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1.
Int J Syst Evol Microbiol ; 69(11): 3362-3367, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31622228

RESUMO

A novel Gram-stain-negative bacterium, designated as SCSIO 06110T, was isolated from a deep-sea sediment of the West Pacific Ocean. Cells were 0.5-0.8 µm in width and 3.0-4.0 µm in length, spore-forming, rod-shaped with peritrichous flagella. Positive for catalase and urease, negative for oxidase and nitrate reduction. Growth occurred at 15-37 °C, pH 6-9 and 1-5 % (w/v) NaCl, with optimum growth at 28 °C, pH 7 and 3 % (w/v) NaCl. MK-7 was the only menaquinone. The strain possessed diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two unidentified phospholipids. Iso-C16 : 0, iso-C15 : 0 and iso-C14 : 0 were the major fatty acids. The novel isolate clustered with genera in the family Paenibacillaceae, but formed a separated branch with the closest relative Chengkuizengella sediminis J15A17T (91.1 % sequence similarity) when compared in a phylogenetic analysis of 16S rRNA gene sequences. The DNA G+C content of strain SCSIO 06110T was 38.5 mol%. Based on the polyphasic data presented, a new genus, Longirhabdus gen. nov., is proposed in the family Paenibacillaceae with the type species Longirhabdus pacifica sp. nov. and the type strain SCSIO 06110T (=DSM 105158T=CGMCC 1.16550T).


Assuntos
Bacillales/classificação , Sedimentos Geológicos/microbiologia , Fontes Hidrotermais/microbiologia , Filogenia , Bacillales/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Oceano Pacífico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Água do Mar/microbiologia , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
2.
Int J Syst Evol Microbiol ; 69(11): 3644-3649, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31622232

RESUMO

A novel Gram-stain-negative, strictly aerobic bacterium that has a rod-like shape with a single polar flagellum in the exponential phase of growth and a spherical or ovoid shape without a flagellum in the stationary phase was isolated from a mangrove wetland sediment sample collected at Beilun Estuary National Nature Reserve, Guangxi Province, PR China and designated strain ZS-4T. This strain grew optimally at pH 6.0-8.0, at a temperature of 37 °C and in the presence of 3-4 % (w/v) NaCl. Its polar lipid profile included phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminophospholipid and two uncharacterized lipids. Ubiquinone 8 (Q-8) was the sole respiratory quinone and the cellular fatty acids were dominated by C17 : 1ω8c and C16 : 0. A phylogenetic analysis based on the 16S rRNA gene sequence showed that strain ZS-4T exhibited its highest similarities to the type strains Thalassotalea litorea HMF4135T (97.8 %) and Thalassotalea ponticola GJSW-36T (95.9 %). A whole genome-level comparison of strain ZS-4T with T. litorea MCCC 1K03283T revealed an average nucleotide identity value of 75.6 % and a calculated DNA-DNA hybridization value of 19.6 %. In addition, the genomic DNA G+C content of strain ZS-4T was 45.9 mol%. Thus, based on analyses of its morphology, physiology, fatty acid composition and 16S rRNA gene sequence, strain ZS-4T should be considered a novel species of the genus Thalassotalea, with the proposed name Thalassotaleamangrovi sp. nov. The type strain is ZS-4T (=KCTC 72399T=MCCC 1K03630T).


Assuntos
Gammaproteobacteria/classificação , Sedimentos Geológicos/microbiologia , Filogenia , Áreas Alagadas , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Estuários , Ácidos Graxos/química , Gammaproteobacteria/isolamento & purificação , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
3.
Int J Syst Evol Microbiol ; 69(7): 2108-2113, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31663498

RESUMO

Strain M8-2T, which was isolated from brackish lake water (Lake Sanaru) in Japan, was characterized for representation of a novel species in the genus Algoriphagus. Cells of strain M8-2T were aerobic, Gram-stain-negative and curved-rod-shaped (0.2-0.5 µm wide and 0.7-1.9 µm long). Strain M8-2T grew optimally at 30 °C, pH 6.5-7.5 and in the presence of 0.5-1.0 % (w/v) NaCl. MK-7 was the sole isoprenoid quinone. The major polar lipids were phosphatidylethanolamine, an unidentified phospholipid and an unidentified polar lipid. The predominant cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. Phylogenetic analysis based on its 16S rRNA gene sequence showed that strain M8-2T belonged to the genus Algoriphagus and was closely related to Algoriphagus aquatilis A8-7T, Algoriphagus boseongensis BS-R1T, Algoriphagus aquaeductus T4T, Algoriphagus olei CC-Hsuan-617T, Algoriphagusshivajiensis NIO-S3T and Algoriphagus mannitolivorans DSM 15301T with sequence similarities of 96.6-97.4 %. Results of average nucleotide identity (<75 %) and digital DNA-DNA hybridization (<19 %) studies showed that M8-2T was distinct from its phylogenetic relatives. Based on the results of tests for acid production, the predominant cellular fatty acid composition, the DNA G+C content and phylogenetic position, a novel species in the genus Algoriphagus, with the name Algoriphagussanaruensis sp. nov., is proposed for strain M8-2T (=JCM 31446T=LMG 29969T).


Assuntos
Bacteroidetes/classificação , Lagos/microbiologia , Filogenia , Técnicas de Tipagem Bacteriana , Bacteroidetes/isolamento & purificação , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Japão , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
4.
Int J Syst Evol Microbiol ; 69(11): 3519-3523, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31483241

RESUMO

A Gram-stain-positive, rod-shaped and motile bacterium with lateral flagellum, designated T3246-1T, was isolated from an ice core, which was drilled from Hariqin Glacier on the Tibetan Plateau, PR China. It grew optimally at 20 °C, pH 7-8 and in the presence of 3 % (w/v) NaCl. The major fatty acid of strain T3246-1T was anteiso-C15 : 0. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. MK-8 was the dominant isoprenoid quinone. The whole-cell sugars were rhamnose, xylose and mannose. The major cell-wall peptidoglycan was lysine. The genomic DNA G+C content of the strain was 71.4 mol%. Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain T3246-1T formed a lineage within the genus Haloactinobacterium and was closely related to Haloactinobacterium album YIM 93306T with 95.99 % similarity. The average nucleotide identity value between strain T3246-1T and Haloactinobacterium album YIM 93306T was 76.65 %. Based on phenotypic and chemotaxonomic characteristics, strain T3246-1T was considered to represent a novel species of the genus Haloactinobacterium, for which the name Haloactinobacterium glacieicola sp. nov. is proposed. The type strain is T3246-1T (=CGMCC 1.13535T=JCM 32923T).


Assuntos
Actinobacteria/classificação , Camada de Gelo/microbiologia , Filogenia , Actinobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , Parede Celular/química , China , DNA Bacteriano/genética , Ácidos Graxos/química , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
5.
Int J Syst Evol Microbiol ; 69(11): 3616-3622, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31502946

RESUMO

The use of gnotobiotics has attracted wide interest in recent years due to technological advances that have revealed the importance of host-associated microbiomes for host physiology and health. One of the oldest and most important gnotobiotic mouse model, the altered Schaedler flora (ASF) has been used for several decades. ASF comprises eight different bacterial strains, which have been characterized to different extent, but only a few are available through public strain collections. Here, the isolation of a close relative of one of the less-studied ASF strains, Clostridium species ASF 502, from faeces of C57BL/6J mice is reported. Isolate TLL-A1T shares 99.5 % 16S rRNA gene sequence identity with Clostridium species ASF 502 and phylogenetic analyses indicate that both strains belong to the uncultured so-called 'Lachnospiraceae UCG 006' clade. The rare sugar d-arabinose was used as a sole carbon source in the anaerobic isolation medium. Results of growth experiments with TLL-A1T on different carbon sources and analysis of its ~6.5 Gb indicate that TLL-A1T harbours a large gene repertoire that enables it to utilize a variety of carbohydrates for growth. Comparative genome analyses of TLL-A1T and Clostridium species ASF 502 reveal differences in genome content between the two strains, in particular with regards to carbohydrate-activating enzymes. Based on genomic, molecular and phenotypic differences, we propose to classify strain TLL-A1T (DSM 106076T=KCTC 15657T) as a representative of a new genus and a new species, for which we propose the name Schaedlerella arabinosiphila gen. nov., sp. nov.


Assuntos
Arabinose/metabolismo , Clostridiales/classificação , Fezes/microbiologia , Camundongos Endogâmicos C57BL/microbiologia , Filogenia , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , Clostridiales/isolamento & purificação , DNA Bacteriano/genética , Camundongos , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
6.
Int J Syst Evol Microbiol ; 69(11): 3356-3361, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31502948

RESUMO

A bacterial strain M05W1-28T was isolated from a well that collected water for irrigation from a deep aquifer at a depth of 400 m. Cells were observed to be rod-shaped, non-motile, aerobic, stained Gram-negative. Optimal growth was obtained at pH 7.0 (range: 6.0-9.0), 28 °C (range: 15-37 °C) and 0 % NaCl (range: 0-1.5 %, w/v) in modified tryptic soy broth (mTSB) without added NaCl and R2A. The cells were found to be positive for catalase and oxidase activities. The major fatty acids (>10 %) were identified as summed feature 3 (C16 : 1 ω7c / C16 : 1 ω6c) and iso-C15 : 0. The major polar lipids were phosphatidylethanolamine, glycolipid, phosphoglycolipids, phospholipids, and unidentified lipids. The major respiratory quinone was menaquinone-7 (MK-7). The genomic G+C content of strain M05W1-28T was 40.7 %. Based on similarities of 16S rRNA gene sequences, strain M05W1-28T was affiliated with the genus Sphingobacterium, exhibiting the highest sequence similarities with S. multivorum LMG 8342T (97.5 %), S. ginsenosidimutans THG07T (97.1 %) and less than 97.0 % to other members of the genus. The average nucleotide identity (ANI) and digital DNA-DNA hybridisation values (dDDH) between M05W1-28T and S. multivorum LMG 8342T were 78.1 and 22.5 %, respectively. Phenotypic characteristics including enzyme activities and carbon source utilisation differentiated the strain from other Sphingobacterium species. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strain M05W1-28T represented a novel species within the genus Sphingobacterium, for which the name Sphingobacterium puteale sp. nov. is proposed. The type strain is M05W1-28T (=CGMCC 1.13711T=KCTC 72027T).


Assuntos
Água Subterrânea/microbiologia , Filogenia , Sphingobacterium/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Sphingobacterium/isolamento & purificação , Vitamina K 2/análogos & derivados , Vitamina K 2/química
7.
Int J Syst Evol Microbiol ; 69(11): 3629-3635, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31511125

RESUMO

Two Gram-stain-positive, irregular rod-shaped (0.2-0.5×1.3-2.5 um) strains, HY056T and HY057, were isolated from the faeces of Equus kiang (the largest of the wild asses) collected at different regions from the Qinghai-Tibetan Plateau of PR China. Phylogenetic analyses indicated that strains HY056T and HY057 belong to the genus Nocardioides by sharing a similarity ranging from 96.3 to 97.0 % in the 16S rRNA gene sequence and forming a distinct cluster with Nocardioides daphniae JCM 16608T, Nocardioides houyundeii 78T, Nocardioides solisilvae Ka25T and Nocardioides gilvus XZ17T. The digital DNA-DNA hybridization value of strain HY056T was 96.9 % with strain HY057, but less than 30.0 % with the above four closest relatives. MK-8(H4) was the predominant (91.6 %) respiratory quinone. The cell wall contained ll-2,6-diaminopimelic acid as the diamino acid of the peptidoglycan. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phospholipid. The predominant fatty acids (>10.0 %) were C18 : 1ω9c and iso-C16:0. The DNA G+C contents of strains HY056T and HY057 were 68.9 and 69.1 mol%, respectively. ß-Glucosidase expression was positive, and acid was produced from d-fructose. Strain HY056T (=CGMCC 4.7563T=JCM 33399T) is assigned as the type strain of a novel species within the genus Nocardioides, for which the name Nocardioidesyefusunii sp. nov is proposed.


Assuntos
Actinobacteria/classificação , Equidae/microbiologia , Fezes/microbiologia , Filogenia , Actinobacteria/isolamento & purificação , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Tibet , Vitamina K 2/análogos & derivados , Vitamina K 2/química
8.
Rev Inst Med Trop Sao Paulo ; 61: e51, 2019 Sep 12.
Artigo em Inglês | MEDLINE | ID: mdl-31531629

RESUMO

A drug resistance survey involving Mycobacterium tuberculosis isolated from patients of a tertiary Hospital in the Rio de Janeiro city (RJ), Brazil, between the years 1996 and 1998 revealed a high frequency of isoniazid (HR) resistance. These isolates were revisited and genotyped. Patients came from different RJ neighborhoods and municipalities, and 70% were outpatients. Applying the 3' and 5' IS 6110 -RFLP and the Spoligotype genotyping methods, the clonal structure of this population was investigated obtaining a snapshot of past epidemiological events. The 3' clusters were subsequently 5' IS 6110 -RFLP typed. Spoligotyping was analyzed in the SITVIT2 database. Epidemiological relationships were investigated. The major lineage was T (54.4%), and SIT 53/T1 and SIT 535/T1 were the most frequent. The T1 sublineage comprises 12.8% of resistant strains and SIT 535 were assigned for 31.8% of them. Orphan patterns corresponded to 12% and 73.3% and belonged to the T lineage. One pattern was unlisted in the SITVIT2. The 5' IS 6110 -RFLP did not confirm 3/12 of the 3' IS 6110 -RFLP clusters. A combination of all methods decreased the number of clusters to three. Nosocomial transmission was associated with one cluster involving a hospital cupbearer. This event was suspected in a multidrug resistant-TB inpatient caregiver who harbored a mixed infection. The 3' IS 6110 clusters were associated with HR (p=0.046). These genotypic retrospective data may reflect a fraction of more extensive recent transmission in different communities that may be corroborated by the concentration of HR patients, and may serve as a database for further evolutionary and characterization evaluation of circulating strains and together with epidemiological data favors a more effective transmission control.


Assuntos
Elementos de DNA Transponíveis/genética , Farmacorresistência Bacteriana/genética , Mycobacterium tuberculosis/genética , Tuberculose/microbiologia , Adolescente , Adulto , Técnicas de Tipagem Bacteriana , Brasil , DNA Bacteriano/genética , Feminino , Genótipo , Técnicas de Genotipagem , Humanos , Masculino , Mycobacterium tuberculosis/classificação , Mycobacterium tuberculosis/isolamento & purificação , Polimorfismo de Fragmento de Restrição , Estudos Retrospectivos
9.
Rev Soc Bras Med Trop ; 52: e20190243, 2019 Sep 05.
Artigo em Inglês | MEDLINE | ID: mdl-31508786

RESUMO

INTRODUCTION: In recent decades, the prevalence of carbapenem-resistant Acinetobacter isolates has increased, and the production of oxacillinase (OXA)-type carbapenemases is the main mechanism underlying resistance. We evaluated OXA production from 114 Acinetobacter isolates collected between March and December 2013 from different clinical specimens of patients in two hospitals (Hospital 1 [n = 61] and Hospital 2 [n = 53]) located in Niterói, Rio de Janeiro, Brazil. We also evaluated the genetic diversity of OXA-producing isolates. METHODS: All the isolates were identified through the automated system Vitek II and matrix-assisted laser desorption ionization-time of flight mass spectrometry MALDI-TOF MS as belonging to the A. baumannii-A. calcoaceticuscomplex. Antimicrobial susceptibility profiles were verified through agar diffusion tests. The presence of OXA-encoding genes was confirmed by PCR. The genetic diversity of isolates positive for carbapenemase production was analyzed through pulsed-field gel electrophoresis. RESULTS: There was a high rate of resistance to carbapenems in the isolates (imipenem: 96%; meropenem: 92%) from both hospitals. Moreover, a high percentage (95.6%) of OXA-23-positive isolates was observed for both hospitals, indicating that this was the main mechanism of carbapenem-resistance among the studied population. In addition, most isolates (96.5%) were positive for bla OXA-51. A high genetic diversity and a few major genotypes were found among the OXA-23-positive isolates analyzed. Only intra-hospital dissemination was observed. CONCLUSIONS: The elevated dissemination of bla OXA-23-like observed among Acinetobacter isolates from both the studied hospitals highlights the need for continuous epidemiological surveillance in these institutions.


Assuntos
Infecções por Acinetobacter/microbiologia , Acinetobacter/enzimologia , beta-Lactamases/biossíntese , Acinetobacter/efeitos dos fármacos , Acinetobacter/genética , Antibacterianos/farmacologia , Técnicas de Tipagem Bacteriana , Brasil , DNA Bacteriano/genética , Eletroforese em Gel de Campo Pulsado , Hospitais Gerais , Humanos , Testes de Sensibilidade Microbiana , Reação em Cadeia da Polimerase , beta-Lactamases/efeitos dos fármacos
10.
Int J Syst Evol Microbiol ; 69(9): 2735-2738, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31483242

RESUMO

Early characterization of strains designated into the genera Entomoplasma and Mesoplasma was based upon biological and chemical characteristics. With the advent of 16S rRNA gene sequence analysis as an added taxonomic character, it became clear that the two genera did not form distinct and separate monophyletic clusters. A genome-level analysis of all 17 validly published species within the family Entomoplasmataceae has recently been performed. Phylogenetic analyses, comparisons of gene content, and the lack of genus-specific genes supported that species from the two genera are intermixed and should not be taxonomically separated. This level of analysis clearly reveals the necessity to revise the taxonomy of this family by merging the two genera into one, Entomoplasma. Additionally, it was definitively determined that the strain originally designated as Acholeplasma multilocale resides in this cluster and should be formally renamed as Entomoplasma multilocale. Merging Mesoplasma and Entomoplasma yields a paraphyletic genus, but is supported by cell morphology and ecology to be distinguished from the genera Spiroplasma and Mycoplasma.


Assuntos
Entomoplasmataceae/classificação , Genoma Bacteriano , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
11.
Int J Syst Evol Microbiol ; 69(11): 3377-3384, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31368883

RESUMO

A Gram-negative, aerobic, rod-shaped, non-spore-forming bacterium, designated as strain BML3T, was isolated from a sputum sample of a hospital patient in Japan. Strain BML3T grew at temperatures from 4 to 40 °C, in 1.0-7.0 % (w/v) NaCl and at pH 6.0-9.0. Results of phylogenetic analysis based on the sequences of housekeeping genes, including the 16S rRNA gene and rpoB, rpoD and gyrB, showed that strain BML3T was part of the Pseudomonas putida group and located close to Pseudomonas asiatica, Pseudomonas monteiliiand P. putida . Whole-genome comparisons, using average nucleotide identity and digital DNA-DNA hybridization, confirmed strain BML3T to be a distinct species among the P. putida group. Phenotypic characterization tests demonstrated that the utilization of phenylmercuric acetate could distinguish this strain from other closed species of the P. putida group. Based on genetic and phenotypic evidence, strain BML3T should be classified as a novel species, for which the name Pseudomonas juntendi sp. nov. is proposed. The type strain is BML3T (=DSM 109244T,=JCM 33395T), with a DNA G+C content of 62.66 mol %.


Assuntos
Filogenia , Pseudomonas/classificação , Escarro/microbiologia , Urina/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Genes Bacterianos , Humanos , Japão , Mianmar , Hibridização de Ácido Nucleico , Pseudomonas/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
12.
Int J Syst Evol Microbiol ; 69(11): 3392-3398, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31373894

RESUMO

Strains A31/70T, CCUG 58779 and SD129 were Gram-stain-negative, short rods, motile by one polar flagellum and isolated from clinical specimens in Botswana, Sweden and Spain, respectively. The 16S rRNA sequence similarity values grouped them in the Pseudomonas stutzeri phylogenetic group of species. The DNA G+C content ranged from 65.5 to 65.7 mol%. The strains were characterized phenotypically by the API 20NE and Biolog GEN III tests, and chemotaxonomically by their whole-cell MALDI-TOF MS protein profiles and by their fatty acid contents. The absence of the arginine dihydrolase and the hydrolysis of gelatin differentiated these strains from the closest species, Pseudomonas azotifigens. The major fatty acid contents were summed feature 8 (38.6 %), C16 : 0 (22.6 %), summed feature 3 (20.5 %) and C12 : 0 (8.4 %). Multilocus sequence analysis with three housekeeping gene sequences (rpoD, gyrB and 16S rRNA) together with whole-genome comparisons indicated that these strains cluster together in the phylogenetic analysis and their similarity values were lower than the thresholds established for species in the genus Pseudomonas. These results permit us to conclude that strains A31/70T, CCUG 58779 and SD129 belong to a novel species in the genus Pseudomonas for which the name Pseudomonas nosocomialis sp. nov. is proposed. The type strain is A31/70T (=CECT 9981T=CCUG 73638T).


Assuntos
Filogenia , Pseudomonas/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , Botsuana , DNA Bacteriano/genética , Ácidos Graxos/química , Genes Bacterianos , Humanos , Tipagem de Sequências Multilocus , Hibridização de Ácido Nucleico , Pseudomonas/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Espanha , Suécia
13.
Int J Syst Evol Microbiol ; 69(11): 3405-3413, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31373895

RESUMO

Strain CECT 7735T, a marine Gram-reaction negative, aerobic, non-motile bacterium, was isolated from coastal seawater in Valencia, Spain. Strain CECT 7735T is chemoorganotrophic, mesophilic, slightly halophilic, grows at 15-28 °C but not at 4 or 37 °C, requires seawater for growth and grows up to 6 % salinity. The major cellular fatty acid is summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The G+C content of the genome is 55.7 mol%. Comparative analysis of the 16S rRNA gene sequence shows the strain is affiliated to the family Rhodobacteraceae, in the class Alphaproteobacteria, with highest similarities to Phaeobacter species (97.0-97.5 %), Shimia species (96.5-97.3 %) and Pseudopelagicola gijangensis (96.5 %). Further phylogenomic analysis through the up-to-date-bacterial core gene (UBCG) set showed P. gijangensis to be its closest relative. Average nucleotide identity and in silico DNA-DNA hybridization values are lower than 85 and 21 %, respectively, with its phylogenetic relatives, suggesting that strain CECT 7735T represents a new species. The average amino acid identity value was over 70 % with the genome of the type strain of P. gijangensis and with all those of Shimia species. These values, together with UBCG set trees, suggest that the new species and P. gijangensisbelong to the same genus and that Pseudopelagicola should be reclassified as a Shimia species. We conclude that strain CECT 7735T represents a new species in the genus Shimia, for which we propose the name Shimiathalassica sp. nov. In addition, Pseudopelagicola gijangensis is reclassified as Shimiagijangensis comb. nov. From the same phylogenomic study, it can be concluded that Thalassobius activus should be reclassified in the genus Cognatishimia as Cognatishimiaactiva comb. nov.


Assuntos
Filogenia , Rhodobacteraceae/classificação , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Espanha
14.
Int J Syst Evol Microbiol ; 69(11): 3399-3404, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31380735

RESUMO

A white-coloured, Gram-stain-negative, aerobic, rod-shaped bacterium (designated strain SY21T) was isolated from waste-activated sludge. Optimal growth occurred at 28 °C and pH 7.0. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain SY21T exhibited 16S rRNA gene sequence similarities of 95.5-98.0 % to Thermomonas species and clustered with the type species of the genus Thermomonas. In strain SY21T, the predominant respiratory quinone was ubiquinone Q-8, and the cellular fatty acids consisted mainly of iso-C15 : 0, C16 : 0, iso-C11 : 0 3-OH, summed feature 3 and summed feature 9. The major polar lipids were phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The genomic DNA G+C content was determined to be 67.9 mol% and the DNA-DNA relatedness between strain SY21T and the closest phylogenetically related strain, Thermomonas carbonis KCTC 42013T, was 35.0±0.1 %. Based on the distinct phenotypic, chemotaxonomic and phylogenetic properties, strain SY21T represents a novel species of the genus Thermomonas, for which the name Thermomonas aquatica sp. nov. is proposed. The type strain is SY21T (=KCTC 62191T=NBRC 113114T).


Assuntos
Filogenia , Esgotos/microbiologia , Águas Residuárias/microbiologia , Xanthomonadaceae/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Ubiquinona/química , Xanthomonadaceae/isolamento & purificação
15.
Int J Syst Evol Microbiol ; 69(11): 3414-3419, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31380736

RESUMO

A Gram-negative bacterium, namely strain ANRC-JHZ47T, was isolated from a seawater sample collected at Biological Bay, Fildes Peninsula, Antarctica. Cells of strain ANRC-JHZ47T were rod-shaped and motile by a single polar flagellum. Strain ANRC-JHZ47T was aerobic, oxidase-negative, and catalase-positive. The strain grew at 4-37 °C (optimum, 25 °C), pH at 3.5-10.0 (optimum, pH 5.5) and in NaCl at 1-7.0 % (w/v; optimum, 2-3 %). Strain ANRC-JHZ47T used Q-8 as the predominant respiratory quinone. Its predominant fatty acids were C16 : 0 (21.9 %), C12 : 0 (12.6 %), C19 : 0cyclo ω8c (12.4 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 13.1 %), C10 : 0 3-OH (11.3 %) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 6.0 %). Its major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, one unidentified aminolipid and five unknown polar lipids. The DNA G+C content was 42.6 mol%. Strain ANRC-JHZ47T showed the highest 16S rRNA gene sequence similarity to Marinomonas arenicola KMM 3893T (97.9 %), followed by Marinomonas primoryensis KMM 3633T (97.6 %), Marinomonas profundimaris D104T (97.2 %) and Marinomonas pollencensis IVIA-Po-185T (97.0 %). Furthermore, the average nucleotide identity values between strain ANRC-JHZ47T and M. arenicola KMM 3893T, M. primoryensis KMM 3633T and M. profundimaris D104T were 79.8, 74.0, and 74.1 %, respectively. The in silico DNA-DNA hybridization values between them were 22.5±2.5, 20.4±2.3 and 19.9±2.3 %, respectively. Based on the results of phenotypic and phylogenetic analyses, strain ANRC-JHZ47T is considered to represent a novel species of the genus Marinomonas, for which the name Marinomonas flavescens sp. nov. is proposed. The type strain is ANRC-JHZ47T (=MCCC 1K03604T=KCTC 72113T).


Assuntos
Marinomonas/classificação , Filogenia , Água do Mar/microbiologia , Regiões Antárticas , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Marinomonas/isolamento & purificação , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
16.
Int J Syst Evol Microbiol ; 69(11): 3437-3442, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31385781

RESUMO

A Gram-stain-negative, non-motile, aerobic, short rod-shaped bacterium, designated OD32T, was isolated from a soil sample taken from the rhizosphere of Silene acaulis collected from the Arctic tundra. The novel strain, OD32T, was able to grow at 15-37 °C (optimum, 33 °C), pH 6.5-9.5 (pH 7.5-8.0) and 0-0.5 % NaCl (0 %, w/v). A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain OD32T was most closely related to the genus Deinococcus; it shared the highest sequence similarity (95.7 %) with Deinococcus grandis ATCC 43672T. Genomic DNA G+C content of the strain OD32T was 68.2 mol%. The predominant respiratory quinone was menaquinone 8 (MK-8). The major fatty acids were summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), C15 : 1 ω6c, C17 : 1 ω6c, C17 : 0, C16 : 0 and iso-C17 : 0. Based on phylogenetic inference and genotypic characteristics, strain OD32T represents a novel species of the genus Deinococcus, for which the name Deinococcus arcticus sp. nov. is proposed. The type strain is OD32T (=KCTC 33972T=CICC 24671T).


Assuntos
Deinococcus/classificação , Filogenia , Rizosfera , Silene/microbiologia , Microbiologia do Solo , Tundra , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Deinococcus/isolamento & purificação , Ácidos Graxos/química , Genótipo , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Svalbard
17.
Int J Syst Evol Microbiol ; 69(11): 3420-3425, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31385782

RESUMO

A novel Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium was isolated from Lake Dajiaco on the Tibetan Plateau. Strain DJCT grew without NaCl and tolerated up to 3 % (w/v) NaCl. Growth occurred at pH 6.0-10.0 (optimum, pH 7.0-8.0) and 15-37 °C (optimum, 25-30 °C). Vitamins were not required for growth. The main polar lipids of strain DJCT were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant respiratory quinone was Q-10. The major fatty acid was C18 : 1ω7c. Genome sequencing revealed a genome size of 4.61 Mbp and a G+C content of 62.9 mol%. Analysis of 16S rRNA sequences showed that strain DJCT belonged to the genus Tabrizicola, with the closest neighbour Tabrizicola aquatica RCRI19T (97.5 %). DNA-DNA relatedness between strain DJCT and the closest phylogenetically related strain T. aquatica RCRI19T was 40.8 %. Stain DJCT was clearly distinguished from the type strain mentioned above through phylogenetic analysis, DNA-DNA hybridization, fatty acid composition data and a range of physiological and biochemical characteristic comparisons. Based on its phenotypic and chemotaxonomic characteristics, strain DJCT could be classified as a representative of a novel species of the genus for which the name Tabrizicola alkalilacus sp. nov. is proposed. The type strain is DJCT (=CICC 24242T=KCTC 62173T).


Assuntos
Lagos/microbiologia , Filogenia , Rhodobacteraceae/classificação , Álcalis , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Concentração de Íons de Hidrogênio , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Rhodobacteraceae/isolamento & purificação , Análise de Sequência de DNA , Tibet , Ubiquinona/análogos & derivados , Ubiquinona/química
18.
Int J Syst Evol Microbiol ; 69(11): 3368-3376, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31391144

RESUMO

Twenty-two cream-coloured bacterial strains were isolated from oak trees affected by acute oak decline (AOD) in Southern England. Isolates were Gram-negative, motile, slightly curved rods, aerobic, non-spore-forming, catalase positive and oxidase positive. 16S rRNA gene sequence analysis placed the strains in two separate phylogenetic clusters in the Pseudomonas straminea group, with Pseudomonas flavescens as the closest phylogenetic relative. Multilocus sequence analyses of the gyrB, rpoD and rpoB genes supported the delineation of the strains into two separate taxa, which could be differentiated phenotypically and chemotaxonomically from each other, and their closest relatives. Average nucleotide identity and in silico DNA-DNA hybridization values revealed percentages of genome similarity below the species threshold (95 and 70 %, respectively) between the two taxa and the closest relatives, confirming their novel species status. Therefore, on the basis of this polyphasic approach we propose two novel Pseudomonas species, Pseudomonasdaroniae sp. nov. (type strain FRB 228T=LMG 31087T=NCPPB 4672T) and Pseudomonasdryadis sp. nov. (type strain FRB 230T=LMG 31087T=NCPPB 4673T).


Assuntos
Filogenia , Doenças das Plantas/microbiologia , Pseudomonas/classificação , Quercus/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Genes Bacterianos , Tipagem de Sequências Multilocus , Hibridização de Ácido Nucleico , Pseudomonas/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Reino Unido
19.
Int J Syst Evol Microbiol ; 69(11): 3426-3436, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31395106

RESUMO

A Micromonospora strain, designated 5R2A7T, isolated from a high altitude Atacama Desert soil was examined by using a polyphasic approach. Strain 5R2A7T was found to have morphological, chemotaxonomic and cultural characteristics typical of members of the genus Micromonospora. The cell wall contains meso- and hydroxy-diaminopimelic acid, the major whole-cell sugars are glucose, ribose and xylose, the predominant menaquinones MK-10(H4), MK-10(H6), MK-10(H8) and MK-9(H6), the major polar lipids diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and an unknown glycolipid, and the predominant cellular fatty acids iso-C16 : 0, iso-C15 : 0 and 10-methyl C17 : 0. The digital genomic DNA G+C content is 72.3 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain 5R2A7T was closely related to Micromonospora coriariae DSM 44875T (99.8 %) and Micromonospora cremea CR30T (99.7 %), and was separated readily from the latter, its closest phylogenetic neighbour, based on gyrB and multilocus sequence data, by low average nucleotide identity (92.59 %) and in silico DNA-DNA relatedness (51.7 %) values calculated from draft genome assemblies and by a range of chemotaxonomic and phenotypic properties. Consequently, strain 5R2A7T is considered to represent a novel species of Micromonospora for which the name Micromonospora acroterricola sp. nov. is proposed. The type strain is 5R2A7T (=LMG 30755T=CECT 9656T).


Assuntos
Altitude , Clima Desértico , Micromonospora/classificação , Filogenia , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Composição de Bases , Parede Celular/química , Chile , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Glicolipídeos/química , Micromonospora/isolamento & purificação , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/química
20.
Int J Syst Evol Microbiol ; 69(11): 3472-3477, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31418668

RESUMO

A Gram-stain-negative, strictly aerobic, motile, yellow, rod-shaped bacterium, designated ZDH117T, was isolated from soilsampled atthe Danxialandformin Guangdong Province, PR China. The 16S rRNA gene sequence of strain ZDH117T had highest similarityvalues to Sphingomonas adhaesivaDSM 7418T (97.5 %), SphingomonasdesiccabilisCP1DT (97.3 %) and Sphingomonas ginsenosidimutans KACC 14949T (97.2 %). However, phylogenetic analyses based on 16S rRNA gene sequences demonstrated that strain ZDH117T clustered with Sphingomonas zeicaulis 541T (96.17 %) and Sphingomonas sanxanigenens DSM 19645T (95.95 %). The genomic average nucleotide identity values of ZDH117T with S. adhaesiva DSM 7418T, S. desiccabilis CP1DTand S. ginsenosidimutans KACC TT were 75.1, 75.2 and 75.0 %, respectively. The G+C content of the genomic DNA was 67.6 mol%. Strain ZDH117T was characterized to have ubiquinone-10 as the predominant respiratory quinone, sym-homospermidine as the major polyamine and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c), C14 : 0-2OH, C16 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) as the major cellular fatty acids (>5 % of total). The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid, an unidentified phospholipid and three unidentified lipids. On the basis of its phenotypic, chemotaxonomic and phylogenetic characteristics, strain ZDH117T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas gilva sp. nov. is proposed. The type strain is ZDH117T (=KCTC 62894T=CCTCCAB 2018262T).


Assuntos
Filogenia , Microbiologia do Solo , Sphingomonas/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Fosfolipídeos/química , Pigmentação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Espermidina/análogos & derivados , Espermidina/química , Sphingomonas/isolamento & purificação , Ubiquinona/química
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