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1.
Antonie Van Leeuwenhoek ; 112(12): 1739-1745, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31346832

RESUMO

A novel strain, YIM 131921T, was isolated from a Physcia sp. lichen collected from the South Bank Forest of the Baltic Sea. The strain is Gram-negative, catalase positive and oxidase negative, strictly aerobic, asporogenous, non-motile and reddish brown in colour. The temperature and pH for growth were found to be 20-30 °C (optimum 28 °C) and pH 6.5-12.0 (optimum pH 7.0 ± 0.5). No growth was observed in the presence of NaCl. Based on 16S rRNA gene sequence similarity, strain YIM 131921T shares high similarities with Rubellimicrobium roseum YIM 48858T (98.3%), followed by Rubellimicrobium mesophilum MSL-20T (96.8%), Rubellimicrobium aerolatum 5715S-9T (96.1%) and Rubellimicrobium thermophilum DSM 16684T (96.0%). Phylogenetic trees showed YIM 131921T forms a cluster with type strains of the genus Rubellimicrobium. The predominant cellular fatty acids (> 20%) were identified as summed feature 8 (C18:1ω7c) and C16:0. Q-10 was found to be the predominant respiratory ubiquinone. The polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, glycolipid, phospholipids and an unidentified aminolipid. The DNA G + C content of the draft genome sequence is 66.6 mol%. Strain YIM 131921T showed an average nucleotide identity value of 80.3% and a digital DNA-DNA hybridizations value of 26.1% with the reference strain R. roseum YIM 48858T based on draft genome sequences. Based on comparative analyses of phenotypic, molecular, chemotaxonomic data and genomic comparisons, strain YIM 131921T is concluded to represent a novel species of the genus Rubellimicrobium, for which the name Rubellimicrobium rubrum sp. nov. is proposed. The type strain is YIM 131921T (= CGMCC 1.13958T = NBRC 114054T = KCTC 72461T).

2.
Antonie Van Leeuwenhoek ; 112(10): 1567-1575, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31147966

RESUMO

A novel Gram-negative bacterium, non-motile and short rod-shaped, designated strain GY511T, was isolated from the intestines of fish collected from Maowei Sea, China. Growth occurred at pH 6.0-9.0 (optimum 7.0), 4-37 °C (optimum 28 °C) and at 0-2.5% (w/v) NaCl (optimum 1.0%). The result of 16S rRNA gene sequence analysis showed that strain GY511T is closely related to O. oryzae NBRC 113109T (97.6%), O. konkukae DSM 105395T (97.4%), Ottowia beijingensis CGMCC 1.12324T (95.9%), Ottowia pentelensis DSM 21699T (95.2%) and Ottowia thiooxydans DSM 14619T (95.0%). The DNA-DNA hybridization values of strain GY511T with O. oryzae NBRC 113109T and O. konkukae DSM 105395T were 35.4 ± 3.1% and 26.3 ± 1.8%, respectively. The major fatty acids (> 10%) were identified as summed feature 3 (C16:1ω7c and/or C16:1ω6c), C16:0 and summed feature 8 (C18:1ω7c and/or C18:1ω6c) and the major respiratory quinone was ubiquinone-8 (Q-8). The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmethylethanolamine, two unidentified aminolipids and an unidentified phospholipid. The G+C content of the genomic DNA was 62.9 mol%. Thiosulfate could be utilized as co-substrate for aerobic growth and was oxidised to sulfate. On the basis of phenotypic, chemotaxonomic and molecular data, strain GY511T is considered to represent a novel species of the genus Ottowia, for which the name Ottowia flava sp. nov. is proposed. The type strain is GY511T (= NBRC 113500T = DSM 107425T = CGMCC 1.13650T).

3.
Zhongguo Dang Dai Er Ke Za Zhi ; 21(4): 387-392, 2019 Apr.
Artigo em Chinês | MEDLINE | ID: mdl-31014434

RESUMO

OBJECTIVE: To investigate the current status of empirical antibiotic therapy for children with Staphylococcus aureus sepsis and the effect of therapeutic paradigm on prognosis based on a retrospective analysis. METHODS: A total of 78 children with Staphylococcus aureus sepsis who were admitted from January 2014 to August 2017 were enrolled. According to the preferred empirical antibiotics before the detection of Staphylococcus aureus by blood culture, these children were divided into a carbapenem group with 16 children, a ß-lactam group with 37 children, a vancomycin group with 15 children and a vancomycin+ß-lactam group with 10 children. A retrospective analysis was performed for related clinical data including general status, underlying diseases, Acute Physiology and Chronic Health Evaluation II (APACHE II) score, history of use of immunosuppressant, drug resistance to methicillin and prognosis. A logistic regression analysis was used to investigate the effect of empirical antibiotic therapy on the clinical outcome and prognosis of children with Staphylococcus aureus sepsis. RESULTS: There were no significant differences among these groups in general status, underlying diseases, history of use of immunosuppressant, APACHE II score, nosocomial infection and detection rate of methicillin-resistant Staphylococcus aureus (P>0.05). There were significant differences in the incidence rate of septic shock and in-hospital mortality among these four groups (P<0.05). The carbapenem group had the highest incidence rate of septic shock and in-hospital mortality (69% and 50% respectively). The multivariate logistic regression analysis showed that empirical antibiotic therapy with different antibiotics had different risks for septic shock and in-hospital death in children with Staphylococcus aureus sepsis (P<0.05), and that an APACHE II score of ≥15 was an independent risk factor for septic shock in these children (P<0.05). The carbapenem group had significantly higher risks of septic shock and in-hospital death than the vancomycin group (P<0.05). CONCLUSIONS: Inappropriate empirical use of antibiotics may lead to a poor prognosis in children with Staphylococcus aureus sepsis. Empirical use of carbapenems is not recommended for children suspected of Staphylococcus aureus sepsis.


Assuntos
Antibacterianos/uso terapêutico , Staphylococcus aureus Resistente à Meticilina , Sepse , Infecções Estafilocócicas , Criança , Humanos , Estudos Retrospectivos , Infecções Estafilocócicas/tratamento farmacológico , Staphylococcus aureus
4.
Curr Microbiol ; 75(2): 213-222, 2018 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-29127454

RESUMO

Huge numbers of bacteria reside in the digestive tract of host and these microorganisms play a vital role in the host health, especially in the digestion of food and the development of immune system. Host phylogeny and diet, especially long-term diet, both have great influence on the gut bacterial community. Other aspects of host, such as gender, age, and the geography and weather they lived, are also correlated to their gut bacterial community. Feces are usually used for gut bacteria study and fecal bacteria can represent the distal gut bacteria. In order to determine the influence of the host phylogeny and diet on the composition of distal gut bacterial community and to interpret bacterial population and diversity in the intestinal of animals, the distal gut bacterial community of four kinds of primates and five kinds of carnivora (including herbivorous, omnivorous, and carnivorous) were investigated using high-throughput sequencing and the isolation of the Actinobacteria from fresh feces of several primates was processed. The results showed the host phylogeny had a greater influence on the distal gut bacterial community of the primates and carnivora than the host diet. A total of 44 bacteria phyla and two archaea phyla were detected, which indicated that the distal gut bacteria of these animals were abundant. The distal gut bacteria were relatively stable and wildly shared in primates and carnivora. The difference in distal gut bacteria of the two animal orders is mainly determined by relative abundance of most distal gut bacteria rather than by the taxa of these bacteria.


Assuntos
Archaea/classificação , Bactérias/classificação , Carnívoros , Microbioma Gastrointestinal , Trato Gastrointestinal/microbiologia , Primatas , Actinobacteria , Animais , Archaea/genética , Bactérias/genética , Fezes/microbiologia , Sequenciamento de Nucleotídeos em Larga Escala
5.
Int J Syst Evol Microbiol ; 67(11): 4801-4807, 2017 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-28984560

RESUMO

Two novel actinobacteria, designated YIM 121936T and YIM 121940T, were isolated from alkaline sediment in Yuanjiang, China. The cells of the novel strains were Gram-stain-positive, aerobic, motile, non-spore-forming and coccus-shaped. The two strains both contained meso-diaminopimelic acid as the diagnostic diamino acid. The whole-cell sugars were arabinose, galactose, glucose, mannose and ribose. The predominant menaquinone was MK-9(H2). The polar lipid profile of both strains comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, one unknown phosphoglycolipid and five unknown phospholipids. The predominant fatty acids of both strains were anteiso-C15 : 0. The genomic DNA G+C contents of strains YIM 121936T and YIM 121940T were 74.7 and 75.2 %, respectively. Strain YIM 121936T was closely related to Kineococcus aurantiacus IFO 15268T (97.19 %), Kineococcus gypseus YIM 121300T (97.00 %) and Kineococcus mangrovi NBRC 110933T (97.00 %). Strain YIM 121940T was closely related to K. aurantiacus IFO 15268T (97.41 %), Kineococcus endophytica KLBMP 1274T (97.18 %), Kineococcus rhizosphaerae RP-B16T (97.09 %), Kineococcus radiotolerans SRS 30216T (97.09 %), K. gypseus YIM 121300T (97.00 %) and K. mangrovi NBRC 110933T (97.00 %). Strain YIM 121936T shared high 16S rRNA gene sequence similarity (99 %) with YIM 121940T. Similarities of two strains with other species of the genus Kineococcus were <97 %. The DNA-DNA hybridization values were below 70 % among all the strains studied. YIM 121936T and YIM 121940T are representatives of two new species in the genus Kineococcus, for which names Kineococcus terreus sp. nov. (type strain YIM 121936T=KCTC 39738T=DSM 102155T) and Kineococcus aureolus sp. nov. (type strain YIM 121940T=KCTC 39739T=DSM 102158T) are proposed, respectively.


Assuntos
Actinomycetales/classificação , Sedimentos Geológicos/microbiologia , Filogenia , Actinomycetales/genética , Actinomycetales/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Concentração de Íons de Hidrogênio , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Salinidade , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
6.
Int J Syst Evol Microbiol ; 67(7): 2253-2257, 2017 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-28671530

RESUMO

A novel actinobacterium, designated YIM 101593T, was isolated from the faeces of a primate (Rhinopithecus roxellanae) living in Yunnan Wild Animal Park in Yunnan province, south-west China. The isolate was Gram-stain-positive, facultatively anaerobic, coccus-shaped, oxidase-negative and motile. The cell wall contained meso-diaminopimelic acid as its diagnostic diamino acid, and mannose, ribose, glucose, galactose and arabinose were detected as the main whole-cell sugars. The predominant menaquinone was MK-8(H2). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two glycolipids, three unidentified phospholipids and two unidentified lipids. The major fatty acids were C17 : 1ω8c, C15 : 0 and summed feature 4 (anteiso-C17 : 1 B and/or iso-C17 : 1 I). The DNA G+C content was 69.8 mol%. The 16S rRNA gene sequence similarity between strain YIM 101593T and Mobilicoccus pelagius was 97.9 %, and the two strains formed a distinct lineage stably on the basis of phylogenetic analysis. In addition, DNA-DNA relatedness between the two strains was 49.0±5.1 %. On the basis of chemotaxonomical and physiological characteristics and the phylogenetic analysis, strain YIM 101593T should be considered to represent a novel species of the genus Mobilicoccus, for which we propose the name Mobilicoccus caccae sp. nov., with the type strain YIM 101593T (=DSM 27611T=CCTCC AB 2013229T).


Assuntos
Actinomycetales/classificação , Fezes/microbiologia , Filogenia , Primatas/microbiologia , Actinomycetales/genética , Actinomycetales/isolamento & purificação , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , DNA Ribossômico/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
7.
Antonie Van Leeuwenhoek ; 110(4): 553-562, 2017 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-28032205

RESUMO

A novel strain, YIM 100770T, was isolated from Rhinoceros unicornis faeces collected from Yunnan Wild Animal Park, China. The taxonomic status was determined based on the physiological, biochemical and phylogenetic characteristics. Strain YIM 100770T was observed to be rod-shaped, non-motile, Gram-stain negative and aerobic. The G+C content of the genomic DNA was determined to be 68.5 mol%. The cells of strain YIM 100770T contain ubiquinone Q-10 as the respiratory quinone. The major fatty acids (>1%) were identified as Summed feature 8 (C18:1 ω7c and/or C18:1 ω6c; 78.1%), Summed feature 4 (iso-C17:1-I and/or anteiso-C17:1-B; 12.9%), C19:0 cyclo ω8c (2.8%), C16:0 (2.2%) and C18:0 (2.2%). Comparison of 16S rRNA gene sequences revealed the strain show high similarities with the members of the genera Psychroglaciecola (94.5%), Methylobacterium (90.5-94.1%) and Microvirga (92.0-93.3%) in the family Methylobacteriaceae. In addition, the strain also showed high similarities with the members of the genera Chelatococcus (93.7-94.0%) and Pseudochelatococcus (93.1-93.7%) in the family Beijerinckiacea, and the genus Bosea (93.1-93.8%) in the family Bradyrhizobiaceae. The phylogenetic analysis, combined with the chemical characteristics, suggest that the strain represents a novel genus in the order Rhizobiales of the class Alphaproteobacteria, for which the name Enterovirga rhinocerotis gen. nov., sp. nov. is proposed. The type strain of E. rhinocerotis is YIM 100770T (=DSM 25903T = CCTCC AB 2012048T).


Assuntos
Alphaproteobacteria/classificação , Alphaproteobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana , Perissodáctilos/microbiologia , Alphaproteobacteria/genética , Animais , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/análise , Fezes/microbiologia , RNA Ribossômico 16S/genética
8.
Int J Syst Evol Microbiol ; 66(11): 4445-4450, 2016 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-27498962

RESUMO

A novel, yellow, aerobic strain, YIM 101168T, isolated from the faeces of a dove (Columba livia), was studied to determine its taxonomic position. Cells were Gram-stain-positive, short rod-shaped, oxidase-negative, catalase-positive and non-motile. The strain could grow at 7-37 °C, at pH 6-10 and in the presence of 0-13 % (w/v) NaCl. The strain had a 16S rRNA gene sequence similarity and DNA-DNA hybridization relatedness value with Microbacteriumgubbeenense NCIMB 30129T of 97.8 % and 41.5±8.7 %, respectively. Ornithine was detected as the diagnostic amino acid in the hydrolysate of the cell wall. Whole-cell sugars were found to be galactose, glucose, rhamnose, mannose and ribose. Major fatty acids (>10 %) were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. Major menaquinones were identified as MK-10, MK-11 and MK-12. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, glycolipids and four unidentified lipids. The phylogenetic analyses as well as the chemotaxonomic and phenotypic characteristics indicate that strain YIM 101168T represents a novel species of the genus Microbacterium; the name Microbacterium faecale sp. nov. is proposed for the novel species and the type strain is YIM 101168T (=DSM 27232T=KCTC 39554T=CGMCC 1.15152T).


Assuntos
Actinomycetales/classificação , Columbidae/microbiologia , Filogenia , Actinomycetales/genética , Actinomycetales/isolamento & purificação , Aminoácidos/química , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Fezes/microbiologia , Glicolipídeos/química , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/química
9.
Antonie Van Leeuwenhoek ; 109(9): 1177-83, 2016 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-27260265

RESUMO

A novel aerobic, non-motile, Gram-positive, rod-shaped actinobacterium, designated YIM 100951(T), was isolated from the faeces of civets (Viverra zibetha) living in the National Nature Protect Region in Selangor, Malaysia. Strain YIM 100951(T) shows high similarities with Microbacterium barkeri DSM 20145(T) (97.6 %), Microbacterium oryzae MB10(T) (97.3 %), Microbacterium lemovicicum ViU22(T) (97.1 %) and Microbacterium indicum BBH6(T) (97.0 %) based on their 16S rRNA genes. However, phylogenetic analysis showed that strain YIM 100951(T) formed a clade with Microbacterium halotolerans YIM 70130(T) (96.7 %), Microbacterium populi 10-107-8(T) (96.7 %) and Microbacterium sediminis YLB-01(T) (96.9 %). DNA-DNA hybridization was carried out between strains YIM 100951(T) and M. barkeri DSM 20145(T), the result showed a value of 23.2 ± 4.5 %. In addition, some of the physiological, biochemical and chemotaxonomic characteristics of strain YIM 100951(T) are different from the closely related strains. Thus, we suggest that strain YIM 100951(T) represents a novel species of the genus Microbacterium, for which the name Microbacterium gilvum sp. nov. is proposed. The type strain is YIM 100951(T) (=DSM 26235(T) = CCTCC AB 2012971(T)).


Assuntos
Actinomycetales/classificação , Actinomycetales/isolamento & purificação , Fezes/microbiologia , Filogenia , Viverridae/microbiologia , Actinomycetales/genética , Actinomycetales/metabolismo , Animais , Parede Celular/química , DNA Bacteriano/genética , DNA Ribossômico/genética , Ácidos Graxos/metabolismo , Malásia , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Especificidade da Espécie , Vitamina K 2/metabolismo
10.
Int J Syst Evol Microbiol ; 66(7): 2478-2483, 2016 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-27073837

RESUMO

A Gram-stain-positive, facultatively anaerobic, short rod-shaped, oxidase-negative and non-motile novel strain, designated YIM 101505T, was isolated from the faeces of a primate, Assamese macaque, and was studied to determine its taxonomic position. The cell wall contained meso-diaminopimelic acid and short-chain mycolic acids. Whole cell sugars were mannose, galactose and arabinose as major components. The major fatty acids (>10 %) were C18 : 1ω9c, C16 : 0 and C17 : 1ω8c and the major menaquinone was MK-9(H2). The polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, glycolipid and six unidentified lipids. The new isolate shared most of the typical chemotaxonomic characteristics of members of the genus Corynebacterium. The closest related species was Corynebacterium efficiens based on 16S rRNA gene (98.1 % similarity) and partial rpoB gene (91.4 % similarity) sequences. Similarities with other species of this genus were below 97 % based on the 16S rRNA gene. The DNA-DNA hybridization value between YIM 101505T and C. efficiens DSM 44549T was 47.7±3.6 %. Moreover, the physiological and biochemical characteristics of YIM 101505T and C. efficiens DSM 44549T were different. Thus, strain YIM 101505T is considered to represent a novel member of the genus Corynebacterium, for which the name Corynebacterium faecale sp. nov. is proposed. The type strain is YIM 101505T (=DSM 45971T=CCTCC AB 2013226T).


Assuntos
Corynebacterium/classificação , Corynebacterium/isolamento & purificação , Fezes/microbiologia , Macaca/microbiologia , Animais , Técnicas de Tipagem Bacteriana , China , Corynebacterium/química , Corynebacterium/citologia , DNA Bacteriano/genética , Fosfolipídeos/análise , Filogenia , Análise de Sequência de DNA
11.
Int J Syst Evol Microbiol ; 66(2): 922-927, 2016 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-26621119

RESUMO

A novel Gram-stain-positive, non-spore-forming, irregular rod-shaped, non-motile and facultatively anaerobic actinobacterium, designated strain YIM 101269T, was isolated from the faeces of Rhinoceros unicornis living in Yunnan Wild Animal Park, Yunnan province, south-west China. The isolate grew at 10-35 °C, at pH 6-12 and with 0-9 % (w/v) NaCl. The cell-wall peptidoglycan of the organism contained ll-diaminopimelic acid as the diagnostic diamino acid. The polar lipids detected were diphosphatidylglycerol, phosphatidylglycerol, three unidentified polar lipids, one unidentified aminophospholipid and three unknown glycolipids. The major cellar fatty acid was anteiso-C15 : 0.MK-10(H4) was the predominant menaquinone. The DNA G+C content was 69.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain YIM 101269T belonged to the genus Tessaracoccus, closely related to Tessaracoccus flavescens DSM 18582T (97.4 % similarity). Based on the evidence from the present study, strain YIM 101269T is considered to represent a novel species of the genus Tessaracoccus, for which the name Tessaracoccus rhinocerotis sp. nov. is proposed. The type strain is YIM 101269T ( = DSM 27579T = CCTCC AB 2013217T).

12.
Antonie Van Leeuwenhoek ; 108(6): 1477-1483, 2015 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-26423082

RESUMO

Two novel actinobacteria, designated strains YIM 101617(T) and YIM 101632(T), were isolated from Lama pacos (alpaca) and Viverra zibetha (civet) faeces in Yunnan Wild Animal Park in Yunnan province, southwestern China. Both strains should be placed in genus Enteractinococcus based on phylogenetic analysis. Based on 16S rRNA gene sequence analysis, strain YIM 101617(T) exhibits high similarity to Enteractinococcus fodinae DSM 22966(T) (97.70 %) and Enteractinococcus coprophilus YIM 100590(T) (97.45 %), whilst YIM 101632(T) exhibits high similarity to Enteractinococcus coprophilus YIM 100590(T) (97.25 %), and the similarity between YIM 101617(T) and YIM 101632(T) is 95.90 %. However, DNA-DNA hybridization values of the two strains with the type strains in the genus Enteractinococcus were low (<70 %). Most morphological and chemotaxonomic characteristics of the two strains were found to be similar to those of species in the genus Enteractinococcus but also some differences were observed. The DNA G+C contents of strains YIM 101617(T) and YIM 101632(T) were determined to be 55.9 and 56.4 mol%, respectively. Based on these data, the two strains are concluded to represent two different novel species in the genus Enteractinococcus. The names Enteractinococcus lamae sp. nov. (type strain YIM 101617(T)=DSM 27612(T)=CCTCC AB 2013230(T)) and Enteractinococcus viverrae sp. nov. (type strain YIM 101632(T)=KCTC 39552(T)=CCTCC AB 2013280(T)) are proposed, respectively.


Assuntos
Fezes/microbiologia , Micrococcaceae/classificação , Micrococcaceae/isolamento & purificação , Animais , Animais de Zoológico/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , Camelídeos Americanos/microbiologia , China , Análise por Conglomerados , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Micrococcaceae/genética , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Viverridae/microbiologia
13.
Antonie Van Leeuwenhoek ; 108(5): 1099-105, 2015 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-26303282

RESUMO

A novel Gram-negative, strictly aerobic, short rod-shaped, non-motile bacterium, designated YIM 101302(T), was isolated from the faeces of Rhinoceros unicornis dwelling in the Yunnan Wild Animal Park, Yunnan province, South-West China. The 16S rRNA gene sequence analysis revealed a clear affiliation of strain YIM 101302(T) to the genus Sphingobacterium. The newly isolated bacterium was found to be closely related to Sphingobacterium composti T5-12(T) (97.1% 16S rRNA sequence identity) and Sphingobacterium alimentarium WCC 4521(T) (95.6% 16S rRNA sequence identity) forming a distinct clade with these two species. Polar lipids of strain YIM 101302(T) were identified as phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unidentified aminophospholipid, and three unidentified polar lipids; the predominant menaquinone as MK-7 and the major fatty as iso-C15:0. The genomic DNA G+C content was determined to be 38.9 mol%. The DNA-DNA hybridization values between strain YIM 101302(T) and S. composti T5-12(T), was 53.6 ± 5.8%. These results indicates that strain YIM 101302(T) represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium rhinocerotis sp. nov. is proposed. The type strain is YIM 101302(T) (=CCTCC AB 2013218(T) = KCTC 42533(T)).


Assuntos
Fezes/microbiologia , Perissodáctilos/microbiologia , Sphingobacterium/classificação , Animais , Metabolismo dos Lipídeos , Filogenia , RNA Ribossômico 16S/genética , Sphingobacterium/genética , Sphingobacterium/isolamento & purificação , Sphingobacterium/metabolismo
14.
Int J Syst Evol Microbiol ; 59(Pt 10): 2575-81, 2009 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-19622654

RESUMO

Two Gram-negatively stained, facultatively anaerobic, non-motile, vibrioid and rod-shaped, chemoheterotrophic bacterial strains, designated YIM D82(T) and YIM D812(T), were isolated from a salt mine in Yunnan, south-west China. DNA-DNA hybridization, genomic DNA G+C content and phylogenetic analyses based on 16S rRNA gene sequences divided the two isolates into two distinct genospecies that were also clearly differentiated by fatty acid profiles, carbon source utilization patterns, antibiotic susceptibility and biochemical characteristics. The two isolates grew in the presence of 1.5-20 % NaCl, and optimally at 28 degrees C and pH 7.5. The genomic DNA G+C contents of strains YIM D82(T) and YIM D812(T) were 61.5 and 62.3 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains YIM D82(T) and YIM D812(T) were members of the family Rhodospirillaceae and showed 90.5-90.6 % and 90.1-90.2 % similarities with their closest relatives, Rhodovibrio sodomensis and Rhodovibrio salinarum, respectively. Differential phenotypic and genotypic characteristics of the two isolates from recognized genera showed that the two strains should be classified as representing a new genus and two novel species for which the names Fodinicurvata sediminis gen. nov., sp. nov. (type strain YIM D82(T)=DSM 21159(T)=KCTC 22351(T)) and Fodinicurvata fenggangensis sp. nov. (type strain YIM D812(T)=CCTCC AA 208037(T)=DSM 21160(T)) are proposed.


Assuntos
Hidroxibutiratos/metabolismo , Poliésteres/metabolismo , Rhodospirillaceae/isolamento & purificação , Rhodospirillaceae/metabolismo , Microbiologia do Solo , China , DNA Bacteriano/genética , DNA Ribossômico/genética , Ácidos Graxos/química , Ácidos Graxos/metabolismo , Dados de Sequência Molecular , Filogenia , RNA Ribossômico 16S/genética , Rhodospirillaceae/classificação , Rhodospirillaceae/genética
15.
Int J Syst Evol Microbiol ; 59(Pt 6): 1382-6, 2009 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-19502320

RESUMO

A novel Gram-negative, non-sporulating, moderately halophilic, facultatively alkaliphilic, catalase- and oxidase-positive, obligately aerobic bacterium, strain YIM-Y25(T), was isolated from a subterranean brine sample collected from a salt mine in Yunnan, south-west China. Cells were spirilla, motile by monopolar flagella, with meso-diaminopimelic acid in the cell-wall peptidoglycan. Growth occurred with 1-15 % (w/v) NaCl (optimum 5 %), at pH 6.0-10.0 (optimum pH 8.0) and at 15-50 degrees C (optimum 35-40 degrees C). Ubiquinone Q-8 was the predominant respiratory quinone. Polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylamine and an unidentified phospholipid. The major cellular fatty acids were C(18 : 1)omega7c, iso-C(16 : 0), C(16 : 0) and C(16 : 1). The genomic DNA G+C content was 58.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM-Y25(T) was most closely related to the type strain of the sole recognized species of the genus Saccharospirillum, Saccharospirillum impatiens EL-105(T) (sequence similarity 97.0 %), and these two strains formed a robust lineage in the phylogenetic tree. The level of DNA-DNA relatedness between them was 12.6 %. The combination of phylogenetic analysis, phenotypic differences, chemotaxonomic properties and DNA-DNA hybridization data supported the view that this strain represents a novel species of the genus Saccharospirillum, for which the name Saccharospirillum salsuginis sp. nov. is proposed, with YIM-Y25(T) (=CCTCC AA 207033(T) =KCTC 22169(T)) as the type strain.


Assuntos
Gammaproteobacteria/classificação , Cloreto de Sódio , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/análise , DNA Ribossômico/análise , Ácidos Graxos/análise , Gammaproteobacteria/genética , Gammaproteobacteria/isolamento & purificação , Gammaproteobacteria/fisiologia , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , Fenótipo , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Especificidade da Espécie
16.
Int J Syst Evol Microbiol ; 59(Pt 4): 874-9, 2009 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-19329623

RESUMO

A novel Gram-positive-staining, catalase- and oxidase-positive, non-motile, non-spore-forming coccus, designated YIM-Y21(T), was isolated from a salt mine in Yunnan, south-west China. The strain was moderately halophilic, facultatively alkaliphilic and obligately aerobic. Colonies were white. Growth occurred with 1.0-30.0 % NaCl (optimum, 10.0 % NaCl), at pH 6.0-10.0 (optimum, pH 8.5) and at 5-40 degrees C (optimum, 25 degrees C). The major amino acid constituents of the cell wall were glycine and lysine. The major cellular fatty acids were anteiso-C(15 : 0), anteiso-C(17 : 0) and iso-C(15 : 0). MK-6 was the predominant respiratory quinone, with MK-7 present in minor amounts. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and an unidentified phospholipid. The DNA G+C content was 46.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain YIM-Y21(T) was most closely related to the type strains of the nine recognized species of the genus Salinicoccus. The sequence similarities between the isolate and the type strains of members of this genus were in the range of 90.6-93.8 %, which indicated that strain YIM-Y21(T) is a representative of a novel species within the genus Salinicoccus. Together with the phenotypic characteristics and chemotaxonomic differences, these results support the proposal of a novel species of the genus Salinicoccus, Salinicoccus albus sp. nov., with YIM-Y21(T) (=CCTCC AA 207024(T) =DSM 19776(T) =KCTC 13192(T)) as the type strain.


Assuntos
Microbiologia do Solo , Staphylococcaceae/classificação , Staphylococcaceae/isolamento & purificação , Aminoácidos/análise , Técnicas de Tipagem Bacteriana , Composição de Bases , Parede Celular/química , China , Análise por Conglomerados , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Ácidos Graxos/análise , Concentração de Íons de Hidrogênio , Dados de Sequência Molecular , Filogenia , Quinonas/análise , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Homologia de Sequência do Ácido Nucleico , Cloreto de Sódio/metabolismo , Staphylococcaceae/genética , Staphylococcaceae/fisiologia , Temperatura Ambiente
17.
Wei Sheng Wu Xue Bao ; 47(4): 571-7, 2007 Aug.
Artigo em Chinês | MEDLINE | ID: mdl-17944352

RESUMO

The microbial diversity of cultivable bacteria, isolated from the ancient salt deposits from the Yipinglang Salt Mine (YPL) in the Yunnan Province, P. R. China,was investigated by using conventional culture-dependent method and phylogenetic analyses based on 16S rRNA gene sequence comparisons. 38 bacteria strains were isolated from the brine, halite and saline soil samples on MBA (marine broth agar 2216, Difco) and ISP 2 (International Streotomyces Project medium 2) media supplemented with 0.5-3.5 mol/L NaCl. The genomic DNAs of the isolates were extracted and their 16S rRNA genes were amplified by PCR using bacterial universal primers. The resulting 16S rRNA gene sequences were compared with sequences obtained from public databases to find the most closely related species. Phylogenetic analyses were performed using the software packages MEGA after multiple alignment of sequence data by CLUSTAL X. The evolutional instances (corrected by Kimura's 2-parameter model) were calculated and clustering was performed with the neighbor-joining method. The results showed that the isolates are members of twenty-four genera (Acinetobacter, Agromyces, Arthrobacter, Bacillus, Brevundimonas, Chromohalobacter, Dietzia, Erythrobacter, Exiguobacterium, Halomonas, Idiomarina, Kocuria, Marinobacter, Micrococcus, Paracoccus, Planomicrbium, Porphyrobacter, Pseudomonas, Psychrobacter, Roseivivax, Saccharospirillum, Salegentibactor, Salinicoccus, Streptomyces) of seventeen families (Alteromonadaceae, Bacillaceae, Caulobacteraceae, Flavobacteriaceae, Halomonadaceae, Idiomarinaceae, Microbacteriaceae, Micrococcaceae, Moraxellaceae, Planococcaceae, Pseudomonadaceae, Rhodobacteraceae, Dietziaceae, Saccharospirillaceae, Sphingomonadaceae, Staphylococcaceae, Streptomycetaceae) in four major phylogenetic groups (Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria). The most abundant and diverse isolates were within the phyla of Proteobacteria (47.3%; Gamma-Proteobacteria, 31.5%; Alpha-Proteobacteria, 15.8%) and Firmicutes (34.2%). The phylogenetic distance matrix results suggested that out of 38 isolates 32 are different strains of 27 known species, and that at least 3 stains represent new species within 3 characterized genera. Y3 (Accession No. EF177665) and Y25 (EF177670) represent new species of the genera Idiomarina and Saccharospirillum, respectively. Y15 (DQ837380), Y16 (EF177680) and Y22 (EF177689) represent a new species of the genus Salinicoccus. And strain Y21 (EF177692) may represent a novel species of a possible new genus of the family Staphylococcaceae. The results presented above shown that there are abundant bacterial species diversity and phylogenetic diversity in the ancient salt deposits from the Yipinglang Salt Mine.


Assuntos
Bactérias/classificação , Bactérias/isolamento & purificação , Biodiversidade , Filogenia , Cloreto de Sódio/metabolismo , Bactérias/genética , Bactérias/metabolismo , China , Técnicas de Cultura , DNA Bacteriano/genética , DNA Ribossômico/genética , Dados de Sequência Molecular , RNA Ribossômico 16S/genética
18.
Wei Sheng Wu Xue Bao ; 47(2): 295-300, 2007 Apr.
Artigo em Chinês | MEDLINE | ID: mdl-17552238

RESUMO

The prokaryotic microbial diversity of the ancient salt deposits in the Kunming Salt Mine, PR China was investigated using PCR-DGGE and rRNA approaches. Total community DNA was extracted and purified by a direct method, which yielded amplified DNA of high molecular weight for samples. A variable region of 16S rRNA gene was then amplified by PCR with bacterial and archaeal primers and analyzed by denaturing gradient gel electrophoresis (DGGE). Twenty-seven major bands were detected in the bacterial DGGE profile of the sample, but only one band of pure culture strains of bacteria isolated from the Kunming Salt Mine matched with one band of sample. No band of pure culture strains of archaea isolated from the Kunming Salt Mine matched with 18 major bands of sample. The results indicated that most of microbes in this environment are likely uncultivable. Clones on the plate were not the predominant species in the community. Two 16S rRNA gene clone libraries (bacteria and archaea) were also constructed, and 36 and 20 clones were selected for amplified ribosomal DNA restriction analysis (ARDRA). ARDRA with enzymes Afa I, Hha I, Hae III revealed 10 bacterial operational taxonomic units (OTUs), with three most abundant OTUs accounting for 38.9%, 25.0%, 16.7% of all the bacterial 16S rDNA clones, respectively. The remaining 7 OTUs presented at low levels, were represented by a single clone. Eight archaeal OTUs were obtained but no predominant OTUs. Some clones were sequenced and each sequence was compared with all nucleotide sequences in GenBank database. Examination of 16S rDNA clones showed that the ancient salt deposits in the Kunming Salt Mine contained a phylogenetically diverse population of organisms from the Bacteria domain with members of three major lineages represented: alpha-proteobacteria, gamma-Proteobacteria and Actinobacteria, especially Pseudomonas. Surprisingly, we recovered a variety of sequence closely related to Actinobacteria which was not found in other salt deposits. All of archaeal clones are from Halorubrum, Haloterrigena and uncultured archaea. The results of DGGE and clone library profiling analysis both indicated that microbial community of the Kunming Salt Mine had higher diversity. In this initial survey, our polyphasic approaches demonstrated that novel and uncultured microbes thrive in the ancient salt deposits of the Kunming Salt Mine. Molecular analysis of the microbial diversity in salt deposits provides foundation for better application of microbial resources.


Assuntos
Archaea/classificação , Bactérias/classificação , Microbiologia da Água , Archaea/genética , Bactérias/genética , Mineração , RNA Ribossômico 16S/genética , Cloreto de Sódio
19.
Wei Sheng Wu Xue Bao ; 46(6): 967-72, 2006 Dec.
Artigo em Chinês | MEDLINE | ID: mdl-17302163

RESUMO

In order to understand the diversity of culturable bacteria, 44 bacteria strains inhabiting brines and salt crystals in the Kunming Salt Mine, P. R. China were isolated and cultured. Results showed that the numbers of the bacteria isolated from salt crystals (3.1 x 10(3) - 3.7 x 10(6) CFU/g) were higher than those from brines (1.3 - 6.3 x 10(3) CFU/L). A neighbor-joining tree of the partial 16S rDNA sequences (about 600bp of 5'-end) showed that 44 strains were phylogenetically clustered into 4 major groups and 44 distinct lineages or species (the similarities of 16S rDNA sequences <97%): 24 strains of Firmicutes (54.6%), 2 strains of alpha-Proteobacteria (4.6%), 4 strains of gamma-Proteobacteria (9.1%) and 14 strains of Actinobacteria (31.7%). Strains of the genus Bacillus (26.1% and 59.9%) were the most predominant microorganisms among brines and salt crystals. Additionally, seven potential novel species were found, based on the similarities of 16S rDNA sequences to those of previously published species, and seven strains with bioactivities against pathogenic microorganisms were isolated. The conclusion is that there are a number of novel species and bioactive strains, as well as great diversity in Kunming Salt Mine.


Assuntos
Bactérias/isolamento & purificação , Mineração , Cloreto de Sódio , Actinobacteria/isolamento & purificação , Alphaproteobacteria/isolamento & purificação , Bactérias/classificação , Bactérias/crescimento & desenvolvimento , Gammaproteobacteria/isolamento & purificação , Filogenia
20.
Wei Sheng Wu Xue Bao ; 46(6): 1018-22, 2006 Dec.
Artigo em Chinês | MEDLINE | ID: mdl-17302174

RESUMO

Two different direct DNA extraction methods and one indirect DNA extraction method were applied to recover environmental DNA from six mat samples, which were sampled closely around a high-temperature spring vent in Tengchong Rehai of the western Yunnan province. As the criteria, quantity and purity of the extracted crude DNA, the result of PCR amplification for denaturing gradient gel electrophoresis (DGGE) before and after crude DNA purification, and the Shannon-wiener index of DGGE profiles were used to evaluate the direct and indirect DNA extraction methods. For the samples of less biomass, the indirect method yielded available crude DNA with high purity, and the DNA was amplified without purification by PCR for DGGE. The two direct methods extracted less DNA than indirect method from the samples of less biomass, and the crude DNA extraction could not be amplified by PCR. Despite the lower quantity of DNA yield, the indirect DNA extraction method for the other' mat samples presented more diverse bacterial community than that of the direct DNA extraction methods according to the Shannon-wiener index of the PCR-DGGE profiles.


Assuntos
DNA Bacteriano/isolamento & purificação , Microbiologia Ambiental , Fontes Termais/microbiologia , Eletroforese em Gel de Poliacrilamida , Reação em Cadeia da Polimerase , Microbiologia do Solo
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