,4)-7-hydroxy-2,4,7-trimethyl-2,4-octadienoic acid (), and one prenylated tryptophan derivative, 6-(3,3-dimethylallyl)--acetyl-ʟ-tryptophan ().