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1.
Isolate RS1 T isolated from used metalworking fluid was found to be a Gram-negative, motile, and non-spore forming rod. Based on phylogenetic
analyses with 16S rRNA, isolate RS1 T was placed into the mendocina sublineage of Pseudomonas. The major whole cell fatty acids were C 18:1ω7c (32.6%), C 16:0 (25.5%), and C 15:0 ISO 2OH/C 16:1ω7c (14.4%). The sequence similarities of isolate RS1 T based on gyrB and rpoD genes were 98.9 and 98.0% with Pseudomonas pseudoalcaligenes, and 98.5 and 98.1% with Pseudomonas oleovorans, respectively. The ribotyping pattern showed a 0.60 similarity with P. oleovorans ATCC 8062 T and 0.63 with P. pseudoalcaligenes ATCC17440 T. The DNA G + C content of isolate RS1 T was 62.2 mol.%. The DNA–DNA relatedness was 73.0% with P. oleovorans ATCC 8062 T and 79.1% with P. pseudoalcaligenes ATCC 17440 T. On the basis of morphological, biochemical, and molecular studies, isolate RS1 T is considered to represent a new subspecies of P. oleovorans. Furthermore, based on the DNA–DNA relatedness (>70%), chemotaxonomic, and molecular profile, P. pseudoalcaligenes ATCC 17440 T and P. oleovorans ATCC 8062 T should be united under the same name; according to the rules of priority, P. oleovorans, the first described species, is the earlier synonym and P. pseudoalcaligenes is the later synonym. As a consequence, the division of the species P. oleovorans into two novel subspecies is proposed: P. oleovorans subsp. oleovorans subsp. nov. (type strain ATCC 8062 T = DSM 1045 T = NCIB 6576 T), P. oleovorans subsp. lubricantis subsp. nov. (type strain RS1 T = ATCC BAA-1494 T = DSM 21016 T). 相似文献
2.
Microbiota analysis of blown pack spoiled salami revealed five distinguishable Lactobacillus isolates we could not assign to a known species. Two of the isolates (TMW 1.2172 T and TMW 1.1920) are rod-shaped, whilst three isolates (TMW 1.2098 T, TMW 1.2118 and TMW 1.2188) appear coccus shaped or as short rods. All isolates are Gram-stain positive, facultative anaerobic, catalase and oxidase negative, non-motile and non-sporulating. Phylogenetic analysis of the 16S rRNA, dnaK, pheS and rpoA gene sequences revealed two distinct lineages within the genus Lactobacillus (L.). The isolates are members of the Lactobacillus alimentarius group with Lactobacillus ginsenosidimutans DSM 24154 T (99.4% 16S similarity ), Lactobacillus versmoldensis DSM 14857 T (97.9%) and Lactobacillus furfuricola DSM 27174 T (97.7%) as phylogenetic closest related species and L. alimentarius DSM 20249 T (97.7%) and Lactobacillus paralimentarius DSM 13961 T (97.5%) as closest relatives, respectively. Average Nucleotide Identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the isolates and their close related type strains are lower than 80% and 25%, respectively. For both designated type strains, the peptidoglycan type is A4α l-Lys-d-Asp and the major fatty acids are C 16:0, C 18:1ω9c and summed feature 7. Based on phylogenetic, phenotypic and chemotaxonomic analysis we demonstrated that the investigated isolates belong to two novel Lactobacillus species for which we propose the names Lactobacillus salsicarnum with the type strain TMW 1.2098 T = DSM 109451 T = LMG 31401 T and Lactobacillus halodurans with the type strain TMW 1.2172 T = DSM 109452 T = LMG 31402 T. 相似文献
3.
Strain OCN044T was isolated from the homogenised tissue and mucus of an apparently healthy Acropora cytherea coral fragment collected from the western reef terrace of Palmyra Atoll in the Northern Line Islands and was taxonomically evaluated with a polyphasic approach. The morphological and chemotaxonomic properties are consistent with characteristics of the genus Vibrio: Gram-stain-negative rods, oxidase- and catalase-positive, and motile by means of a polar flagellum. Strain OCN044T can be differentiated as a novel subspecies based on 21 differences among chemotaxonomic features (e.g., fatty acids percentages for C12:0 and C18:1 ω7c), enzymatic activities (e.g., DNase and cystine arylamidase), and carbon sources utilized (e.g., L-xylose and D-melezitose) from its nearest genetic relative. Phylogenetic analysis and genomic comparisons show close evolutionary relatedness to Vibrio tetraodonis A511T but the overall genomic relatedness indices identify strain OCN044T as a distinct subspecies. Based on a polyphasic characterisation, differences in genomic and taxonomic data, strain OCN044T represents a novel subspecies of V. tetraodonis A511T, for which the name Vibrio tetraodonis subsp. pristinus subsp. nov. is proposed. The type strain is OCN044T (=?LMG 31895T?=?DSM 111778T). 相似文献
4.
Twelve isolates from jeotgal, a Korean high-salt-fermented seafood, identified as Staphylococcus equorum were compared by phenotypic and genotypic methods to determine their precise taxonomic identities at the subspecies level. Four strains and three strains had complete 16S rRNA gene sequence matches with S. equorum subsp. equorum DSM 20674 T and S. equorum subsp. linens DSM 15097 T, respectively. Five strains showed 99.9 % identity with the sequences of both type strains. In our DNA–DNA hybridization analyses among two type strains and two isolates, the similarities were over 72 % and were higher than the similarities presented at the subspecies proposal. Physiological characteristics such as sugar utilization, β-galactosidase activity, novobiocin resistance and salt tolerance, which were adopted for subspecies separation, could not be applied to assign the isolates to a taxonomic unit. Antibiotic susceptibility, hemolytic activity, biofilm formation and protein profiles did not present markers to divide the isolates into either of the subspecies. Multilocus sequence typing of the sequences of the 16S rRNA gene and five housekeeping genes did not produce any coherent relationship among the isolates and type strains. Repetitive element-PCR fingerprinting using ERIC (enterobacterial repetitive intergenic consensus) primers classified 12 isolates to three genotypes, and the genotypes of both type strains coincided with two isolates expressing different characteristics. Based on these phenotypic and genotypic analyses results, we propose to unify the present two subspecies of S. equorum into one species, S. equorum. 相似文献
5.
A total of 26 Gram-negative, motile, gently curved, and rod-shaped isolates were recovered, during a study to determine the faeco-prevalence of Helicobacter spp. in urban wild birds. Pairwise comparisons of the 16S rRNA gene sequences indicated that these isolates belonged to the genus Helicobacter and phylogenetic analysis based on the 16S rRNA gene sequences showed that the isolates were separated into two divergent groups. The first group consisted of 20 urease-positive isolates sharing the highest 16S rRNA gene sequence identity levels of 98.5–98.6% to H. mustelae ATCC 43772 T, while the second group contained six urease-negative isolates with the sequence identity level of 98.5% to the type strain of H. pametensis ATCC 51478 T. Five isolates were chosen and subjected to comparative whole-genome analysis. The phylogenetic analysis of the 16S rRNA, gyrA and atpA gene sequences showed that Helicobacter isolates formed two separate phylogenetic clades, differentiating the isolates from the other Helicobacter species. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses between strains faydin-H8 T, faydin-H23 T and their close neighbors H. anseris MIT 04-9362 T and H. pametensis ATCC 51478 T, respectively, confirmed that both strains represent novel species in the genus Helicobacter. The DNA G+C contents of the strains faydin-H8 T and faydin-H23 T are 32.0% and 37.6%, respectively. The results obtained for the characterization of the wild bird isolates indicate that they represent two novel species, for which the names Helicobacter anatolicus sp. nov., and Helicobacter kayseriensis sp. nov., are proposed, with faydin-H8 T(=LMG 32237 T = DSM 112312 T) and faydin-H23 T(=LMG 32236 T = CECT 30508 T) as respective type strains. 相似文献
6.
Gram-negative, facultatively anaerobic bacteria were isolated from symptomatic oak tissue in the UK and USA. Partial gyrB sequencing placed ten strains in the genus Brenneria, with B. goodwinii as the closest phylogenetic relative. The strains were investigated further using a polyphasic approach including MLSA (based on partial gyrB, rpoB, infB and atpD gene sequences), 16S rRNA gene sequencing, DNA–DNA relatedness studies and both phenotypic and chemotaxonomic assays. The MLSA and 16S rRNA gene analyses separated the strains into two groups based on origin, suggesting that they belong to Brenneria as two novel species. However, the DNA–DNA relatedness values revealed a closer relationship between the groups and indicated that they should belong to the same species. As the two groups of strains from the UK and USA can be differentiated from each other phenotypically and by ERIC PCR fingerprints, it is proposed to classify them as novel subspecies of a novel Brenneria species. The name Brenneria roseae sp. nov. (FRB 222 T = LMG 27714 T = NCPPB 4581 T) is proposed, with Brenneria roseae subsp. roseae ssp. nov. (FRB 222 T = LMG 27714 T = NCPPB 4581 T) for the strains from the UK and Brenneria roseae subsp. americana ssp. nov. (FRB 223 T = LMG 27715 T = NCPPB 4582 T) for the strains from the USA. 相似文献
7.
Thirteen coagulase-negative, oxidase-negative, and novobiocin-susceptible staphylococci were isolated from human clinical specimens. The isolates were differentiated from known staphylococcal species on the basis of 16S rRNA, hsp60, rpoB, dnaJ, tuf, and gap gene sequencing, automated ribotyping, (GTG) 5-PCR fingerprinting, and MALDI-TOF MS analysis. Phylogenetic analysis based on the 16S rRNA gene sequence indicated phylogenetic relatedness of the analyzed strains to Staphylococcus haemolyticus, Staphylococcus hominis, Staphylococcus devriesei, and Staphylococcus lugdunensis. DNA–DNA hybridization experiments between representative strains CCM 8418 T, CCM 8421 T, and the closest phylogenetic neighbors confirmed that the isolates represent novel Staphylococcus species, for which the name Staphylococcus petrasii sp. nov. is proposed. Genotypic and phenotypic analyses unambiguously split the strains into two closely related subclusters. Based on the results, two novel subspecies S. petrasii subsp. petrasii subsp. nov. and S. petrasii subsp. croceilyticus subsp. nov. are proposed, with type strains CCM 8418 T (=CCUG 62727 T) and CCM 8421 T (=CCUG 62728 T), respectively. 相似文献
8.
A novel bacterium capable of fixing nitrogen was isolated from plantain rhizosphere soil in China. The isolate, designated YN-83 T, is Gram-positive, aerobic, motile and rod-shaped (0.4–0.6 μm × 1.9–2.6 μm). Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain YN-83 T was a member of the genus Cohnella. High similarity of 16S rRNA gene sequence was found between YN-83 T and Cohnella ginsengisoli DSM18997 T (97.99%), whereas the similarity was below 96.0% between YN-83 T and the other Cohnella species. DNA–DNA relatedness between strain YN-83 T and C. ginsengisoli DSM18997 T was 27.4 ± 6.2%. The DNA G+C content of strain YN-83 T was 59.3 mol%. The predominant isoprenoid quinone was MK-7 and the major fatty acids were anteiso-C 15:0 (44.3%), iso-C 15:0 (11.3%), iso-C 16:0 (18.6%) and C 16:0 (7.7%). The polar lipids of strain YN-83 T consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, lyso- phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. On the basis of phenotypic and chemotaxonomic properties, 16S rRNA gene sequence, G+C content and DNA–DNA hybridization, strain YN-83 T represents a novel species of the genus Cohnella, for which the name Cohnella plantaginis sp. nov. (type strain YN-83 T = DSM 25424 T = CGMCC 1.12047 T) is proposed. 相似文献
9.
Four red-pigmented isolates, with optimum growth temperatures of approximately 55–60 °C and an optimum pH for growth between 7.5 and 8.5, were recovered from hot springs in Central France. Phylogenetic analysis of the 16S rRNA gene sequences showed that these organisms represented a new species of the genus Meiothermus. The new isolates could be distinguished from other strains of the species of the genus Meiothermus primarily by the glycolipid profile and fatty acid composition because these organisms lacked the hydroxy fatty acids and the glycolipid variant GL-1a found in all other isolates of the species of Meiothermus examined. On the basis of the results presented here we propose the name Meiothermus rufus for the new species, which is represented by strains CAL-4 T (=DSM 22234 T=LMG 24878 T) and CAL-12 (=DSM 22235=LMG 24879). We also propose emending the genus Meiothermus to include strains that have only one glycolipid instead of two glycolipid variants. 相似文献
10.
Two red-pigmented isolates, with optimum growth temperatures between 45 and 50 °C, were recovered from a hot spring in the Furnas, Área da Fonte 1825 on the Island of São Miguel in the Azores. Phylogenetic analysis of the 16S rRNA gene sequences showed that these organisms represented a new species of the genus Meiothermus. These new isolates could be distinguished from other strains of the species of the genus Meiothermus primarily by the fatty acid composition and polar lipid pattern, since they did not possess 2-OH fatty acids or glycolipid variant GL-1a. Moreover, the two new isolates had the lowest growth temperature range of any of the known species of the genus Meiothermus. On the basis of the results presented here we propose the name Meiothermus granaticius for the new species represented by strains AF-68 T (=DSM 23260 T = LMG 25524 T) and AF-49 (=DSM 23259 = LMG 25525). 相似文献
11.
A novel actinomycete, designated strain KLBMP 1111 T, was isolated from the root of the oil-seed plant Jatropha curcas L. collected from Sichuan Province, south-west China. Strain KLBMP 1111 T formed a distinct branch in the 16S rRNA gene phylogenetic tree together with the type strains in the genus Kibdelosporangium, with the highest similarity to Kibdelosporangium aridum subsp. aridum DSM 43828 T (98.8%), K. aridum subsp. largum DSM 44150 T (98.1%) and Kibdelosporangium philippinense DSM 44226 T (98.1%). The organism produced sporangium-like structures, the typical morphological characteristic of the genus Kibdelosporangium. The chemotaxonomic properties of this strain were also consistent with those of the genus Kibdelosporangium: the peptidoglycan contained meso-diaminopimelic acid; the predominant menaquinone was MK-9(H 4); phospholipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylinositol
and an unknown phospholipid; iso-C 16:0, C 16:0, anteiso-C 15:0 and iso-C 15:0 as the predominant cellular fatty acids and the G+C content was 67.2 mol%. DNA–DNA hybridization values between strain KLBMP
1111 T and the three Kibdelosporangium species were less than 50%. This strain had the ability to produce a siderophore, utilized 1-aminocyclopropane-1-carboxylic
acid (ACC) as sole source of nitrogen and possessed ACC deaminase enzyme. Based on genotypic and phenotypic data, strain KLBMP
1111 T represents a novel species in the genus Kibdelosporangium. We propose the name Kibdelosporangium phytohabitans sp. nov. for this species. The type strain is the strain KLBMP 1111 T (=KCTC 19775 T = CCTCC AA 2010001 T). 相似文献
13.
A polyphasic taxonomic study was performed on seven Bacillus-like bacteria isolated from three hypersaline and alkaline lakes located in China, Kenya and Tanzania. All strains were moderately halophilic and alkaliphilic, Gram positive, motile rods. The DNA G+C content from the seven isolates ranged from 42.2 to 43.4 mol% and their major fatty acid was anteiso-C 15:0. Strain CG1 T, selected as representative strain of the isolates, possesses meso-diaminopimelic acid in the cell wall peptidoglycan, MK-7 as the predominant menaquinone and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. Comparative 16S rRNA gene sequence analysis indicated that the isolates belonged to the genus Bacillus. The seven isolates shared 97.7–99.9% 16S rRNA gene sequence similarity, and formed a branch that was distinct from the type strains of the recognized species of the genus Bacillus. They were most closely related to Bacillus agaradhaerens DSM 8721 T (92.6–93.8% 16S rRNA sequence similarity). DNA–DNA hybridization values between the seven isolates were 85–100%. According to the polyphasic characterization, the strains represent a novel species, for which the name Bacillus locisalis sp. nov. is proposed. The type strain is CG1 T (CCM 7370 T = CECT 7152 T = CGMCC 1.6286 T = DSM 18085 T). 相似文献
14.
Association between bacteria Photorhabdus and their nematode hosts Heterorhabditis represents one of the emerging models in symbiosis studies. In this study, we isolated the bacterial symbionts of the nematode
Heterorhabditis georgiana. Using gyrB sequences for phylogenetic analysis, these strains were shown to be part of the species of Photorhbdus luminescens but with clear separation from currently recognized subspecies. Physiological properties and DNA–DNA hybridization profiles
also supported the phylogenetic relationship of these strains. Therefore, a new subspecies, Photorhabdus luminescens subsp. kleinii subsp. nov., is proposed with the type strain KMD37 T (=DSM 23513 =ATCC =NRRL B-59419). 相似文献
15.
Social bees harbor a community of gut mutualistic bacteria, among which bifidobacteria occupy an important niche. Recently, four novel species have been isolated from guts of different bumblebees, thus allowing to suppose that a core bifidobacterial population may be present in wild solitary bees. To date there is sparse information about bifidobacteria in solitary bees such as Xylocopa and Osmia spp., this study is therefore focused on the isolation and characterization of bifidobacterial strains from solitary bees, in particular carpenter bee ( Xylocopa violacea), builder bee ( Osmia cornuta), and red mason bee ( Osmia rufa). Among the isolates from Osmia spp. no new species have been detected whereas among Xylocopa isolates four strains (XV2, XV4, XV10, XV16) belonging to putative new species were found. Isolated strains are Gram-positive, lactate- and acetate-producing and possess the fructose-6-phosphate phosphoketolase enzyme. Full genome sequencing and genome annotation were performed for XV2 and XV10. Phylogenetic relationships were determined using partial and complete 16S rRNA sequences and hsp60 restriction analysis that confirmed the belonging of the new strains to Bifidobacterium genus and the relatedness of the strains XV2 and XV10 with XV16 and XV4, respectively. Phenotypic tests were performed for the proposed type strains, reference strains and their closest neighbor in the phylogenetic tree. The results support the proposal of two novel species Bifidobacterium xylocopae sp. nov. whose type strain is XV2 (=DSM 104955 T = LMG 30142 T), reference strain XV16 and Bifidobacterium aemilianum sp. nov. whose type strain is XV10 (=DSM 104956 T = LMG 30143 T), reference strain XV4. 相似文献
16.
The status of two mesophilic filamentous actinomycetes isolated from an arid Australian soil sample was determined using a polyphasic taxonomic approach. The isolates had chemical and morphological properties consistent with their classification in the genus Amycolatopsis, assignments that were supported by analysis of 16S rRNA gene sequence data. Isolate SF26 T formed a distinct phyletic line and hence was sharply separated from its nearest phylogenetic neighbour, Amycolatopsis sacchari DSM 44468 T. In contrast, isolate SF27 T formed a subclade in the Amycolatopsis tree with Amycolatopsis vancoresmycina DSM 44592 T but was separated readily from the latter by DNA:DNA pairing data. The two isolates were distinguished from one another and from their respective nearest phylogenetic neighbours using a range of phenotypic properties. These data indicate that the two isolates should be recognized as new species in the genus Amycolatopsis. The names proposed for these new taxa are Amycolatopsis bartoniae sp. nov. and Amycolatopsis bullii sp. nov. with isolates SF26 T (=NCIMB 14706 T = NRRL B-2846 T) and SF27 T (=NCIMB 14707 T = NRRL B-24847 T) as the respective type strains. 相似文献
17.
The genus Agrobacterium was initially described as mainly phytopathogenic strains. Nowadays, the genus includes phytopathogenic and non-phytopathogenic bacteria that are distinctive among the Rhizobiaceae family. Recently we have isolated two closely related strains, LMG 31531 T and LMG 31532, from soil and plant roots, respectively. Both strains differ from previously reported species based on the genomic and phenotypic data. A. arsenijevicii KFB 330 T and A. fabacearum LMG 31642 T showed the highest 16S rRNA similarity (98.9 %), followed by A. nepotum LMG 26435 T (98.7 %). A clear genomic feature that distinguishes LMG 31531 T and LMG 31532 from other Agrobacterium species is the absence of a linear chromid. Nevertheless, typical values of the core-proteome Average Amino Acid Identity (cpAAI > 85 %) and 16S rRNA gene sequence similarity (>96 %) when compared to other members of the genus confirm the position of these two strains as part of the Agrobacterium genus. They are therefore described as Agrobacterium divergens sp. nov. Besides, our comparative genomic study and survey for clade-specific markers resulted in the discovery of conserved proteins that provide insights into the functional evolution of this genus. 相似文献
19.
The bacterial symbiont Verminephrobacter eiseniae colonizes nephridia, the excretory organs, of the lumbricid earthworm Eisenia fetida. E. fetida transfers V. eisenia into the egg capsule albumin during capsule formation and V. eiseniae cells migrate into the earthworm nephridia during embryogenesis, where they bind and persist. In order to characterize the mechanistic basis of selective tissue colonization, methods for site-directed mutagenesis and colonization competence were developed and used to evaluate the consequences of individual gene disruptions. Using these newly developed tools, two distinct modes of bacterial motility were shown to be required for V. eiseniae colonization of nascent earthworm nephridia. Flagella and type IV pili mutants lacked motility in culture and were not able to colonize embryonic earthworms, indicating that both twitching and flagellar motility are required for entrance into the nephridia. 相似文献
20.
An ultraviolet-radiation-resistant, Gram-positive, orange-pigmented, thermophilic and strictly aerobic cocci was isolated
from Saharan water hot spring in Tunisia. The newly isolated bacterium, designated HAN-23 T, was identified based on polyphasic taxonomy including genotypic, phenotypic and chemotaxonomic characterization. Phylogenetic
analysis based on 16S rRNA gene sequences placed this strain within Deinococcus genus. However, strain HAN-23 T is different from recognized species of the genus Deinococcus, showing less than 94.0% similarity values to its closest relatives. The predominant cellular fatty acids determined by gas
chromatography were iso-C 15:0, iso-C 17:0 and iso C 17:1 ω9c. The major respiratory quinone was MK-8. The DNA G + C content was 66.9 mol%. DNA–DNA hybridization measurements revealed
low DNA relatedness (6%) between the novel isolate and its closest neighbor, the type strain Deinococcus geothermalis DSM 11300. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain HAN-23 T represents a novel species of the genus Deinococcus, for which the name Deinococcus sahariens sp. nov. is proposed, the type strain being HAN-23 T (=DSM 18496 T; LMG 23756 T). 相似文献
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