- Volume 64, Issue Pt_2, 2014
Volume 64, Issue Pt_2, 2014
- Notification List
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Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 63, part 11, of the IJSEM
More LessThis listing of names of prokaryotes published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles).
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- Special Collection: Genomics for Next-Generation Taxonomy and Phylogenetics of Micro-Organisms
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- Reviews
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Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea
More LessThe polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA–DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the Bacteria and Archaea coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of International Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.
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Use of gene sequence analyses and genome comparisons for yeast systematics
More LessDetection, identification and classification of yeasts have undergone a major transformation in the past decade and a half following application of gene sequence analyses and genome comparisons. Development of a database (barcode) of easily determined gene sequences from domains 1 and 2 (D1/D2) of large subunit rRNA and from the internal transcribed spacer (ITS) now permits many laboratories to identify species accurately and this has led to a doubling in the number of known species of yeasts over the past decade. Phylogenetic analysis of gene sequences has resulted in major revision of yeast systematics, resulting in redefinition of nearly all genera. Future work calls for application of genomics to refine our understanding of the species concept and to provide a better understanding of the boundaries of genera and higher levels of classification. This increased understanding of phylogeny is expected to allow prediction of the genetic potential of various clades and species for biotechnological applications and adaptation to environmental changes.
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Applications of next-generation sequencing to unravelling the evolutionary history of algae
More LessFirst-generation Sanger DNA sequencing revolutionized science over the past three decades and the current next-generation sequencing (NGS) technology has opened the doors to the next phase in the sequencing revolution. Using NGS, scientists are able to sequence entire genomes and to generate extensive transcriptome data from diverse photosynthetic eukaryotes in a timely and cost-effective manner. Genome data in particular shed light on the complicated evolutionary history of algae that form the basis of the food chain in many environments. In the Eukaryotic Tree of Life, the fact that photosynthetic lineages are positioned in four supergroups has important evolutionary consequences. We now know that the story of eukaryotic photosynthesis unfolds with a primary endosymbiosis between an ancestral heterotrophic protist and a captured cyanobacterium that gave rise to the glaucophytes, red algae and Viridiplantae (green algae and land plants). These primary plastids were then transferred to other eukaryotic groups through secondary endosymbiosis. A red alga was captured by the ancestor(s) of the stramenopiles, alveolates (dinoflagellates, apicomplexa, chromeridae), cryptophytes and haptophytes, whereas green algae were captured independently by the common ancestors of the euglenophytes and chlorarachniophytes. A separate case of primary endosymbiosis is found in the filose amoeba Paulinella chromatophora, which has at least nine heterotrophic sister species. Paulinella genome data provide detailed insights into the early stages of plastid establishment. Therefore, genome data produced by NGS have provided many novel insights into the taxonomy, phylogeny and evolutionary history of photosynthetic eukaryotes.
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- Methods
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Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
More LessAmong available genome relatedness indices, average nucleotide identity (ANI) is one of the most robust measurements of genomic relatedness between strains, and has great potential in the taxonomy of bacteria and archaea as a substitute for the labour-intensive DNA–DNA hybridization (DDH) technique. An ANI threshold range (95–96 %) for species demarcation had previously been suggested based on comparative investigation between DDH and ANI values, albeit with rather limited datasets. Furthermore, its generality was not tested on all lineages of prokaryotes. Here, we investigated the overall distribution of ANI values generated by pairwise comparison of 6787 genomes of prokaryotes belonging to 22 phyla to see whether the suggested range can be applied to all species. There was an apparent distinction in the overall ANI distribution between intra- and interspecies relationships at around 95–96 % ANI. We went on to determine which level of 16S rRNA gene sequence similarity corresponds to the currently accepted ANI threshold for species demarcation using over one million comparisons. A twofold cross-validation statistical test revealed that 98.65 % 16S rRNA gene sequence similarity can be used as the threshold for differentiating two species, which is consistent with previous suggestions (98.2–99.0 %) derived from comparative studies between DDH and 16S rRNA gene sequence similarity. Our findings should be useful in accelerating the use of genomic sequence data in the taxonomy of bacteria and archaea.
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Taxonomic use of DNA G+C content and DNA–DNA hybridization in the genomic age
More LessThe G+C content of a genome is frequently used in taxonomic descriptions of species and genera. In the past it has been determined using conventional, indirect methods, but it is nowadays reasonable to calculate the DNA G+C content directly from the increasingly available and affordable genome sequences. The expected increase in accuracy, however, might alter the way in which the G+C content is used for drawing taxonomic conclusions. We here re-estimate the literature assumption that the G+C content can vary up to 3–5 % within species using genomic datasets. The resulting G+C content differences are compared with DNA–DNA hybridization (DDH) similarities calculated in silico using the GGDC web server, with 70 % similarity as the gold standard threshold for species boundaries. The results indicate that the G+C content, if computed from genome sequences, varies no more than 1 % within species. Statistical models based on larger differences alone can reject the hypothesis that two strains belong to the same species. Because DDH similarities between two non-type strains occur in the genomic datasets, we also examine to what extent and under which conditions such a similarity could be <70 % even though the similarity of either strain to a type strain was ≥70 %. In theory, their similarity could be as low as 50 %, whereas empirical data suggest a boundary closer (but not identical) to 70 %. However, it is shown that using a 50 % boundary would not affect the conclusions regarding the DNA G+C content. Hence, we suggest that discrepancies between G+C content data provided in species descriptions on the one hand and those recalculated after genome sequencing on the other hand ≥1 % are due to significant inaccuracies of the applied conventional methods and accordingly call for emendations of species descriptions.
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Genotype to phenotype: identification of diagnostic vibrio phenotypes using whole genome sequences
Vibrios are ubiquitous in the aquatic environment and can be found in association with animal or plant hosts. The range of ecological relationships includes pathogenic and mutualistic associations. To gain a better understanding of the ecology of these microbes, it is important to determine their phenotypic features. However, the traditional phenotypic characterization of vibrios has been expensive, time-consuming and restricted in scope to a limited number of features. In addition, most of the commercial systems applied for phenotypic characterization cannot characterize the broad spectrum of environmental strains. A reliable and possible alternative is to obtain phenotypic information directly from whole genome sequences. The aim of the present study was to evaluate the usefulness of whole genome sequences as a source of phenotypic information. We performed a comparison of the vibrio phenotypes obtained from the literature with the phenotypes obtained from whole genome sequences. We observed a significant correlation between the previously published phenotypic data and the phenotypic data retrieved from whole genome sequences of vibrios. Analysis of 26 vibrio genomes revealed that all genes coding for the specific proteins involved in the metabolic pathways responsible for positive phenotypes of the 14 diagnostic features (Voges–Proskauer reaction, indole production, arginine dihydrolase, ornithine decarboxylase, utilization of myo-inositol, sucrose and l-leucine, and fermentation of d-mannitol, d-sorbitol, l-arabinose, trehalose, cellobiose, d-mannose and d-galactose) were found in the majority of the vibrios genomes. Vibrio species that were negative for a given phenotype revealed the absence of all or several genes involved in the respective biochemical pathways, indicating the utility of this approach to characterize the phenotypes of vibrios. The absence of the global regulation and regulatory proteins in the Vibrio parahaemolyticus genome indicated a non-vibrio phenotype. Whole genome sequences represent an important source for the phenotypic identification of vibrios.
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Conserved signature indels and signature proteins as novel tools for understanding microbial phylogeny and systematics: identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria
More LessGenome sequences are enabling applications of different approaches to more clearly understand microbial phylogeny and systematics. Two of these approaches involve identification of conserved signature indels (CSIs) and conserved signature proteins (CSPs) that are specific for different lineages. These molecular markers provide novel and more definitive means for demarcation of prokaryotic taxa and for identification of species from these groups. Genome sequences are also enabling determination of phylogenetic relationships among species based upon sequences for multiple proteins. In this work, we have used all of these approaches for studying the phytopathogenic bacteria belonging to the genera Dickeya , Pectobacterium and Brenneria . Members of these genera, which cause numerous diseases in important food crops and ornamental plants, are presently distinguished mainly on the basis of their branching in phylogenetic trees. No biochemical or molecular characteristic is known that is uniquely shared by species from these genera. Hence, detailed studies using the above approaches were carried out on proteins from the genomes of these bacteria to identify molecular markers that are specific for them. In phylogenetic trees based upon concatenated sequences for 23 conserved proteins, members of the genera Dickeya , Pectobacterium and Brenneria formed a strongly supported clade within the other Enterobacteriales . Comparative analysis of protein sequences from the Dickeya , Pectobacterium and Brenneria genomes has identified 10 CSIs and five CSPs that are either uniquely or largely found in all genome-sequenced species from these genera, but not present in any other bacteria in the database. In addition, our analyses have identified 10 CSIs and 17 CSPs that are specifically present in either all or most sequenced Dickeya species/strains, and six CSIs and 19 CSPs that are uniquely found in the sequenced Pectobacterium genomes. Finally, our analysis also identified three CSIs and one CSP that are specifically shared by members of the genera Pectobacterium and Brenneria , but absent in species of the genus Dickeya , indicating that the former two genera shared a common ancestor exclusive of Dickeya . The identified CSIs and CSPs provide novel tools for identification of members of the genera Dickeya and Pectobacterium and for delimiting these taxa in molecular terms. Descriptions of the genera Dickeya and Pectobacterium have been revised to provide information for these molecular markers. Biochemical studies on these CSIs and CSPs, which are specific for these genera, may lead to discovery of novel properties that are unique to these bacteria and which could be targeted to develop antibacterial agents that are specific for these plant-pathogenic bacteria.
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- Review
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A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species
Currently, bacterial taxonomy relies on a polyphasic approach based on the combination of phenotypic and genotypic characteristics. However, the current situation is paradoxical in that the genetic criteria that are used, including DNA–DNA hybridization, 16S rRNA gene sequence nucleotide similarity and phylogeny, and DNA G+C content, have significant limitations, but genome sequences that contain the whole genetic information of bacterial strains are not used for taxonomic purposes, despite the decreasing costs of sequencing and the increasing number of available genomes. Recently, we diversified bacterial culture conditions with the aim of isolating uncultivated bacteria. To classify the putative novel species that we cultivated, we used a polyphasic strategy that included phenotypic as well as genomic criteria (genome characteristics as well as genomic sequence similarity). Herein, we review the pros and cons of genome sequencing for taxonomy and propose that the incorporation of genome sequences in taxonomic studies has the advantage of using reliable and reproducible data. This strategy, which we name taxono-genomics, may contribute to the taxonomic classification of bacteria.
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- New Taxa
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- Archaea
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Methanobacterium movilense sp. nov., a hydrogenotrophic, secondary-alcohol-utilizing methanogen from the anoxic sediment of a subsurface lake
A novel strain of methanogenic archaea, designated MC-20T, was isolated from the anoxic sediment of a subsurface lake in Movile Cave, Mangalia, Romania. Cells were non-motile, Gram-stain-negative rods 3.5–4.0 µm in length and 0.6–0.7 µm in width, and occurred either singly or in short chains. Strain MC-20T was able to utilize H2/CO2, formate, 2-propanol and 2-butanol as substrate, but not acetate, methanol, ethanol, dimethyl sulfide, monomethylamine, dimethylamine or trimethylamine. Neither trypticase peptone nor yeast extract was required for growth. The major membrane lipids of strain MC-20T were archaeol phosphatidylethanolamine and diglycosyl archaeol, while archaeol phosphatidylinositol and glycosyl archaeol were present only in minor amounts. Optimal growth was observed at 33 °C, pH 7.4 and 0.08 M NaCl. Based on phylogenetic analysis of 16S rRNA gene sequences, strain MC-20T was closely affiliated with Methanobacterium oryzae FPiT (similarity 97.1 %) and Methanobacterium lacus 17A1T (97.0 %). The G+C content of the genomic DNA was 33.0 mol%. Based on phenotypic and genotypic differences, strain MC-20T was assigned to a novel species of the genus Methanobacterium for which the name Methanobacterium movilense sp. nov. is proposed. The type strain is MC-20T ( = DSM 26032T = JCM 18470T).
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Methanospirillum psychrodurum sp. nov., isolated from wetland soil
More LessA psychrotolerant methanogenic strain, X-18T, was isolated from the soil of the Madoi wetland at Qinghai, Tibetan plateau, China. Cells were wavy rods (11–62 µm long) with blunt tapered ends and Gram-stain-negative. Strain X-18T grew strictly anaerobically and produced methane exclusively from H2/CO2. Growth occurred in the temperature range of 4–32 °C and optimally at 25 °C. Growth pH ranged from 6.5 to 8.0 and the optimum was 7.0. The G+C content of the genomic DNA of strain X-18T was 44.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences and the alpha subunit of methyl-coenzyme M reductase indicated that strain X-18T was affiliated to the genus Methanospirillum and was most closely related to Methanospirillum lacunae Ki8-1T, with 96.3 % 16S rRNA gene sequence similarity. However, strain X-18T could be distinguished from the existing species of the genus Methanospirillum by its lower growth temperature and obligate hydrogenotrophic methanogenesis. On the basis of phenotypic characteristics and phylogenetic analysis, strain X-18T represents a novel species of the genus Methanospirillum , for which the name Methanospirillum psychrodurum sp. nov. is proposed and strain X-18T is assigned as the type strain ( = CGMCC 1.5186T = JCM 19216T).
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- Actinobacteria
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Arthrobacter gyeryongensis sp. nov., isolated from soil of a Gynostemma pentaphyllum field
More LessA Gram-stain-positive, flagellate, rod-shaped, catalase- and oxidase-positive bacterium, designated DCY72T, was isolated from the soil of a Gynostemma pentaphyllum field. Growth occurred at 4–34 °C (optimum 30 °C), at pH 4–10 (optimum pH 7), and with 0–5 % NaCl (w/v). The major menaquinones of strain DCY72T were MK-9(H2) (81.0 %) and MK-10(H2) (12.2 %). The major amino acid present in the cell-wall peptidoglycan was l-lysine. The major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The genomic DNA G+C content was 64.5 mol%. 16S rRNA gene sequence analysis revealed that strain DCY72T belonged to the family Micrococcaceae and was most closely related to Arthrobacter ramosus CCM 1646T (98.2 % similarity). The DNA–DNA relatedness between strain DCY72T and A. ramosus KACC 14391T (98.2 % 16S rRNA gene sequence similarity), Arthrobacter nitroguajacolicus KACC 14581T (97.6 %), Arthrobacter nicotinovorans KACC 20508T (97.3 %) and Arthrobacter aurescens KACC 20528T (97.3 %). was 12.9 %±0.3, 25.6 %±0.3, 26.6 %±0.5 and 23.2 %±0.9, respectively. On the basis of the phenotypic characteristics, genotypic analysis and physiological characteristics, strain DCY72T represents a novel species of the genus Arthrobacter , for which the name Arthrobacter gyeryo ngensis sp. nov. is proposed. The type strain is DCY72T ( = KCTC 33072T = JCM 18514T).
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Bifidobacterium moukalabense sp. nov., isolated from the faeces of wild west lowland gorilla (Gorilla gorilla gorilla)
Gram-staining-positive anaerobic rods were isolated from the faeces of a wild lowland gorilla (Gorilla gorilla gorilla) in Moukalaba-Doudou National Park, Gabon, and strain GG01T was taxonomically investigated. Based on phylogenetic analyses and specific phenotypic characteristics, the strain belonged to the genus Bifidobacterium . Phylogenetic analysis of its 16S rRNA gene sequence revealed that strain GG01T formed a single monophyletic cluster and had a distinct line of descent. Based on 16S rRNA gene sequence similarity, the type strains of Bifidobacterium catenulatum JCM 1194T (98.3 %) and Bifidobacterium pseudocatenulatum (98.1 %) JCM 1200T were the most closely related to this novel strain, although it was clear that they belonged to different species. hsp60 sequences also supported these relationships. The DNA G+C content of this novel strain was 60.1 mol%. Bifidobacterium moukalabense sp. nov. (type strain GG01T = JCM 18751T = DSM 27321T) is proposed.
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Actinomyces haliotis sp. nov., a bacterium isolated from the gut of an abalone, Haliotis discus hannai
More LessA novel, Gram-staining-positive, facultatively anaerobic, non-motile and coccus-shaped bacterium, strain WL80T, was isolated from the gut of an abalone, Haliotis discus hannai, collected from the northern coast of Jeju in Korea. Optimal growth occurred at 30 °C, pH 7–8 and with 1 % (w/v) NaCl. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that strain WL80T fell within the cluster of the genus Actinomyces , with highest sequence similarity to the type strains of Actinomyces radicidentis (98.8 % similarity) and Actinomyces urogenitalis (97.0 % similarity). The major cellular fatty acids were C18 : 1ω9c and C16 : 0. Menaquinone-10 (H4) was the major respiratory quinone. The genomic DNA G+C content of the isolate was 70.4 mol%. DNA–DNA hybridization values with closely related strains indicated less than 7.6 % genomic relatedness. The results of physiological, biochemical, chemotaxonomic and genotypic analyses indicated that strain WL80T represents a novel species of the genus Actinomyces , for which the name Actinomyces haliotis sp. nov. is proposed. The type strain is WL80T ( = KACC 17211T = JCM 18848T).
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Micromonospora polyrhachis sp. nov., an actinomycete isolated from edible Chinese black ant (Polyrhachis vicina Roger)
A novel actinomycete, designated strain NEAU-ycm2T, was isolated from edible Chinese black ants (Polyrhachis vicina Roger) and characterized using a polyphasic approach. The organism was found to have morphological and chemotaxonomic characteristics typical of the genus Micromonospora . The 16S rRNA gene sequence of strain NEAU-ycm2T showed highest similarity to those of Micromonospora sonneratiae 274745T (99.12 %), Micromonospora pattaloongensis TJ2-2T (98.85 %), Micromonospora pisi GUI 15T (98.76 %), Polymorphospora rubra TT 97-42T (98.42 %) and Micromonospora eburnea LK2-10T (98.21 %). Phylogenetic analysis based on the 16S rRNA gene and gyrB gene demonstrated that strain NEAU-ycm2T is a member of the genus Micromonospora and supported the close phylogenetic relationship to M. sonneratiae 274745T, M. pattaloongensis JCM 12833T and M. pisi GUI 15T. Furthermore, a combination of DNA–DNA hybridization and some physiological and biochemical properties indicated that the novel strain could be readily distinguished from its closest phylogenetic relatives. Therefore, it is proposed that NEAU-ycm2T represents a novel species of the genus of Micromonospora , for which the name Micromonospora polyrhachis sp. nov. is proposed. The type strain is NEAU-ycm2T ( = CGMCC 4.7100T = DSM 45886T).
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Streptomyces graminilatus sp. nov., isolated from bamboo litter
More LessA Gram-stain-positive, novel actinobacterium, designated strain JL-6T, was isolated from the litter of a bamboo (Sasa borealis) forest in Damyang, Korea. Strain JL-6T had white‐grey, smooth, cylindrical spores that were borne in straight, long spore-chains. The novel strain grew aerobically at 15–28 °C (optimum, 28 °C), pH 4.0–8.0 (optimum, pH 5.5) and with 0–1.5 % (w/v) NaCl. The cell-wall peptidoglycan contained ll-diaminopimelic acid, glutamic acid, alanine and glycine. The predominant menaquinones were MK-9(H6) and MK-9(H8). Whole-cell hydrolysates mainly contained glucose and ribose. Phosphatidylinositol and phosphatidylcholine were the diagnostic phospholipids. The G+C content of the genomic DNA was 72.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JL-6T belonged to the genus Streptomyces with sequence similarities ranging from 97.3 % to 98.3 %. However, DNA–DNA hybridization between JL-6T and the closest related strain, Streptomyces turgidiscabies , ATCC 700248T and other closely related species in the genus Streptomyces showed <50 % relatedness. Based on these observations, strain JL-6T is proposed to represent a novel species of the genus Streptomyces , for which the name Streptomyces graminilatus sp. nov. is proposed. The type strain is JL-6T ( = KACC 16470T = NBRC 108882T).
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Description of Galbitalea soli gen. nov., sp. nov., and Frondihabitans sucicola sp. nov.
Bacterial strains KIS82-1T and GRS42T were isolated from soil and from sap of Acer mono, respectively, in the Republic of Korea. Both strains were aerobic, Gram-stain-positive, mesophilic, rod-shaped and motile. Phylogenetically, both strains belonged to the family Microbacteriaceae of the phylum Actinobacteria . The 16S rRNA gene sequence of strain KIS82-1T showed the highest similarity to those of Frondihabitans peucedani RS-15T (97.6 %), Frigoribacterium mesophilum MSL-08T (97.2 %) and Labedella gwakjiensis KSW2-17T (97.0 %), while strain GRS42T showed the highest 16S rRNA gene sequence similarity to Frondihabitans peucedani RS-15T (98.7 %), Frondihabitans cladoniiphilus CafT13T (98.4 %), Frondihabitans australicus E1HC-02T (98.2 %) and Frigoribacterium faeni 801T (97.3 %). The 16S rRNA gene sequence similarity between GRS42T and KIS82-1T was 97.0 %. Phylogenetic trees indicated that strain GRS42T was firmly grouped into the genus Frondihabitans , while strain KIS82-1T did not show a clear affiliation to any genus within the family Microbacteriaceae . Strain KIS82-1T showed type B1β peptidoglycan with 2,4-diamino-l-butyric acid as the diamino acid. It had MK-11, MK-10 and MK-12 as respiratory quinones, anteiso-C15 : 0, iso-C16 : 0 and iso-C14 : 0 as major cellular fatty acids and diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid as predominant polar lipids. The peptidoglycan of strain GRS42T was of type B2β with d-ornithine as the diamino acid. The strain contained MK-8, MK-9 and MK-7 as respiratory quinones, summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) as major cellular fatty acid and diphosphatidylglycerol, phosphatidylglycerol and three unknown glycolipids as predominant polar lipids. Strain GRS42T revealed low DNA–DNA hybridization (<50 % relatedness) with closely related strains. Based on the data obtained in the present polyphasic taxonomic study, we propose that strain KIS82-1T represents a novel genus and species and that strain GRS42T represents a novel species in the family Microbacteriaceae . The genus Galbitalea gen. nov. is proposed, with strain KIS82-1T ( = KACC 15520T = NBRC 108727T) as the type strain of the type species, Galbitalea soli sp. nov. Strain GRS42T ( = KACC 15521T = NBRC 108728T) is proposed as the type strain of Frondihabitans sucicola sp. nov.
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Glaciihabitans tibetensis gen. nov., sp. nov., a psychrotolerant bacterium of the family Microbacteriaceae, isolated from glacier ice water
More LessA Gram-stain-positive, aerobic, non-spore-forming, short-rod-shaped bacterium, designated strain MP203T, was isolated from ice water of Midui Glacier in Tibet Autonomous Region, China. The strain was psychrotolerant, growing at 0–25 °C. 16S rRNA gene sequence analysis showed that strain MP203T was most similar to Frigoribacterium faeni NBRC 103066T, Compostimonas suwonensis KACC 13354T, Frigoribacterium mesophilum KCTC 19311T, Marisediminicola antarctica CCTCC AB 209077T and Alpinimonas psychrophila JCM 18951T, with similarities of 97.4, 97.2, 97.2, 97.1 and 97.1 %, respectively. The maximum-likelihood phylogenetic tree indicated that strain MP203T clustered with nine genera of the family Microbacteriaceae , namely Frigoribacterium , Compostimonas , Marisediminicola , Alpinimonas , Frondihabitans , Clavibacter , Subtercola , Klugiella and Agreia . However, bootstrap analysis showed that there was no significance in the branching pattern of the linage comprising strain MP203T and any existing generic lineage of the family Microbacteriaceae . DNA–DNA hybridization results indicated levels of relatedness between strain MP203T and Marisediminicola antarctica CCTCC AB 209077T, Frigoribacterium faeni NBRC 103066T, Frigoribacterium mesophilum KCTC 19311T, Compostimonas suwonensis KACC 13354T and Alpinimonas psychrophila JCM 18951T were 25.8±7.3, 29.6±7.6, 19.7±6.7, 16.0±4.2 and 12.4±5.1 % (mean±sd), respectively. The G+C content of the genomic DNA was 64.1 mol%. Analysis of the cell-wall peptidoglycan revealed that the peptidoglycan structure of strain MP203T was B10 type with Gly[l-Hse]–d-Glu–d-DAB, containing 2, 4-diaminobutyric acid (DAB) as a diagnostic amino acid. The cell-wall sugars were rhamnose, ribose, mannose and glucose. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso A-C15 : 1. An unusual compound identified as anteiso-C15 : 0-DMA (1, 1-dimethoxy-anteiso-pentadecane) was also present in strain MP203T. The predominant menaquinone was MK-10. Diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), one unknown glycolipid and four unknown lipids were detected in the polar lipid extracts. As strain MP203T was distinguishable from phylogenetically related genera in the family Microbacteriaceae in terms of its physiological and chemotaxonomic characteristics and phylogenetic position, it was considered to represent a novel species of a new genus. Thus, the name Glaciihabitans tibetensis gen. nov., sp. nov. is proposed. The type strain of Glaciihabitans tibetensis is MP203T ( = CGMCC 1.12484T = KCTC 29148T).
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Emended description of Actinoplanes friuliensis and description of Actinoplanes nipponensis sp. nov., antibiotic-producing species of the genus Actinoplanes
In 2000, an actinomycete strain that showed strong antibacterial activity in culture extracts was isolated from a soil sample. The antibiotic activity corresponds to a lipopeptide complex that was named friulimycin, as the producing micro-organism was isolated from a soil sample from the region of Friaul in Italy. Taxonomic investigations showed that the producer strain belonged to a novel species of the genus Actinoplanes , for which the name Actinoplanes friuliensis was proposed. During further taxonomic studies, another antibiotic-producing isolate belonging to the genus Actinoplanes , FH 2241T, was characterized; in a patent, the name ‘Actinoplanes nipponensis’ was proposed for this strain. This organism was shown to be related to A. friuliensis . ‘A. nipponensis’ was never described in detail and the name was never validly published. Here we present a complete description of Actinoplanes nipponensis sp. Nov. (type strain FH 2241T = ATCC 31145T = DSM 43867T) and an emended description of Actinoplanes friuliensis (type strain HAG 010964T = DSM 45797T = CCUG 63250T).
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- Firmicutes and Related Organisms
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Brevibacillus fulvus sp. nov., isolated from a compost pile
More LessTwo strains, designated K2814T and K282, were isolated from a compost pile in Japan. These strains were Gram-stain-variable, aerobic, motile and endospore-forming rods. The strains produced a characteristic brown non-diffusible pigment. The 16S rRNA gene sequences of the strains were 100 % identical and had high similarity to that of Brevibacillus levickii LMG 22481T (97.3 %). Phylogenetic analyses based on 16S rRNA gene sequences revealed that these strains belong to the genus Brevibacillus . Strains K2814T and K282 contained meso-diaminopimelic acid in their cell walls. Strains K2814T and K282 contained MK-7 (96.0 and 97.2 %, respectively) and MK-8 (4.0 and 2.8 %, respectively) as the major and minor menaquinones, respectively. Their major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0 and iso-C17 : 0. The DNA G+C contents of strains K2814T and K282 were 48.8 and 49.8 mol%, respectively. Polar lipids of strain K2814T were composed of phosphatidyl-N-methylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, three unidentified polar lipids, an unidentified aminophospholipid and an unidentified aminolipid. The level of DNA–DNA relatedness between strains K2814T and K282 was 99 or 100 %, and levels between strain K2814T and the type strains of seven related species of the genus Brevibacillus , including Brevibacillus levickii LMG 22481T, were below 59 %. From the chemotaxonomic and physiological data and the levels of DNA–DNA relatedness, these two strains should be classified as representing a novel species of the genus Brevibacillus , for which the name Brevibacillus fulvus sp. nov. (type strain K2814T = JCM 18162T = ATCC BAA-2417T = DSM 25523T) is proposed.
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Kurthia huakuii sp. nov., isolated from biogas slurry, and emended description of the genus Kurthia
A novel facultatively anaerobic bacterium, designated strain LAM0618T, was isolated from biogas slurry samples collected from the large-scale anaerobic digester of Modern Farming Corporation in Hebei Province, China. Cells of strain LAM0618T were Gram-stain-positive, motile, non-spore-forming and short-rod-shaped. The optimal temperature and pH for growth were 30 °C and 7.0, respectively. The strain did not require NaCl for growth but tolerated up to 70 g NaCl l−1. The major fatty acids of strain LAM0618T were iso-C15 : 0, anteiso-C15 : 0, iso-C14 : 0, C16 : 0 and C18 : 0. The predominant menaquinones of strain LAM0618T were menaquinone 7 (MK-7) and menaquinone 6 (MK-6). The main polar lipids of strain LAM0618T were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and six unknown glycolipids. The genomic DNA G+C content was 41 mol% as determined by the T m method. Analysis of the 16S rRNA gene sequence revealed that strain LAM0618T was a member of the genus Kurthia , and was most closely related to ‘ Kurthia massiliensis’ DSM 24639, Kurthia zopfii DSM 20580T, Kurthia gibsonii DSM 20636T and Kurthia sibirica DSM 4747T, with 96.9, 95.7, 95.6 and 94.9 % sequence similarity, respectively. Based on its phenotypic and genotypic properties, strain LAM0618T is suggested to represent a novel species of the genus Kurthia , for which the name Kurthia huakuii sp. nov. is proposed. The type strain is LAM0618T ( = ACCC 06121T = JCM 19187T).
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- Proteobacteria
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Sulfitobacter porphyrae sp. nov., isolated from the red alga Porphyra yezoensis
Gram-stain-negative, aerobic, halophilic bacteria, designated SCM-1T, LCM10-1 and CTBL-B-147, were isolated from modified half-strength SWM-III medium, PES medium and thalli after laboratory cultivation of a red alga, Porphyra yezoensis. Phylogenetic analysis of 16S rRNA gene sequences indicated that the new isolates were affiliated to the genus Sulfitobacter of the class Alphaproteobacteria , and the 16S rRNA gene sequence similarity of the new isolates with the closest related species, Sulfitobacter mediterraneus CH-B427T, was 98.8 %. The DNA G+C contents of the new isolates were in the range of 61.4–62.3 mol%. DNA–DNA relatedness values of strain SCM-1T with other type strains of the genus Sulfitobacter were less than 15.9 %. The new isolates contained Q-10 as the predominant ubiquinone, phosphatidylcholine, phosphatidylglycerol, an unidentified amino lipid and an unidentified lipid as the main polar lipids, and C18 : 1ω7c, C19 : 1ω7c and C16 : 0 as the major fatty acids (>10 % of the total). Strain SCM-1T could be differentiated from Sulfitobacter mediterraneus JCM 21792T by 35 morphological and phenotypic characteristics. On the basis of the phylogenetic, genetic and phenotypic properties of the new isolates, the name Sulfitobacter porphyrae sp. nov. is proposed, with strain SCM-1T ( = LMG 27110T = NBRC 109054T) as the type strain.
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Pseudoalteromonas xiamenensis sp. nov., a marine bacterium isolated from coastal surface seawater
More LessA Gram-negative, oxidase- and catalase-positive, rod-shaped, non-spore-forming, motile, aerobic bacterium, designated Y2T, was isolated from surface seawater of Yundang Lake, Xiamen, China. The strain was able to grow in the presence of 0.5–6.0 % NaCl (optimum 1.0–1.5 %), at pH 5–10 (optimum pH 8) and at 10–40 °C (optimum 25 °C). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Y2T belongs to the genus Pseudoalteromonas , with the highest sequence similarity of 94.9 % to Pseudoalteromonas tunicata D2T; within the genus Pseudoalteromonas , it showed the lowest similarity of 92.8 % to Pseudoalteromonas denitrificans ATCC 43337T. The G+C content of the chromosomal DNA of strain Y2T was 45.1 mol%. The predominant fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0, C12 : 0 3-OH and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c). The only respiratory quinone detected was Q-8. Based on the phylogenetic and phenotypic characteristics, strain Y2T represents a novel species of the genus Pseudoalteromonas , for which the name Pseudoalteromonas xiamenensis sp. nov. is proposed; the type strain is Y2T ( = CGMCC 1.12157T = JCM 18779T).
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Methyloceanibacter caenitepidi gen. nov., sp. nov., a facultatively methylotrophic bacterium isolated from marine sediments near a hydrothermal vent
A moderately thermophilic, methanol-oxidizing bacterium (strain Gela4T) was isolated from methane-utilizing mixed-culture originating from marine sediment near a hydrothermal vent. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain Gela4T was closely related to members of the genus ‘Methyloligella’ (94.7 % similarity) within the class Alphaproteobacteria . Strain Gela4T was a Gram‐staining‐negative and aerobic organism. Cells were rod-shaped and non-motile. The temperature range for growth of strain Gela4T was 19–43 °C (optimal growth at 35 °C). Strain Gela4T tolerated up to 9 % NaCl with an optimum at 1 %. The organism was a facultative methylotroph that could utilize methanol, methylamine, trimethylamine and a variety of multi-carbon compounds. The major cellular fatty acid and major respiratory quinone were C18 : 1ω7c and ubiquinone-10, respectively. The predominant phospholipids were phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 63.9 mol%. On the basis of the morphological, physiological, biochemical and genetic information, a novel genus and species, Methyloceanibacter caenitepidi is proposed, with Gela4T ( = NBRC 109540T = DSM 27242T) as the type strain.
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Photobacterium aquae sp. nov., isolated from a recirculating mariculture system
More LessA Gram-staining-negative, heterotrophic, facultatively anaerobic bacterium, designated AE6T, was isolated from a grouper (Epinephelus malabaricas) culture tank in a recirculating mariculture system located in Tianjin, China. Strain AE6T was able to grow at 15–40 °C (optimum, 30–35 °C), at pH 5.5–10.0 (optimum, pH 7.0–7.5) and in the presence of 0.5–7 % (w/v) NaCl (optimum, 2–3 %). It contained Q-8 as the predominant respiratory quinone, phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) as the major polar lipids and C16 : 1ω7c/C16 : 1ω6c (40.4 %), C18 : 1ω7c (15.5 %) and C16 : 0 (13.5 %) as the predominant cellular fatty acids. The genomic DNA G+C content was 47.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain AE6T belonged to the genus Photobacterium (94.2–96.8 % of 16S rRNA gene sequence similarity) and formed a distinct phylogenetic lineage within the genus and exhibited the highest sequence similarity to Photobacterium aphoticum CECT 7614T (96.8 %). Multilocus sequence analysis (MLSA) using four loci (gyrB, rpoA, pyrH and recA) also revealed that strain AE6T was phylogenetically related to the genus Photobacterium . Based on the phylogenetic, chemotaxonomic and phenotypic evidence, strain AE6T is considered to represent a novel species of the genus Photobacterium , for which the name Photobacterium aquae sp. nov. is proposed. The type strain is AE6T ( = CGMCC 1.12159T = JCM 18480T).
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Cellvibrio diazotrophicus sp. nov., a nitrogen-fixing bacteria isolated from the rhizosphere of salt meadow plants and emended description of the genus Cellvibrio
More LessTwo Gram-reaction-negative, aerobic, nitrogen-fixing, rod-shaped bacteria, designated strains E20 and E50T, were isolated from the rhizosphere of salt meadow plants Plantago winteri and Hordeum secalinum, respectively, near Münzenberg, Germany. Based on the 16S rRNA gene sequence analysis both strains E20 and E50T are affiliated with the genus Cellvibrio , sharing the highest similarity with Cellvibrio gandavensis LMG 18551T (96.4 %) and (97.1 %), respectively. Strains E20 and E50T were oxidase and catalase-positive, grew at a temperature range between 16 and 37 °C and in the presence of 0–5 % NaCl (w/v). The DNA G+C contents were 52.1 mol% (E20) and 51.6 mol% (E50T). Major fatty acids of strains E20 and E50T were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C18 : 1ω7c, C12 : 0, C18 : 0 and C12 : 0 3-OH. The DNA–DNA relatedness of the strains to Cellvibrio gandavensis LMG 18551T was 39 % for strain E20 and 58 % for strain E50T. The nitrogen fixation capability of strains E20 and E50T was confirmed by the acetylene reduction assay. On the basis of our polyphasic taxonomic study, strains E20 and E50T represent a novel species of the genus Cellvibrio , for which the name Cellvibrio diazotrophicus is proposed. The type strain of Cellvibrio diazotrophicus is E50T ( = LMG 27267T = KACC 17069T). An emended description of the genus Cellvibrio is proposed based on the capability of fixing nitrogen and growth in presence of up to 5 % NaCl (w/v).
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Marinomonas fungiae sp. nov., isolated from the coral Fungia echinata from the Andaman Sea
More LessA novel aerobic marine bacterium, strain AN44T, was isolated from the coral Fungia echinata sampled from the Andaman Sea, India. Cells were Gram-negative, motile and rod-shaped. Oxidase and catalase tests were positive. Heterotrophic growth was observed at pH 5.5–10 and at 16–42 °C, with optimum growth at pH 7–8 and 28 °C. Strain AN44T grew in the presence of 0.5–11 % (w/v) NaCl; the optimal NaCl concentration for growth was 3–5 %. The DNA G+C content was 47.8 mol%. Predominant cellular fatty acids of strain AN44T were C18 : 1ω7c, C16 : 1ω7c/C16 : 1ω6c, C16 : 0, C10 : 0 3-OH, C12 : 0, C10 : 0, C14 : 0 and C18 : 0. The sole isoprenoid ubiquinone was Q-8. The polar lipids were an unidentified phospholipid, an unidentified aminophospholipid and two unidentified glycolipids. 16S rRNA gene sequence comparisons revealed that strain AN44T clustered within the radiation of the genus Marinomonas and showed similarity of 97.9 % with Marinomonas ostreistagni UST010306-043T, 97.8 % with Marinomonas aquimarina 11SM4T, 97.1 % with Marinomonas brasilensis R-40503T and 97.0 % with Marinomonas communis 8T. However, DNA–DNA relatedness between strain AN44T and closely related type strains was well below 70 %. On the basis of the data from the present polyphasic taxonomic study, strain AN44T is considered to represent a novel species of the genus Marinomonas , for which the name Marinomonas fungiae sp. nov. is proposed. The type strain is AN44T ( = JCM 18476T = LMG 27065T).
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Diaphorobacter aerolatus sp. nov., isolated from air, and emended description of the genus Diaphorobacter
A Gram-stain-negative, non-motile, aerobic rod, designated 8604S-37T, was isolated from an outdoor air sample collected in Suwon region, Republic of Korea. The isolate was catalase-positive and oxidase-negative. 16S rRNA gene sequence analysis indicated that strain 8604S-37T was most closely related to Diaphorobacter nitroreducens NA10BT and Diaphorobacter oryzae RF3T, with which it shared 97.0 % 16S rRNA gene sequence similarity. Strain 8604S-37T grew at 10–37 °C (optimum 28 °C; no growth occurred at 4 or 40 °C) and pH 5–9 (optimum pH 7). The strain tolerated up to 3 % NaCl (w/v) (optimum 0 %). The only respiratory quinone was ubiquinone-8 (Q-8). The polar lipid profile comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one unknown aminolipid. The major fatty acids were C16 : 0, summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C17 : 0 cyclo, and the predominant hydroxy fatty acid was C10 : 0 3-OH. Strain 8604S-37T exhibited less than 50 % DNA–DNA relatedness with Diaphorobacter nitroreducens KACC 13856T and Diaphorobacter oryzae KACC 16857T. The DNA G+C content was 65 mol%. Strain 8604S-37T represents a novel species of the genus Diaphorobacter , for which the name Diaphorobacter aerolatus sp. nov. is proposed. The type strain is 8604S-37T ( = KACC 16536T = NBRC 108926T). An emended description of the genus Diaphorobacter is also proposed.
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Desulfatiferula berrensis sp. nov., a n-alkene-degrading sulfate-reducing bacterium isolated from estuarine sediments
A novel sulfate-reducing bacterium designated strain BE2801T was isolated from oil-polluted estuarine sediments (Berre Lagoon, France). Cells were Gram-stain-negative, motile, slightly curved or vibrioid rods. Optimal growth of strain BE2801T occurred at 30–32 °C, 0.5–1.5% NaCl (w/v) and pH 7.2–7.4. Strain BE2801T grew with C4 to C20 fatty acids or C12 to C20 n-alkenes as electron donors. Acetate and carbon dioxide were the oxidation products. The major cellular fatty acids were C16 : 0, C16 : 1ω7c and C18 : 1ω7. The DNA G+C content was 50.2 mol%. 16S rRNA and dsrAB gene sequence analysis indicated that strain BE2801T was a member of the family Desulfobacteraceae within the class Deltaproteobacteria . DNA–DNA hybridization with the most closely related taxon demonstrated 14.8 % relatedness. Based on phenotypic and phylogenetic evidence, strain BE2801T ( = DSM 25524T = JCM 18157T) is proposed to be a representative of a novel species of the genus Desulfatiferula , for which the name Desulfatiferula berrensis sp. nov. is suggested.
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Paenirhodobacter enshiensis gen. nov., sp. nov., a non-photosynthetic bacterium isolated from soil, and emended descriptions of the genera Rhodobacter and Haematobacter
More LessA Gram-reaction-negative, facultatively anaerobic, non-motile, rod-shaped, non-photosynthetic bacterial strain, DW2-9T, was isolated from soil. The highest 16S rRNA gene sequence similarities were found to Rhodobacter capsulatus ATCC 11166T (97.1 %), Rhodobacter viridis JA737T (96.4 %), Rhodobacter maris JA276T (96.2 %), Rhodobacter veldkampii ATCC 35703T (96.0 %), Haematobacter massiliensis CCUG 47968T (96.0 %), Haematobacter missouriensis CCUG 52307T (95.9 %) and Rhodobacter aestuarii JA296T (95.7 %). The genomic DNA G+C content was 67.2 mol% and the major respiratory quinone was ubiquinone 10 (Q-10). The major cellular fatty acids (>5 %) were C18 : 1ω7c, C16 : 0, C19 : 0 cyclo ω8c and summed feature 3 (one or more of iso-C15 : 0 2-OH, C16 : 1ω6c and C16 : 1ω7c). However, unlike species of the genus Rhodobacter , strain DW2-9T neither formed internal photosynthetic membranes nor produced photosynthetic pigments. DNA–DNA hybridization between strain DW2-9T and R. capsulatus JCM 21090T showed a relatedness of 33 %. Strain DW2-9T contained phosphatidylethanolamine, phosphatidylglycerol and an unknown aminophospholipid as major polar lipids, which differed from those of species of the genera Rhodobacter and Haematobacter . In addition to the differences in phylogenetic position and polar lipid types, strain DW2-9T could be distinguished from species of the genus Haematobacter by the cultivation conditions. On the basis of our polyphasic taxonomic analysis, strain DW2-9T is considered to represent a novel genus and species, for which the name Paenirhodobacter enshiensis gen. nov., sp. nov. is proposed. The type strain of Paenirhodobacter enshiensis is DW2-9T ( = CCTCC AB 2011145T = KCTC 15169T). Emended descriptions of the genera Rhodobacter and Haematobacter are also proposed.
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Pseudomonas kunmingensis sp. nov., an exopolysaccharide-producing bacterium isolated from a phosphate mine
More LessA Gram-stain-negative, rod-shaped, exopolysaccharide-producing, strictly aerobic bacterium with a single polar flagellum, designated strain HL22-2T, was isolated from a phosphate mine situated in a suburb of Kunmming in Yunnan province in south-western China. The taxonomic status of this strain was evaluated by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HL22-2T was related to members of the genus Pseudomonas . 16S rRNA gene sequence similarities between strain HL22-2T and Pseudomonas xanthomarina KMM 1447T, Pseudomonas alcaliphila AL15-21T and Pseudomonas stutzeri ATCC 17588T were 98.9, 98.10 % and 98.06 %, respectively. The major cellular fatty acids were C18 : 1ω7c, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The DNA G+C content was 60.3 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness values, strain HL22-2T represents a novel species of the genus Pseudomonas , for which the name Pseudomonas kunmingensis sp. nov. is proposed. The type strain is HL22-2T ( = CGMCC 1.12273T = DSM 25974T).
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Novosphingobium arabidopsis sp. nov., a DDT-resistant bacterium isolated from the rhizosphere of Arabidopsis thaliana
More LessAn aerobic, Gram-stain-negative, rod-shaped, DDT-resistant bacterium, designated strain CC-ALB-2T, was isolated from the Arabidopsis thaliana rhizosphere. Strain CC-ALB-2T was able to grow at 25–37 °C, at pH 5.0–8.0, with 1.0 % (w/v) NaCl and tolerate up to 200 mg l−1 DDT. 16S rRNA gene sequence analysis of strain CC-ALB-2T showed highest sequence similarity to Novosphingobium stygium KCTC 2891T (97.1 %) and Novosphingobium soli DSM 22821T (96.8 %), and lower levels of similarity (<97.0 %) to other species of the genus Novosphingobium . The major fatty acid profile consisted of C14 : 0 2-OH (13.1 %), C16 : 0 (10.0 %), C15 : 0 iso 3-OH (5.8 %), C16 : 1ω7c/C16 : 1ω6c (summed feature 3, 24.7 %) and C18 : 1ω7c/C18 : 1ω6c (summed feature 8, 42.4 %). The polar lipid profile constitutes sphingoglycolipid, glycolipid, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylglycerol and phosphatidylcholine. The polyamine pattern showed a predominance of spermidine as the major polyamine. The predominant quinone system was ubiquinone (Q-10). The DNA G+C content was 68.9±0.1 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic features, strain CC-ALB-2T is proposed to represent a novel species of the genus Novosphingobium for which the name Novosphingobium arabidopsis sp. nov. is proposed. The type strain is CC-ALB-2T ( = BCRC 80571T = JCM 18896T).
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Photobacterium aestuarii sp. nov., a marine bacterium isolated from a tidal flat
More LessA Gram-staining-negative, motile, weakly halophilic and facultatively aerobic bacterium, designated strain YA11T, was isolated from tidal flat sediment at Yeongam Bay, South Korea. Strain YA11T grew at 10–30 °C (optimum, 20 °C), at pH 6.0–10.0 (optimum, pH 6.5–7.5) and in the presence of 1–6 % (w/v) NaCl (optimum, 2–3 %). The major cellular fatty acids of the strain were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The DNA G+C content of the genomic DNA was 44.2 mol%. Strain YA11T contained Q-8 as the sole respiratory quinone. A phylogenetic tree based on 16S rRNA gene sequences showed that strain YA11T formed a distinct phyletic lineage within the genus Photobacterium and the 16S rRNA gene sequence similarities between strain YA11T and the type strains of species of the genus Photobacterium ranged between 94.0 and 96.4 %. Based on the phenotypic, chemotaxonomic and molecular properties, strain YA11T represents a novel species of the genus Photobacterium , for which the name Photobacterium aestuarii sp. nov. is proposed, with strain YA11T( = KACC 16912T = JCM 18592T) as the type strain.
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Altererythrobacter xiamenensis sp. nov., an algicidal bacterium isolated from red tide seawater
A Gram-stain-negative, yellow-pigmented, aerobic bacterial strain, designated LY02T, was isolated from red tide seawater in Xiamen, Fujian Province, China. Growth was observed at temperatures from 4 to 44 °C, at salinities from 0 to 9 % and at pH from 6 to 10. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the isolate was a member of the genus Altererythrobacter , which belongs to the family Erythrobacteraceae . Strain LY02T was related most closely to Altererythrobacter marensis MSW-14T (97.2 % 16S rRNA gene sequence similarity), followed by Altererythrobacter ishigakiensis JPCCMB0017T (97.1 %), Altererythrobacter epoxidivorans JCS350T (97.1 %) and Altererythrobacter luteolus SW-109T (97.0 %). The dominant fatty acids were C18 : 1ω7c, C17 : 1ω6c and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). DNA–DNA hybridization showed that strain LY02T possessed low DNA–DNA relatedness to A. marensis MSW-14T, A. ishigakiensis JPCCMB0017T, A. epoxidivorans JCS350T and A. luteolus SW-109T (mean±sd of 33.2±1.3, 32.1±1.0, 26.7±0.7 and 25.2±1.1 %, respectively). The G+C content of the chromosomal DNA was 61.2 mol%. The predominant respiratory quinone was ubiquinone-10 (Q-10). According to its morphology, physiology, fatty acid composition and 16S rRNA gene sequence data, the novel strain most appropriately belongs to the genus Altererythrobacter , but can readily be distinguished from recognized species. The name Altererythrobacter xiamenensis sp. nov. is proposed (type strain LY02T = CGMCC 1.12494T = KCTC 32398T = NBRC 109638T).
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Luteimonas abyssi sp. nov., isolated from deep-sea sediment
More LessThree Gram-stain-negative, strictly aerobic, rod-shaped with single polar flagellum, yellow-pigmented bacteria, designated strains XH031T, XH038-3 and XH80-1, were isolated from deep-sea sediment of the South Pacific Gyre (41° 51′ S 153° 6′ W) during the Integrated Ocean Drilling Program (IODP) Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolates belonged to the genus Luteimonas and showed the highest 16S rRNA gene sequence similarity with Luteimonas aestuarii B9T (96.95 %), Luteimonas huabeiensis HB2T (96.93 %) and Xanthomonas cucurbitae LMG 690T (96.92 %). The DNA G+C contents of the three isolates were 70.2–73.9 mol%. The major fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C11 : 0 and C16 : 010-methyl and/or iso-C17 : 1ω9c. The major respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one unknown phospholipid. On the basis of data from polyphasic analysis, the three isolates represent a novel species of the genus Luteimonas , for which the name Luteimonas abyssi sp. nov. is proposed. The type strain is XH031T ( = DSM 25880T = CGMCC 1.12611T).
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- Bacteroidetes
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Flavobacterium tructae sp. nov. and Flavobacterium piscis sp. nov., isolated from farmed rainbow trout (Oncorhynchus mykiss)
Four Gram-staining-negative, catalase- and oxidase-positive, pale-orange pigmented bacterial strains (435-08T, 47B-3-09, 412R-09T and 60B-3-09) were isolated from diseased rainbow trout. Analysis of their 16S rRNA gene sequences suggested their adscription to the genus Flavobacterium . Strains formed two phylogenetic groups represented by strains 435-08T and 47B-3-09 (group A), and strains 412R-09T and 60B-3-09 (group B) displaying 16S rRNA sequence similarities greater than 99.8–99.9 % within their respective groups. Strain 435-08T exhibited the highest levels of similarity with Flavobacterium aquidurense WB-1.1.56T (98.6 % sequence similarity) and strain 412R-09T with Flavobacterium frigidimaris KUC-1T and Flavobacterium aquidurense WB-1.1.56T (98.9 % and 98.6 % sequence similarity, respectively). DNA–DNA hybridization studies showed low levels of relatedness between strain 435-08T and strain 412R-09T and between both strains and the most closely related species of the genus Flavobacterium . The genomic DNA G+C contents of strains 435-08T and 412R-09T were 36.2 and 34.3 mol%, respectively. The predominant respiratory quinone of both strains was MK-6 and the major fatty acids were iso-C15 : 0, C16 : 1ω7c and C15 : 0. The two groups of strains could be distinguished from each other and from related species of the genus Flavobacterium by a number of phenotypic properties. Phylogenetic, genotypic and phenotypic evidence indicated that strains of groups A and B represent two novel species of the genus Flavobacterium , for which the names Flavobacterium tructae sp. nov. (type strain 435-08T = CECT 7791T = CCUG 60100T) and Flavobacterium piscis sp. nov. (type strain 412R-09T = CECT 7911T = CCUG 60099T) are proposed.
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Nonlabens antarcticus sp. nov., a psychrophilic bacterium isolated from glacier ice, and emended descriptions of Nonlabens marinus Park et al. 2012 and Nonlabens agnitus Yi and Chun 2012
More LessA Gram-negative, proteorhodopsin-containing, orange pigmented, rod-shaped and strictly aerobic bacterium, designated strain AKS622T, was isolated from a glacier core collected from the coast of King George Island, Antarctica. 16S rRNA gene sequence analysis revealed that strain AKS622T was affiliated to the genus Nonlabens of the family Flavobacteriaceae and showed highest similarity to Nonlabens marinus S1-08T (97.9 %). The level of DNA–DNA relatedness between strain AKS622T and N. marinus S1-08T was 46 %. Optimal growth of strain AKS622T was observed at pH 7.0, at 15 °C and with 2.0 % NaCl. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C16 : 0, iso-C16 : 0 3-OH, C17 : 0 2-OH and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The DNA G+C content was 37.9 mol%. The major respiratory quinone was MK-6. Phosphatidylethanolamine, four unidentified glycolipids, three unidentified aminolipids and one unidentified lipid were detected as major polar lipids. On the basis of the data from this polyphasic taxonomic study, it was concluded that strain AKS622T represents a novel species within the genus Nonlabens , for which the name Nonlabens antarcticus sp. nov. is proposed. The type strain is AKS622T ( = KCCM 43019T = JCM 14068T). Emended descriptions of N. marinus Park et al. 2012 and Nonlabens agnitus Yi and Chun 2012 are given.
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Flavobacterium spartansii sp. nov., a pathogen of fishes, and emended descriptions of Flavobacterium aquidurense and Flavobacterium araucananum
More LessTwo strains (T16T and S12) of a Gram-reaction-negative, rod-shaped, yellow-pigmented bacterium were recovered from kidneys of feral spawning adult Chinook salmon (Oncorhynchus tshawytscha) and the gills of captive-reared Chinook salmon fingerlings suffering a mortality episode, respectively. Polyphasic characterization revealed that these strains possessed gliding motility, contained a flexirubin-type pigment, proteolysed multiple substrates (i.e. gelatin, casein and elastin), and had a mean DNA G+C content of 35.6 mol%. Sequencing of the 16S rRNA gene demonstrated that strains T16T and S12 were nearly identical to one another (>99 % similarity) and were placed within the genus Flavobacterium , with Flavobacterium aquidurense CCUG 59847T (98.3 %), Flavobaterium araucananum CCUG 61031T (98.2 %) and Flavobacterium frigidimaris (AB183888, 98.1 %) being their closest relatives. Subsequent phylogenetic analyses using neighbour-joining, maximum-parsimony and Bayesian methodologies demonstrated that strains T16T and S12 formed a well-supported clade within the genus Flavobacterium that was distinct from other Flavobacterium species. The major fatty acid constituents of strains T16T and S12 were iso-C15 : 0, C16 : 1ω6c and/or C16 : 1ω7c, iso-C17 : 0 3-OH, and iso-C15 : 0 3-OH according to fatty acid methyl ester analysis. The mean level of DNA–DNA relatedness between strain T16T and F. aquidurense CCUG 59847T and F. araucananum CCUG 61031T was 23 and 29 %, respectively. Thus, the data accumulated in this study support the suggestion that strains T16T and S12 represent a novel species of the genus Flavobacterium , for which the name Flavobacterium spartansii sp. nov. is proposed. The type strain is T16T ( = LMG 27337T = ATCC BAA-2541T). Emended descriptions of F. aquidurense and F. araucananum are also proposed.
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Mucilaginibacter soyangensis sp. nov., isolated from a lake
More LessA non-motile, yellow–orange-pigmented bacterial strain, designated HME6664T, was isolated from Lake Soyang, Republic of Korea. The major fatty acids of strain HME6664T were summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c; 44.7 %) and iso-C15 : 0 (20.2 %). The DNA G+C content was 40.8 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HME6664T formed a lineage within the genus Mucilaginibacter . Strain HME6664T was closely related to Mucilaginibacter ximonensis (96.7 %), Mucilaginibacter dorajii (96.5 %) and Mucilaginibacter lappiensis (96.3 %). On the basis of the evidence presented in this study, strain HME6664T represents a novel species of the genus Mucilaginibacter , for which the name Mucilaginibacter soyangensis sp. nov., is proposed. The type strain is HME6664T ( = KCTC 23261T = CECT 7824T).
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Chitinophaga taiwanensis sp. nov., isolated from the rhizosphere of Arabidopsis thaliana
More LessAn aerobic, Gram-stain-negative, rod-shaped bacterium (strain CC-ALB-1T) was isolated from the rhizosphere of Arabidopsis thaliana. Strain CC-ALB-1T was able to grow at 20–30 °C, pH 5.0–8.0 and with up to 1.0 % (w/v) NaCl. 16S rRNA gene sequence analysis showed that strain CC-ALB-1T had the highest sequence similarity to Chitinophaga ginsengisegetis Gsoil 040T (96.9 %) and Chitinophaga niastensis JS16-4T (96.7 %); lower levels of similarity (<97.0 %) were observed to strains of all other species of the genus Chitinophaga . The fatty acid profile consisted of iso-C15 : 0, iso-C17 : 0 3-OH, C15 : 1ω5c, C16 : 1ω5c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The polar lipid profile contained phosphatidylethanolamine, two unidentified aminolipids and five unidentified lipids. The predominant quinone system was menaquinone 7 (MK-7). The DNA G+C content was 53.4±0.4 mol%. Based on its phylogenetic, phenotypic and chemotaxonomic features, strain CC-ALB-1T is proposed to represent a novel species within the genus Chitinophaga , for which the name Chitinophaga taiwanensis sp. nov. is proposed. The type strain is CC-ALB-1T ( = BCRC 80570T = JCM 18895T).
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Wenyingzhuangia marina gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from a recirculating mariculture system
More LessA Gram-stain-negative, strictly aerobic and heterotrophic bacterial strain, designed strain D1T, was isolated from a recirculating mariculture system in Tianjin, China. Its taxonomic position was determined using a polyphasic approach. Cells of strain D1T were non-flagellated short rods, 0.3–0.5 µm wide and 0.5–1.0 µm long. Growth was observed at 15–30 °C (optimum, 25 °C), at pH 5.5–9.0 (optimum, pH 6.5–7.0) and in the presence of 1–8 % (w/v) NaCl (optimum, 2–3 %). Cells contained carotenoid pigments but not flexirubin-type pigments. Strain D1T contained MK-6 as the sole menaquinone and phosphatidylethanolamine (PE) as the sole phospholipid and four unidentified lipids. The major cellular fatty acids (>10 %) were iso-C15 : 0 (23.2 %), iso-C17 : 0 3-OH (15.2 %), C16 : 1ω7c/C16 : 1ω6c (14.3 %), iso-C15 : 0 3-OH (13.5 %) and iso-C15 : 1 G (10.8 %). 16S rRNA gene sequence analyses indicated that strain D1T belonged to the family Flavobacteriaceae and showed closest phylogenetic relationship to the genus Lutibacter , with highest sequence similarity to Lutibacter aestuarii MA-My1T (92.2 %). The DNA G+C content of strain D1T was 35.9 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain D1T was considered to represent a novel species in a new genus of the family Flavobacteriaceae , for which the name Wenyingzhuangia marina gen. nov., sp. nov. is proposed. The type strain of the type species is D1T ( = CGMCC 1.12162T = JCM 18494T).
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Aquimarina amphilecti sp. nov., isolated from the sponge Amphilectus fucorum
A Gram-stain-negative, rod-shaped, orange-coloured, catalase- and oxidase-positive, non-motile bacterium, designated strain 92VT, was isolated from the marine sponge Amphilectus fucorum, collected from Lough Hyne, County Cork, Ireland. 16S rRNA gene sequence analysis revealed that strain 92VT clustered with members of the family Flavobacteriaceae , the closest member being Aquimarina latercula NCIMB 1399T, with a gene sequence similarity of 97.5 %. Strain 92VT required seawater for growth with optimal growth occurring at 25 °C, at pH 6–7 and with 3 % (w/v) NaCl. MK-6 was the sole respiratory quinone present and the major fatty acids were iso-C17 : 0 3-OH, iso-C15 : 0, iso-C17 : 1ω9c and iso-C15 : 0 3-OH. The DNA G+C content was 36.1 mol%. Combined phenotypic differences and phylogenetic analysis indicate that strain 92VT represents a novel species of the genus Aquimarina , for which the name Aquimarina amphilecti sp. nov. is proposed. The type strain is 92VT ( = NCIMB 14723T = DSM 25232T).
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Robertkochia marina gen. nov., sp. nov., of the family Flavobacteriaceae, isolated from surface seawater, and emended descriptions of the genera Joostella and Galbibacter
A Gram-staining-negative, orange-pigmented, strictly aerobic, carotenoid-producing, rod-shaped, non-flagellated, non-spore-forming bacterium, motile by gliding, designated strain CC-AMO-30DT, was isolated from surface seawater collected near Taichung harbour, Taiwan. Strain CC-AMO-30DT shared pairwise 16S rRNA gene sequence similarities of 94.8, 93.7 and 92.5 % with the type strains of the type species of the genera Joostella , Pustulibacterium and Galbibacter , respectively, and formed a distinct monophyletic lineage in phylogenetic trees. The major fatty acids (≥5 % of total) were iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH, iso-C16 : 0 and anteiso-C15 : 0. The polar lipid profile consisted of phosphatidylethanolamine, four unidentified lipids, two unidentified aminolipids and an unidentified phospholipid. The major polyamine was the triamine sym-homospermidine. The DNA G+C content was 47.1 mol% and the predominant respiratory quinone was menaquinone-6 (MK-6). Based on the phylogenetic distinctiveness and distinguishing phenotypic characteristics, strain CC-AMO-30DT represents a novel genus and species of the family Flavobacteriaceae , for which the name Robertkochia marina gen. nov., sp. nov. is proposed; the type strain of the type species Robertkochia marina is CC-AMO-30DT ( = JCM 18552T = BCRC 80469T). Emended descriptions of the genera Joostella and Galbibacter are also proposed.
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Zunongwangia mangrovi sp. nov., isolated from mangrove (Avicennia marina) rhizosphere, and emended description of the genus Zunongwangia
More LessA Gram-stain-negative, strictly aerobic, slightly halophilic, non-motile and rod-shaped bacterial strain, designated P2E16T, was isolated from mangrove (Avicennia marina) rhizosphere, collected at Devipattinam mangroves, Tamil Nadu, India. Strain P2E16T grew optimally at pH 7.0–8.0, at 25–28 °C and in the presence of 2–3 % (w/v) NaCl. 16S rRNA gene analysis showed that strain P2E16T was phylogenetically closely related to the genus Zunongwangia , with Zunongwangia profunda SM-A87T as the closest related type strain (98.2 % 16S rRNA gene sequence similarity) and less than 93 % 16S rRNA gene sequence similarity to all other members of the family Flavobacteriaceae . Strain P2E16T contained MK-6 as the major respiratory quinone, phosphatidylethanolamine as the predominant polar lipid and iso-C15 : 0 (17.8 %), iso-C17 : 0 3-OH (15.1 %), C15 : 0 (12.8 %), iso-C17 : 1ω9c (9.8 %), iso-C15 : 1 G (9.0 %), and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH; 7.1 %) as the major fatty acids. The DNA G+C content was 34.3 mol%. Differential phenotypic properties, together with the phylogenetic distinctiveness and low DNA–DNA relatedness demonstrated that strain P2E16T was distinct from the type strain of Zunongwangia profunda . On the basis of these presented data, strain P2E16T is considered to represent a novel species of the genus Zunongwangia , for which the name Zunongwangia mangrovi sp. nov. is proposed. The type strain is P2E16T ( = DSM 24499T = LMG 26237T = KCTC 23496T). An emended description of the genus Zunongwangia is also provided.
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Mucilaginibacter defluvii sp. nov., isolated from a dye wastewater treatment facility
More LessA non-motile, rod-shaped bacterium, designated strain A5T, was isolated from a dye wastewater treatment facility in the Republic of Korea. Cells were Gram-reaction-negative, aerobic, catalase-positive and oxidase-negative. The major fatty acids were C16 : 0, C18 : 0, iso-C15 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and the major polar lipid was phosphatidylethanolamine. The strain contained MK-7 as the only isoprenoid quinone and the DNA G+C content was 41.2 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain A5T forms an evolutionary lineage within the radiation encompassing the members of genus Mucilaginibacter , with Mucilaginibacter lutimaris BR-3T as its nearest neighbour (96.6 % sequence similarity). A number of phenotypic characteristics distinguished strain A5T from the members of the genus Mucilaginibacter . On the basis of the evidence presented in this study, strain A5T represents a novel species, for which the name Mucilaginibacter defluvii sp. nov. is proposed. The type strain is A5T ( = KCTC 23922T = JCM 18283T).
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Vitellibacter soesokkakensis sp. nov., isolated from the junction between the ocean and a freshwater spring and emended description of the genus Vitellibacter
More LessA Gram-stain-negative, aerobic, non-spore-forming, non-flagellated, motile by gliding and rod-shaped bacterial strain, RSSK-12T, was isolated from the zone where the ocean and a freshwater spring meet at Jeju island, South Korea. Strain RSSK-12T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0–3.0 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain RSSK-12T clustered with the type strains of two Vitellibacter species, with which it exhibited 94.8–96.9 % sequence similarity. Sequence similarities to the type strains of species of the genus Aequorivita and of other recognized species were 94.7–95.5 % and less than 91.9 %, respectively. Strain RSSK-12T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids of strain RSSK-12T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain RSSK-12T was 38.9 mol%. Differential phenotypic properties, together with phylogenetic distinctiveness, revealed that strain RSSK-12T is separate from other Vitellibacter species. On the basis of the data presented, strain RSSK-12T is considered to represent a novel species of the genus Vitellibacter , for which the name Vitellibacter soesokkakensis sp. nov. is proposed. The type strain is RSSK-12T ( = KCTC 32536T = CECT 8398T).
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Cnuella takakiae gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from Takakia lepidozioides
More LessA Gram-staining-negative, rod-shaped and non-spore-forming bacterium, designated strain RG1-1T, was isolated from Takakia lepidozioides collected from Gawalong glacier in Tibet, China, and characterized by using a polyphasic taxonomic approach. The predominant fatty acids of strain RG1-1T were iso-C15 : 0 (19.8 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 17.0 %), C16 : 0 (9.9 %) and iso-C17 : 0 3-OH (9.4 %); its major polar lipids were phosphatidylethanolamine, four unidentified aminolipids, one unidentified phospholipid, one unidentified aminoglycolipid, one unidentified glycolipid, and three unidentified lipids. Strain RG1-1T contained MK-7 as the dominant menaquinone, and the G+C content of its genomic DNA was 49.1 mol%. Strain RG1-1T exhibited the highest 16S rRNA gene sequence similarity (91.8 %) with Flavisolibacter ginsengiterrae Gsoil 492T and Flavisolibacter ginsengisoli Gsoil 643T. Phylogenetic analysis showed that strain RG1-1T was a member of the family Chitinophagaceae , phylum Bacteroidetes . On the basis of 16S rRNA gene sequence analysis, and phenotypic and chemotaxonomic data, strain RG1-1T is considered to represent a novel species of a novel genus, for which the name Cnuella takakiae gen. nov., sp. nov. is proposed. The type strain is RG1-1T ( = CGMCC 1.12492T = DSM 26897T).
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Proposal of Vibrionimonas magnilacihabitans gen. nov., sp. nov., a curved Gram-stain-negative bacterium isolated from lake water
A mesophilic bacterium appearing as curved rod-shaped cells was isolated from Lake Michigan water. It exhibited highest similarities with Sediminibacterium ginsengisoli DCY13T (94.4 %); Sediminibacterium salmoneum NJ-44T (93.6 %) and Hydrotalea flava CCUG 51397 T (93.1 %) while similarities with other recognized species were <92.0 %. The primary polar lipid was phosphatidylethanolamine, with moderate amounts of two unidentified glycolipids, three unknown polar lipids, one unknown aminophospholipid and one aminolipid. The primary respiratory quinone was MK-7 and sym-homospermidine was the primary polyamine. The major cellular fatty acids were iso-C15 : 1G, iso-C15 : 0, iso-C16 : 0 3-OH and iso-C17 : 0 3-OH, with moderate amounts of iso-C16 : 0. The presence of glycolipids differentiated the novel strains from related genera. The DNA mol% G+C content of the type strain MU-2T was 45.2. Results for other phenotypic and molecular analyses indicated that strain MU-2T is a representative of a novel genus and species for which the name Vibrionimonas magnilacihabitans is proposed. The type strain is MU-2T ( = NRRL B-59231 = DSM 22423).
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Myroides xuanwuensis sp. nov., a mineral-weathering bacterium isolated from forest soil
More LessA Gram-reaction-negative, aerobic, non-motile, yellow-pigmented, rod-shaped bacterium, designated strain TH-19T, was isolated from a forest soil sample in Jiangsu province, China. On the basis of 16S rRNA gene sequence similarity, strain TH-19T was shown to belong to the genus Myroides , a member of the phylum Bacteroidetes , and was related to Myroides odoratimimus LMG 4029T (98.7 % similarity), Myroides profundi D25T (98.2 %) and Myroides marinus JS-08T (97.5 %). Strain TH-19T contained menaquinone-6 (MK-6) as the predominant menaquinone, and the dominant fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. The DNA G+C content of strain TH-19T was 37.2 mol%. The DNA–DNA relatedness values of strain TH-19T with Myroides odoratimimus JCM 7460T, Myroides profundi D25T and Myroides marinus JS-08T were below 70 %. Based on phenotypic, genotypic and phylogenetic evidence, it is suggested that strain TH-19T represents a novel species of the genus Myroides , for which the name Myroides xuanwuensis sp. nov. is proposed. The type strain is TH-19T ( = CCTCC AB 2013145T = JCM 19200T).
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Falsiporphyromonas endometrii gen. nov., sp. nov., isolated from the post-partum bovine uterus, and emended description of the genus Porphyromonas Shah and Collins 1988
More LessTwo black-pigmented, anaerobic bacterial strains, designated LMM 40T and LMM 41, were isolated from the bovine post-partum endometrium of two Holstein cows. The 16S rRNA gene sequences of the two strains were identical and showed the highest similarity to the 16S rRNA gene sequence of the type strain of Porphyromonas crevioricanis (90.2 %) but only 85.1 % 16S rRNA gene sequence similarity to the type strain of the type species of the genus Porphyromonas , Porphyromonas asaccharolytica . The major fatty acid profiles of the two strains were similar to those of species of the genus Porphyromonas , containing iso-C15 : 0 as the major component and moderate amounts of anteiso-C15 : 0, iso-C13 : 0, C15 : 0 and C16 : 0. Hydroxylated fatty acids, such as iso-C14 : 0 3-OH, iso-C16 : 0 3-OH and iso-C17 : 0 3-OH, were also detected. The quinone profiles were dominated by the menaquinones MK-8 and MK-9, while spermidine was the major polyamine. The polar lipid profiles contained major amounts of phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminophospholipid and two unidentified lipids and minor amounts of phosphatidylglycerol, an unidentified aminolipid, a second unidentified aminophospholipid and an unidentified glycolipid. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The genomic DNA G+C contents of LMM 40T and LMM 41 were 40.7 and 41.3 mol%, respectively. Based on a polyphasic approach, including phylogenetic analysis, physiological and biochemical tests as well as metabolic fingerprinting, it is proposed that the two strains are members of a novel genus and species, for which the name Falsiporphyromonas endometrii gen. nov., sp. nov. is proposed. The type strain of Falsiporphyromonas endometrii is LMM 40T ( = DSM 27210T = CCUG 64267T). An emended description of the genus Porphyromonas is also presented.
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 40 (1990)
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Volume 39 (1989)
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Volume 36 (1986)
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Volume 31 (1981)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 24 (1974)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 15 (1965)
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Volume 14 (1964)
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Volume 9 (1959)
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Volume 7 (1957)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)