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1.
Microbiol Res ; 236: 126443, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32146293

RESUMO

Recently, the characteristics of prevalent bacterial pathogens causing bovine mastitis have become increasingly complicated, and many commensal or unusual bacterial species have been isolated from milk samples of cows with mastitis. Strain JS20170427COW was isolated dominantly from the milk of Holstein Friesian cows with mastitis in Jiangsu province in China. Colonies of this strain showed a hillock-like protrusion, with a pale-yellow color at the protrusion and a transparent edge, 4-5 mm in diameter after cultivation at 37 °C for 24 h on 5% sheep blood-enriched agar. Although 16 s rRNA analysis showed the closest relationship with the family Flavobacteriaceae containing Elizabethkingia spp., Riemerella sp. and Soonwooa buanensis, the bacterial species of strain JS20170427COW could not be identified adequately because it had a sequence identity of less than 95 % in 16 s rRNA when compared with all the known species of the family Flavobacteriaceae. Unexpectedly, both the first and re-sequencing data determined the whole genome size of strain JS20170427COW to be 2.69 Mb, which is different from the above three closest bacterial species. Therefore, we hypothesized that strain JS20170427COW is a novel taxon of Flavobacteriaceae. Further identification using conserved genes, single-nucleotide polymorphisms (SNPs), phylogenetic and average nucleotide identity analyses based on whole genome data suggested that JS20170427COW was more likely to be an Elizabethkingia-like strain, but that it does not belong to the Elizabethkingia genus. Comparison of the predicted open reading frames (ORFs) revealed that strain JS20170427COW encodes more special genes than Elizabethkingia species. In summary, we identified a novel Flavobacteriaceae taxon showing a close relationship with Elizabethkingia subspecies, which has potential pathogenicity in bovine mastitis.


Assuntos
Infecções por Flavobacteriaceae/diagnóstico , Flavobacteriaceae , Mastite Bovina/microbiologia , Animais , Técnicas de Tipagem Bacteriana , Bovinos , Doenças dos Bovinos/microbiologia , China , DNA Bacteriano/genética , Feminino , Flavobacteriaceae/classificação , Flavobacteriaceae/genética , Flavobacteriaceae/isolamento & purificação , Filogenia , RNA Ribossômico 16S/genética
2.
PLoS One ; 15(1): e0227967, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31945114

RESUMO

Neonates are at high risk for central line associated bloodstream infections (CLABSI). Biofilm formation is universal on indwelling catheters but why some biofilms seed the bloodstream to cause CLABSI is not clearly understood. With the objective to test the hypothesis that catheter biofilm microbiome in neonates with CLABSI differs than those without infection, we prospectively enrolled neonates (n = 30) with infected and uninfected indwelling central catheters. Catheters were collected at the time of removal, along with blood samples and skin swabs at the catheter insertion sites. Microbiomes of catheter biofilms, skin swabs and blood were evaluated by profiling the V4 region of the bacterial 16S rRNA gene using Illumina MiSeq sequencing platform. The microbial DNA load was higher from catheter biofilms of CLABSI patients without differences in alpha diversity when compared to that of the non-CLABSI neonates. Proteus and unclassified Staphylococcaceae were more abundant in infected catheter biofilms while Bradyrhizobium, Cloacibacterium, and Sphingomonas were more abundant in the uninfected catheters. A blood microbiome was detected in uninfected samples. The blood microbiome in CLABSI neonates clustered separately from the uninfected blood samples in beta diversity plots. We found that the microbiome signature in catheter biofilm and blood of neonates with CLABSI is different than the microbiomes of non-CLABSI neonates.


Assuntos
Infecções Bacterianas/genética , Infecções Relacionadas a Cateter/genética , Flavobacteriaceae/genética , Microbiota/genética , Infecções Bacterianas/sangue , Infecções Bacterianas/microbiologia , Infecções Bacterianas/patologia , Biofilmes/crescimento & desenvolvimento , Bradyrhizobium/genética , Bradyrhizobium/patogenicidade , Infecções Relacionadas a Cateter/sangue , Infecções Relacionadas a Cateter/microbiologia , Infecções Relacionadas a Cateter/patologia , Feminino , Flavobacteriaceae/patogenicidade , Humanos , Recém-Nascido , Masculino , RNA Ribossômico 16S/genética , Estudos Retrospectivos , Staphylococcaceae/genética , Staphylococcaceae/patogenicidade
3.
Arch Microbiol ; 202(2): 293-298, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31650196

RESUMO

A Gram-stain negative, aerobic, motile and rod-shaped novel bacterial strain, designated MAH-3T, was isolated from soil sample of a rice field. The colonies were orange pigmented, smooth, circular and 0.4-0.9 mm in diameter when grown on R2A agar for 3 days. Strain MAH-3T was found to grow at 10-40 °C (optimum 30 °C), pH 6.0-8.0 (optimum 7.0) and in the presence of 0-1.0% NaCl (optimum 0%). Cell growth occurs on R2A agar and Luria-Bertani agar, but not on nutrient agar, tryptone soya agar and MacConkey agar. Cells were positive for catalase test but negative for oxidase test. Cells were able to hydrolyze casein, gelatin, DNA and Tween 80. 16S rRNA gene sequence analysis revealed that strain MAH-3T was most closely related to the genus Fluviicola and exhibited the highest sequence similarity to Fluviicola hefeinensis MYL-8T (97.4%), Fluviicola taffensis RW262T (96.2%) and Fluviicola kyonggii CA-1T (95.6%). Strain MAH-3T had a genome size of 4,271,694 bp and the genomic DNA G + C content was determined to be 41.7 mol%. The genome contained 19 contigs encoded by 3,664 protein-coding genes with 34 tRNA and 4 rRNA genes. The genomic ANI value between strain MAH-3T and one of the closely related type strains, F. taffensis DSM 16823T was 76.2%. The predominant isoprenoid quinone of isolated strain MAH-3T was menaquinone-6 (MK-6). The major fatty acids were identified as C15:0 iso, C15:0 2OH and C17:0 iso 3OH. On the basis of these phenotypic, genotypic and chemotaxonomic studies and DNA-DNA hybridization results, the isolated strain MAH-3T represents a novel species, for which the name Fluviicola chungangensis sp. nov. is proposed, with MAH-3T as the type strain (= KACC 19742T = CGMCC 1.13750T).


Assuntos
Flavobacteriaceae/classificação , Oryza/microbiologia , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/análise , Flavobacteriaceae/genética , Genoma Bacteriano/genética , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Especificidade da Espécie
4.
Syst Appl Microbiol ; 43(1): 126045, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31831198

RESUMO

Cultivable bacteria represent only a fraction of the diversity in microbial communities. However, the official procedures for classification and characterization of a novel prokaryotic species still rely on isolates. Nevertheless, due to single cell genomics, it is possible to retrieve genomes from environmental samples by sequencing them individually, and to assign specific genes to a specific taxon, regardless of their ability to grow in culture. In this study, a complete description was performed for uncultured Kordia sp. TARA_039_SRF, a proposed novel species within the genus Kordia, using culture-independent techniques. The type material was a high-quality draft genome (94.97% complete, 4.65% gene redundancy) co-assembled using ten nearly identical single amplified genomes (SAGs) from surface seawater in the North Indian Ocean during the Tara Oceans Expedition. The assembly process was optimized to obtain the best possible assembly metrics and a less fragmented genome. The closest relative of the species was Kordia periserrulae, which shared 97.56% similarity of the 16S rRNA gene, 75% orthologs and 89.13% average nucleotide identity. The functional potential of the proposed novel species included proteorhodopsin, the ability to incorporate nitrate, cytochrome oxidases with high affinity for oxygen, and CAZymes that were unique features within the genus. Its abundance at different depths and size fractions was also evaluated together with its functional annotation, revealing that its putative ecological niche could be particles of phytoplanktonic origin. It could putatively attach to these particles and consume them while sinking to the deeper and oxygen depleted layers of the North Indian Ocean.


Assuntos
Flavobacteriaceae/classificação , Flavobacteriaceae/genética , Proteínas de Bactérias/genética , DNA Bacteriano/genética , Ecossistema , Genoma Bacteriano/genética , Oceano Índico , Metagenômica , Microbiota/genética , Hibridização de Ácido Nucleico , Filogenia , RNA Ribossômico 16S/genética , Rodopsinas Microbianas/genética , Água do Mar/microbiologia , Análise de Sequência de DNA
5.
J Microbiol ; 57(11): 982-990, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31659684

RESUMO

Microalgae and bacteria are known to be closely associated in diverse environments. To isolate dominant bacterial species associated with a green alga, Dunaliella tertiolecta, a photoreactor culture of the microalga was investigated using culture-based and culture-independent approaches. The bacterial community structure of the algal culture showed that the most abundant bacterial species under the culture conditions was related to the genus Winogradskyella. The closely related amplicon sequences, showing ≥ 99.5% 16S rRNA gene sequence similarity to one of the isolates, designated IMCC-33238T, constituted > 49% of the bacterial community and was therefore regarded as the most dominant species in the algal culture. Strain IMCC33238T was characterized by Gramstaining-negative and orange-colored rods. Phylogenetic analyses of the 16S rRNA genes as well as whole genome sequences revealed that strain IMCC33238T belonged to Winogradskyella and shared more than 97.2% 16S rRNA gene sequence similarity with Winogradskyella species. The strain contained iso-C15:1 G, iso-C15:0, iso-C15:0 3-OH, and summed feature 3 (C16:1ω6c and/or C16:1ω7c) as major fatty acids and MK-6 as the predominant quinone. The polar lipids found in strain IMCC33238T were phosphatidylethanolamine, two unidentified aminolipids, and three unidentified lipids. The genome of strain IMCC33238T was 3.37 Mbp in size with 33.9 mol% G + C content and proteorhodopsin. Many genes encoding folate and vitamin production are considered to play an important role in the bacteria-algae interaction. On the basis of phylogenetic and phenotypic characteristics, strain IMCC33238T represents a novel species in the genus Winogradskyella, for which the name Winogradskyella algicola sp. nov. is proposed. The type strain is IMCC33238T (= KACC 21192T = NBRC 113704T).


Assuntos
Clorofíceas/microbiologia , Flavobacteriaceae/classificação , Flavobacteriaceae/genética , Flavobacteriaceae/isolamento & purificação , Filogenia , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , Benzoquinonas/química , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacteriaceae/fisiologia , Fosfatidiletanolaminas/química , RNA Ribossômico 16S/genética , República da Coreia , Rodopsinas Microbianas/química , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química , Sequenciamento Completo do Genoma
6.
J Appl Microbiol ; 127(6): 1635-1645, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31517421

RESUMO

AIM: To study the association of opportunistic infection due to Myroides odoratimimus in piglets immunocompromised by porcine circovirus type 2 (PCV2) infection. METHODS AND RESULTS: The clinical samples (n = 101) were analysed bacteriologically. The isolates were identified by their phenotypes and MALDI TOF-MS analysis as Myroides species. The phylogram constructed based on nucleotide sequences of the 16S rRNA gene showed identity (~99%) with the M. odoratimimus isolates. The minimum inhibitory concentration values for antibiotics revealed M. odoratimimus to be resistant against carbapenem, cephalosporins, aminoglycosides and fluoroquinolones. The presence of PCV2 in affected tissue samples was confirmed by amplification of the 565 bp region of ORF2 of the PCV2 genome. The topology of the phylogenetic tree grouped the PCV2 with cluster-2d. CONCLUSIONS: PCV2 being immunosuppressive in nature might have impaired the immunity thereby increasing the susceptibility of immunocompromised piglets to opportunistic pathogens such as M. odoratimimus leading to disease severity and high mortality. The M. odoratimimus isolates were found to be multidrug resistant and evidenced for uncertain clinical relevance and hence could act as hidden source of public health hazard. SIGNIFICANCE AND IMPACT OF THE STUDY: Myroides odoratimimus is a rarely reported human pathogen. We reported the incidence of infection due to seemingly rare isolates of M. odoratimimus causing an outbreak of pneumonia in piglets. This appears, to the best of authors' knowledge, to be the first outbreak due to Myroides recorded in animal clinical cases described in the literature.


Assuntos
Infecções por Flavobacteriaceae/imunologia , Infecções por Flavobacteriaceae/microbiologia , Flavobacteriaceae/isolamento & purificação , Síndrome Definhante Multissistêmico de Suínos Desmamados/imunologia , Síndrome Definhante Multissistêmico de Suínos Desmamados/microbiologia , Animais , Antibacterianos/farmacologia , Circovirus/classificação , Circovirus/genética , Circovirus/isolamento & purificação , Flavobacteriaceae/classificação , Flavobacteriaceae/efeitos dos fármacos , Flavobacteriaceae/genética , Hospedeiro Imunocomprometido , Testes de Sensibilidade Microbiana , Filogenia , RNA Ribossômico 16S/genética , Suínos , Desmame
7.
J Agric Food Chem ; 67(33): 9307-9313, 2019 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-31352784

RESUMO

Porphyra is one of the most consumed types of red algae. Porphyran is the major polysaccharide extracted from Porphyra, and it is composed of alternating 4-linked α-l-galactopyranose-6-sulfate (L6S) and 3-linked ß-d-galactopyranose (G) residues. ß-Porphyranases are promising tools for degrading porphyran; however, few enzymes have been reported, and the biochemical properties of porphyranases are still unclear. Here, a novel GH16 ß-porphyranase, designated as Por16A_Wf, was cloned from Wenyingzhuangia fucanilytica and expressed in Escherichia coli. Its biochemical properties and hydrolysis pattern were characterized. Por16A_Wf exhibited stable activity on a wide pH scale from 3.5 to 11.0. Glycomics analysis using LC-MS revealed that Por16A_Wf specifically hydrolyzed the glycosidic linkage of G-L6S, whereas it tolerated 3,6-anhydro-α-l-galactopyranose and methyl-d-galactose in -2 and +2 subsites, respectively. Por16A_Wf could be applied as a biotechnological tool for tailoring porphyran, which would serve in directional preparation of its disaccharide, producing products with various molecular weights and facilitating investigation of the structural heterogeneity of Porphyra polysaccharides.


Assuntos
Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Flavobacteriaceae/enzimologia , Glicosídeo Hidrolases/química , Glicosídeo Hidrolases/genética , Água do Mar/microbiologia , Sefarose/análogos & derivados , Sequência de Aminoácidos , Proteínas de Bactérias/metabolismo , Biocatálise , Biotecnologia , Clonagem Molecular , Estabilidade Enzimática , Flavobacteriaceae/classificação , Flavobacteriaceae/genética , Flavobacteriaceae/isolamento & purificação , Glicosídeo Hidrolases/metabolismo , Concentração de Íons de Hidrogênio , Hidrólise , Peso Molecular , Filogenia , Porphyra/química , Porphyra/metabolismo , Sefarose/química , Sefarose/metabolismo , Alinhamento de Sequência
8.
Microb Cell Fact ; 18(1): 122, 2019 Jul 08.
Artigo em Inglês | MEDLINE | ID: mdl-31286972

RESUMO

BACKGROUND: Acetyl xylan esterase plays an important role in the complete enzymatic hydrolysis of lignocellulosic materials. It hydrolyzes the ester linkages of acetic acid in xylan and supports and enhances the activity of xylanase. This study was conducted to identify and overexpress the acetyl xylan esterase (AXE) gene revealed by the genomic sequencing of the marine bacterium Ochrovirga pacifica. RESULTS: The AXE gene has an 864-bp open reading frame that encodes 287 aa and consists of an AXE domain from aa 60 to 274. Gene was cloned to pET-16b vector and expressed the recombinant AXE (rAXE) in Escherichia coli BL21 (DE3). The predicted molecular mass was 31.75 kDa. The maximum specific activity (40.08 U/mg) was recorded at the optimal temperature and pH which were 50 °C and pH 8.0, respectively. The thermal stability assay showed that AXE maintains its residual activity almost constantly throughout and after incubation at 45 °C for 120 min. The synergism of AXE with xylanase on beechwood xylan, increased the relative activity 1.41-fold. CONCLUSION: Resulted higher relative activity of rAXE with commercially available xylanase on beechwood xylan showed its potential for the use of rAXE in industrial purposes as a de-esterification enzyme to hydrolyze xylan and hemicellulose-like complex substrates.


Assuntos
Acetilesterase/metabolismo , Proteínas de Bactérias/metabolismo , Endo-1,4-beta-Xilanases/metabolismo , Fagus/química , Flavobacteriaceae/enzimologia , Xilanos/metabolismo , Acetilesterase/genética , Sequência de Aminoácidos , Proteínas de Bactérias/genética , Sequência de Bases , Estabilidade Enzimática , Flavobacteriaceae/genética , Concentração de Íons de Hidrogênio , Hidrólise , Microbiologia Industrial , Fases de Leitura Aberta , Água do Mar/microbiologia , Especificidade por Substrato , Temperatura
9.
Food Chem ; 299: 125142, 2019 Nov 30.
Artigo em Inglês | MEDLINE | ID: mdl-31325715

RESUMO

Alginate lyases can be used for alginate oligosaccharide production and for structural characterization or modification of alginates. For these applications it is important to obtain detailed information on mode of action and substrate specificities of alginate lyases. In this study, five alginate lyase genes were cloned from Cellulophaga algicola DSM 14237 genomic DNA, heterologously expressed, and characterized by using HPSEC-RI and HPAEC-PAD/MS. It was demonstrated that these analytical approaches can provide detailed information on preferred substrates, extent of hydrolysis, and the liberated products. The recombinant enzymes cleaved alginates endolytically (CaAly1, CaAly2, CaAly3) or exolytically (CaAly4, CaAly5). The three endolytic alginate lyases predominantly hydrolyzed guluronic acid-rich alginates, only CaAly1 also showed activity on mannuronic acid-rich alginates. The oligosaccharide profiles further demonstrated that the endolytic enzymes have rather narrow but slightly different substrate specificities and that the two exolytic alginate lyases mainly cleaved unsaturated guluronic acid oligosaccharides to monomers.


Assuntos
Alginatos/metabolismo , Cromatografia em Gel/métodos , Cromatografia por Troca Iônica/métodos , Flavobacteriaceae/enzimologia , Polissacarídeo-Liase/metabolismo , Alginatos/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Clonagem Molecular , Flavobacteriaceae/genética , Ácidos Hexurônicos/metabolismo , Hidrólise , Polissacarídeo-Liase/genética , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Especificidade por Substrato
10.
Arch Microbiol ; 201(8): 1119-1127, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31165177

RESUMO

Strain KYPW7T, isolated from the Funglin Stream in Taiwan, was characterized using a polyphasic taxonomy approach. Cells of strain KYPW7T were Gram-stain-negative, aerobic, non-spore forming, non-motile rods and formed white colonies. Growth occurred at 15-30 °C (optimum 25 °C), at pH 6-8 (optimum pH 6.5) and with 0-1% NaCl (optimum 0%). Phylogenetic analyses based on 16S rRNA and coding sequences of 92 protein clusters showed that strain KYPW7T represents a novel genus in the family Flavobacteriaceae. The 16S rRNA gene sequence of strain KYPW7T was related to the species of the genera Chryseobacterium (91.8-96.0% sequence similarity), Bergeyella (95.1-95.8%), Cloacibacterium (94.5-95.7%), Daejeonia (95.6%) and Riemerella (94.0-95.0%). Strain KYPW7T showed less than 72% average nucleotide identity and less than 24% digital DNA-DNA hybridization identity compared to the type strains of related genera within the family Flavobacteriaceae. The predominant fatty acids were iso-C15:0 and iso-C17:0 3-OH. The major isoprenoid quinone was MK-6 and the DNA G + C content was 36.8 mol%. The polar lipids had phosphatidylethanolamine, three uncharacterized aminophospholipids and an uncharacterized phospholipid. The polyamines contained homospermidine, putrescine and spermidine. On the basis of the genotypic and phenotypic data, strain KYPW7T represents a novel species of a new genus in the family Flavobacteriaceae, for which the name Amniculibacterium aquaticum gen. nov., sp. nov. is proposed. The type strain is KYPW7T (= BCRC 81123T = LMG 30598T = KCTC 62512T).


Assuntos
Flavobacteriaceae , Rios/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases/genética , DNA Bacteriano/genética , Ácidos Graxos/análise , Flavobacteriaceae/classificação , Flavobacteriaceae/genética , Flavobacteriaceae/isolamento & purificação , Hibridização de Ácido Nucleico , Fosfatidiletanolaminas/análise , Fosfolipídeos/análise , Filogenia , Poliaminas/análise , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Taiwan
11.
Emerg Infect Dis ; 25(7): 1412-1414, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31211685

RESUMO

Using 16S rRNA and rpoB gene sequencing, we identified 6 patients infected with Elizabethkingia bruuniana treated at E-Da Hospital (Kaohsiung, Taiwan) during 2005-2017. We describe patient characteristics and the molecular characteristics of the E. bruuniana isolates, including their MICs. Larger-scale studies are needed for more robust characterization of this pathogen.


Assuntos
Infecções por Flavobacteriaceae/epidemiologia , Infecções por Flavobacteriaceae/microbiologia , Flavobacteriaceae , Idoso , Idoso de 80 Anos ou mais , Antibacterianos/farmacologia , RNA Polimerases Dirigidas por DNA/genética , Feminino , Flavobacteriaceae/classificação , Flavobacteriaceae/efeitos dos fármacos , Flavobacteriaceae/genética , Infecções por Flavobacteriaceae/história , História do Século XXI , Humanos , Masculino , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Taiwan/epidemiologia
12.
Antonie Van Leeuwenhoek ; 112(11): 1645-1653, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31218499

RESUMO

A bacterial strain designated RZ03T was isolated from an intertidal sand sample from the Yellow Sea in China and characterised using a polyphasic taxonomic approach. Cells of strain RZ03T were observed to be Gram-stain negative, aerobic, and oxidase and catalase positive rods showing gliding motility and forming yellow colonies. Growth was found to occur at 7-30 °C (optimum, 25 °C), at pH 5.5-9.5 (optimum, pH 6.5-7.0) and with 0.5-5% NaCl (optimum, 1.5-2%). Phylogenetic analysis based on 16S rRNA gene sequences indicates that strain RZ03T clusters within members of the genus Flavivirga of the family Flavobacteriaceae and is closely related to the type strains Flavivirga amylovorans JCM 17112T and Flavivirga jejuensis JCM 17113T (97.9% and 97.5% similarity, respectively). The predominant cellular fatty acids are iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH and iso-C15:0 3-OH and the major respiratory quinone is MK-6. Polar lipids include phosphatidylethanolamine, three unidentified aminolipids, an unidentified phospholipid and four unidentified lipids. The genome of strain RZ03T is 4.88 Mbp with a G+C content of 32.2 mol%. A total of 4152 genes are predicted, with 4052 protein-coding genes, 51 RNA genes and 49 pseudogenes. This polyphasic study suggests that strain RZ03T represents a novel species in the genus Flavivirga, for which the name Flavivirga rizhaonensis is proposed. The type strain is RZ03T(= KCTC 62833T = MCCC 1K03615T).


Assuntos
Organismos Aquáticos , Flavobacteriaceae/classificação , Flavobacteriaceae/isolamento & purificação , 24975/microbiologia , Composição de Bases , Flavobacteriaceae/química , Flavobacteriaceae/genética , Genoma Bacteriano , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
13.
Curr Microbiol ; 76(9): 975-981, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31144108

RESUMO

A novel Gram-stain-negative bacterium, designated strain BH-SD17T, was isolated from a marine sediment sample in the Bohai Gulf, Yellow Sea, China. Cells of strain BH-SD17T are aerobic, yellow-colored, non-flagellated rods. Growth occurs between 15 and 40 °C (optimum, 30 °C), at pH 6.0-8.5 (optimum, 7.5) and with 1.0-8.0% (w/v) NaCl (optimum, 3.0%). Strain BH-SD17T contains phosphatidylethanolamine and two unidentified lipids as the major polar lipids. The predominant fatty acids are iso-C15:0 (28.5%), iso-C15:1 G (24.4%), and iso-C17:0 3-OH (12.3%). The major respiratory quinone is MK-6. Strain BH-SD17T shows moderate 16S rRNA gene sequence similarity to existing identified strains, is most closely related to the genera Lutimonas (92.1-92.4%), Lutibacter (91.6-92.3%), and Taeania (91.9%). Phylogenetic trees based on 16S rRNA gene sequences show that strain BH-SD17T forms a distinct lineage within the family Flavobacteriaceae. Based on the results of phenotypic, chemotaxonomic and phylogenetic analysis, strain BH-SD17T is considered to represent a novel genus and species in the family Flavobacteriaceae, for which the name Aureibaculum marinum is proposed. The type strain is BH-SD17T (=CCTCC AB 2017072T=KCTC 62204T).


Assuntos
Flavobacteriaceae/isolamento & purificação , Sedimentos Geológicos/microbiologia , Técnicas de Tipagem Bacteriana , DNA Bacteriano , Ácidos Graxos/metabolismo , Flavobacteriaceae/classificação , Flavobacteriaceae/genética , Flavobacteriaceae/metabolismo , Filogenia , RNA Ribossômico 16S/genética , Água do Mar/microbiologia , Cloreto de Sódio/metabolismo
14.
Arch Microbiol ; 201(8): 1019-1024, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31098768

RESUMO

A novel Gelidibacter strain, JCM 31967T, was isolated from seawater collected from the Inland Sea (Setonaikai) in Japan. It was characterized as a Gram-negative, halophilic, oxidase-negative, catalase-positive, aerobic, nonmotile, but gliding, rod-shaped bacterium without flagella. Based on 16S rDNA gene identity, strain JCM 31967T is closely related to Gelidibacter mesophilus (DSM 14095T, 96.6% identity), G. gilvus (IC158T, 96.4%), G. algens (DSM 12408T, 96.1%), G. sediminis (S11-41T, 94.7%), and G. salicanalis (IC162T, 94.7%). The G + C content of strain JCM 31967T DNA was found to be 39.1%. The average nucleotide identity (ANI) values of JCM 31967T against G. algens DSM 12408T and G. mesophilus DSM 14095T were 79.1% and 80.9%, respectively. Strain JCM 31967T phenotypically differed from the closest related Gelidibacter species in its utilization of methyl α-D-mannopyranoside, methyl α-D-glucopyranoside, and D-ribose and in its lack of utilization of L-arginine and D-arabinose. It was further differentiated based on its fatty acid composition, specifically properties of C18:0 and C20:2 ω6c, 9c, which were significantly different from those of G. algens, G. gilvus, G. mesophilus, G. salicanalis, and G. sediminis type strains. Overall, the results of DNA-DNA hybridization and physiological and biochemical analyses differentiated strain JCM 31967T from a previously described species of Gelidibacter. Based on these polyphasic taxonomic findings, it was concluded that strain JCM 31967T is a novel Gelidibacter species, for which the name Gelidibacter japonicus sp. nov. is proposed, with JCM 31967T (= LMG 30063T) as the type strain.


Assuntos
Flavobacteriaceae , Água do Mar/microbiologia , Composição de Bases/genética , DNA Bacteriano/genética , DNA Ribossômico/genética , Ácidos Graxos/análise , Flavobacteriaceae/classificação , Flavobacteriaceae/genética , Flavobacteriaceae/isolamento & purificação , Japão , Hibridização de Ácido Nucleico , Fenótipo , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
15.
mSphere ; 4(2)2019 04 03.
Artigo em Inglês | MEDLINE | ID: mdl-30944210

RESUMO

Elizabethkingia anophelis is an emerging global multidrug-resistant opportunistic pathogen. We assessed the diversity among 13 complete genomes and 23 draft genomes of E. anophelis strains derived from various environmental settings and human infections from different geographic regions around the world from 1950s to the present. Putative integrative and conjugative elements (ICEs) were identified in 31/36 (86.1%) strains in the study. A total of 52 putative ICEs (including eight degenerated elements lacking integrases) were identified and categorized into three types based on the architecture of the conjugation module and the phylogeny of the relaxase, coupling protein, TraG, and TraJ protein sequences. The type II and III ICEs were found to integrate adjacent to tRNA genes, while type I ICEs integrate into intergenic regions or into a gene. The ICEs carry various cargo genes, including transcription regulator genes and genes conferring antibiotic resistance. The adaptive immune CRISPR-Cas system was found in nine strains, including five strains in which CRISPR-Cas machinery and ICEs coexist at different locations on the same chromosome. One ICE-derived spacer was present in the CRISPR locus in one strain. ICE distribution in the strains showed no geographic or temporal patterns. The ICEs in E. anophelis differ in architecture and sequence from CTnDOT, a well-studied ICE prevalent in Bacteroides spp. The categorization of ICEs will facilitate further investigations of the impact of ICE on virulence, genome epidemiology, and adaptive genomics of E. anophelis IMPORTANCE Elizabethkingia anophelis is an opportunistic human pathogen, and the genetic diversity between strains from around the world becomes apparent as more genomes are sequenced. Genome comparison identified three types of putative ICEs in 31 of 36 strains. The diversity of ICEs suggests that they had different origins. One of the ICEs was discovered previously from a large E. anophelis outbreak in Wisconsin in the United States; this ICE has integrated into the mutY gene of the outbreak strain, creating a mutator phenotype. Similar to ICEs found in many bacterial species, ICEs in E. anophelis carry various cargo genes that enable recipients to resist antibiotics and adapt to various ecological niches. The adaptive immune CRISPR-Cas system is present in nine of 36 strains. An ICE-derived spacer was found in the CRISPR locus in a strain that has no ICE, suggesting a past encounter and effective defense against ICE.


Assuntos
Conjugação Genética/genética , Flavobacteriaceae/genética , Flavobacteriaceae/isolamento & purificação , Variação Genética , Genoma Bacteriano , Imunidade Adaptativa , Animais , Proteínas da Membrana Bacteriana Externa/genética , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Culicidae/microbiologia , DNA Intergênico/genética , Flavobacteriaceae/patogenicidade , Infecções por Flavobacteriaceae/microbiologia , Genômica , Saúde Global , Humanos , Filogenia , Virulência/genética
16.
Antonie Van Leeuwenhoek ; 112(8): 1263-1271, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-30941530

RESUMO

A Gram-stain negative, rod-shaped and non-flagellated bacterium, designated strain 1Q3T, was isolated from coastal seawater in Xiamen Island, China, and subjected to taxonomic characterisation using a polyphasic approach. Strain 1Q3T was found to be aerobic, non-gliding and to lack flexirubin-type pigments. Catalase activity was found to be negative and oxidase positive. The strain has the ability to degrade protein. The nearly complete 16S rRNA gene sequence of strain 1Q3T shows high sequence similarities with Nonlabens aestuariivivens OITF-31T (96.1%), Nonlabens halophilus CAU 1131T and Nonlabens spongiae UST030701-156T (95.7% and 95.5%, respectively). Phylogenetic analysis based on 16S rRNA gene sequences and phylogenomic analysis based on a 92 bacterial core gene set indicated that strain 1Q3T should be affiliated to the genus Nonlabens, but forms a distinct monophyletic branch, which is separated from the other members within the genus Nonlabens. The predominant fatty acids (> 10%) were identified as iso-C17:0 3-OH, iso-C15:0 and anteiso-C15:0. The predominant respiratory quinone was found to be MK-6. The polar lipids were identified as phosphatidylethanolamine, a phospholipid, an aminolipid and three unidentified polar lipids. The draft genome size of strain 1Q3T is 3.7 Mb with genomic G + C content of 41.1 mol%. Based on these results, strain 1Q3T is concluded to represent a novel species within the genus Nonlabens, for which the name Nonlabens xiamenensis sp. nov. is proposed with the type strain 1Q3T (= MCCC 1A14023T = KCTC 62889T).


Assuntos
Flavobacteriaceae/classificação , Flavobacteriaceae/isolamento & purificação , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , China , Análise por Conglomerados , Citosol/química , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Ácidos Graxos/análise , Flavobacteriaceae/genética , Flavobacteriaceae/fisiologia , Fosfolipídeos/análise , Filogenia , Quinonas/análise , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
17.
Mar Genomics ; 46: 8-15, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-30852185

RESUMO

The Aquimarina genus is widely distributed throughout the marine environment, however little is understood regarding its ecological role, particularly when in association with eukaryotic hosts. Here, we examine the genomes of two opportunistic pathogens, Aquimarina sp. AD1 and BL5, and a non-pathogenic strain Aquimarina sp. AD10, that were isolated from diseased individuals of the red alga Delisea pulchra. Each strain encodes multiple genes for the degradation of marine carbohydrates and vitamin biosynthesis. These traits are hypothesised to promote nutrient exchange between the Aquimarina strains and their algal host, facilitating a close symbiotic relationship. Moreover, each strain harbours the necessary genes for the assembly of a Type 9 Secretion System (T9SS) and the associated gliding motility apparatus. In addition to these common features, pathogenic strains AD1 and BL5, encode genes for the production of flexirubin type pigments and a number of unique non-ribosomal peptide synthesis (NRPS) gene clusters, suggesting a role for these uncharacterised traits in virulence. This study provides valuable insight into the potential ecological role of Aquimarina in the marine environment and the complex factors driving pathogenesis and symbiosis in this genus.


Assuntos
Flavobacteriaceae/genética , Genômica , Interações Hospedeiro-Patógeno/genética , Microalgas/genética , Microalgas/microbiologia , Rodófitas/genética , Rodófitas/microbiologia , Flavobacteriaceae/patogenicidade , Simbiose
18.
Microbiol Immunol ; 63(3-4): 111-118, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30817020

RESUMO

Two gram-negative, catalase-negative, oxidase-positive strains (PAGU 1467T and PAGU 1468) isolated from patients with infective endocarditis were investigated to determine their taxonomic status. 16S rRNA gene sequence analysis indicated that the two strains were members of the Bergeyella-Chryseobacterium-Riemerella branch of the family Flavobacteriaceae. Strains PAGU 1467T and PAGU 1468 were highly related to each other (98.8% 16S rRNA gene sequence similarity). Phylogenetically closely-related species to PAGU 1467T comprised Bergeyella zoohelcum (95.0% 16S rRNA gene sequence similarity), Riemerella anatipestifer (94.3%) and Cloacibacterium normanense (94.3%). The major fatty acids of the two isolates were iso-C15:0 , iso-C17:0 3-OH and iso-C15:0 3-OH. The presence of C16:0 3-OH and iso-C15:0 2-OH allowed these isolates to be distinguished from B. zoohelcum. Menaquinone MK-6 was the only respiratory quinone in these organisms; this is a consistent characteristic of the family Flavobacteriaceae. The guanine-plus-cytosine content of the genomic DNA was 42.0%, which is higher than that of other close phylogenetic relatives. On the basis of their phenotypic properties and genetic distinctiveness, isolates PAGU 1467T and PAGU 1468 were classified within the novel genus Spodiobacter, as Spodiobacter cordis gen. nov., sp. nov., which is also the type species. The type strain of S. cordis is PAGU 1467T ( = CCUG 65564T = NBRC 109998T ).


Assuntos
Endocardite/microbiologia , Flavobacteriaceae/classificação , Flavobacteriaceae/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/análise , Flavobacteriaceae/genética , Humanos , Filogenia , RNA Ribossômico 16S/genética
19.
Syst Appl Microbiol ; 42(3): 263-274, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30773292

RESUMO

Flavobacteriia are abundant in many marine environments including hadal waters, as demonstrated recently. However, it is unclear how this flavobacterial population adapts to hadal conditions. In this study, extensive comparative genomic analyses were performed for the flavobacterial strain Euzebyella marina RN62 isolated from the Mariana Trench hadal water in low abundance. The complete genome of RN62 possessed a considerable number of carbohydrate-active enzymes with a different composition. There was a predominance of GH family 13 proteins compared to closely related relatives, suggesting that RN62 has preserved a certain capacity for carbohydrate utilization and that the hadal ocean may hold an organic matter reservoir distinct from the surface ocean. Additionally, RN62 possessed potential intracellular cycling of the glycogen/starch pathway, which may serve as a strategy for carbon storage and consumption in response to nutrient pulse and starvation. Moreover, the discovery of higher glycoside hydrolase dissimilarities among Flavobacteriia, compared to peptidases and transporters, suggested variation in polysaccharide utilization related traits as an important ecophysiological factor in response to environmental alterations, such as decreased labile organic carbon in hadal waters. The presence of abundant toxin exporting, transcription and signal transduction related genes in RN62 may further help to survive in hadal conditions, including high pressure/low temperature.


Assuntos
Metabolismo dos Carboidratos/genética , Ecossistema , Flavobacteriaceae/genética , Flavobacteriaceae/metabolismo , Água do Mar/microbiologia , Adaptação Fisiológica/genética , Flavobacteriaceae/classificação , Genes Bacterianos/genética , Genoma Bacteriano/genética , Glicogênio/metabolismo , Filogenia , Polissacarídeos/metabolismo
20.
Antonie Van Leeuwenhoek ; 112(7): 1077-1085, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-30729398

RESUMO

A Gram-stain negative, aerobic, rod-shaped, and non-motile bacterium, designated strain CCMM003T, was isolated from a culture of the green alga Ulva prolifera. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CCMM003T belongs to the family Flavobacteriaceae and exhibits a close relationship to Pseudozobellia thermophila DSM 19858T (92.5%). Optimal growth occurred in the presence of 4% (w/v) NaCl, at pH 7.0 and 30 °C. The polar lipids of strain CCMM003T consisted of phosphatidylethanolamine and six unidentified lipids. The predominant isoprenoid quinone was MK-6. The major fatty acids were iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH and summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH). The DNA G + C content of strain CCMM003T calculated on the basis of the genome sequence was 41.2 mol% and the genome size was 5.9 Mbp. On the basis of data from this polyphasic study, strain CCMM003T is considered to represent a novel genus and species of the family Flavobacteriaceae, for which the name Ulvibacterium marinum gen. nov., sp. nov. is proposed. The type strain is CCMM003T (= MCCC 1K03244T =KCTC 52639T).


Assuntos
Flavobacteriaceae/isolamento & purificação , Água do Mar/microbiologia , Ulva/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Ácidos Graxos/metabolismo , Flavobacteriaceae/classificação , Flavobacteriaceae/genética , Flavobacteriaceae/metabolismo , Filogenia , RNA Ribossômico 16S/genética , Ulva/crescimento & desenvolvimento
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