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1.
Nat Commun ; 11(1): 4648, 2020 09 16.
Artigo em Inglês | MEDLINE | ID: mdl-32938927

RESUMO

Emergence of tigecycline-resistance tet(X) gene orthologues rendered tigecycline ineffective as last-resort antibiotic. To understand the potential origin and transmission mechanisms of these genes, we survey the prevalence of tet(X) and its orthologues in 2997 clinical E. coli and K. pneumoniae isolates collected nationwide in China with results showing very low prevalence on these two types of strains, 0.32% and 0%, respectively. Further surveillance of tet(X) orthologues in 3692 different clinical Gram-negative bacterial strains collected during 1994-2019 in hospitals in Zhejiang province, China reveals 106 (2.7%) tet(X)-bearing strains with Flavobacteriaceae being the dominant (97/376, 25.8%) bacteria. In addition, tet(X)s are found to be predominantly located on the chromosomes of Flavobacteriaceae and share similar GC-content as Flavobacteriaceae. It also further evolves into different orthologues and transmits among different species. Data from this work suggest that Flavobacteriaceae could be the potential ancestral source of the tigecycline resistance gene tet(X).


Assuntos
Antibacterianos/farmacologia , Proteínas de Bactérias/genética , Farmacorresistência Bacteriana/genética , Infecções por Flavobacteriaceae/epidemiologia , Flavobacteriaceae/genética , Tigeciclina/farmacologia , China/epidemiologia , Escherichia coli/efeitos dos fármacos , Escherichia coli/genética , Evolução Molecular , Flavobacteriaceae/efeitos dos fármacos , Flavobacteriaceae/isolamento & purificação , Infecções por Flavobacteriaceae/microbiologia , Humanos , Filogenia
2.
Nucleic Acids Res ; 48(14): 7786-7800, 2020 08 20.
Artigo em Inglês | MEDLINE | ID: mdl-32585009

RESUMO

Marine flavobacteria possess dedicated Polysaccharide Utilization Loci (PULs) enabling efficient degradation of a variety of algal polysaccharides. The expression of these PULs is tightly controlled by the presence of the substrate, yet details on the regulatory mechanisms are still lacking. The marine flavobacterium Zobellia galactanivorans DsijT digests many algal polysaccharides, including alginate from brown algae. Its complex Alginate Utilization System (AUS) comprises a PUL and several other loci. Here, we showed that the expression of the AUS is strongly and rapidly (<30 min) induced upon addition of alginate, leading to biphasic substrate utilization. Polymeric alginate is first degraded into smaller oligosaccharides that accumulate in the extracellular medium before being assimilated. We found that AusR, a GntR family protein encoded within the PUL, regulates alginate catabolism by repressing the transcription of most AUS genes. Based on our genetic, genomic, transcriptomic and biochemical results, we propose the first model of regulation for a PUL in marine bacteria. AusR binds to promoters of AUS genes via single, double or triple copies of operator. Upon addition of alginate, secreted enzymes expressed at a basal level catalyze the initial breakdown of the polymer. Metabolic intermediates produced during degradation act as effectors of AusR and inhibit the formation of AusR/DNA complexes, thus lifting transcriptional repression.


Assuntos
Alginatos/metabolismo , Proteínas de Bactérias/metabolismo , Flavobacteriaceae/genética , Regulação Bacteriana da Expressão Gênica , Proteínas Repressoras/metabolismo , Flavobacteriaceae/metabolismo , Regiões Promotoras Genéticas
3.
Arch Microbiol ; 202(8): 2127-2133, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32506148

RESUMO

A Gram-stain-negative, strictly aerobic, non-flagellated, gliding, rod-shaped bacterium, designated C1T was isolated from the coastal sediment of Xiaoshi Island, Weihai, China. Phylogenetic analysis of the 16S rRNA gene and the genome sequence of the newly isolated strain revealed that it belonged to the genus Psychroflexus within the family Flavobacteriaceae. The 16S rRNA gene sequence similarities between strain C1T and the type strains of Psychroflexus members ranged from 91.6 to 94.9%. The AAI, POCP, ANI and dDDH values between strain C1T and Psychroflexus torquis ATCC 700755T were 67.0%, 53.1%, 70.5% and 20.2%, respectively. The DNA G+C content was 34.0 mol%. Strain C1T grows optimally at 28-30 â„ƒ, at pH 7.5-8.0 and with 3.0-5.0% (w/v) NaCl, and its colonies were orange-colored, convex and circular on the MA plate. Positive for hydrolysis of Tween 20 and catalase activities. The dominant respiratory quinone was menaquinone-6, and the major fatty acids were iso-C17:0 3-OH and iso-C15:0. The polar lipids of strain C1T consisted of phosphatidylethanolamine and three unidentified lipids. On the basis of phylogenetic, phenotypic and chemotaxonomic data, it is considered that strain C1T represents a novel species within the genus Psychroflexus, for which, the name Psychroflexus maritimus sp. nov., is proposed. The type strain is C1T (= MCCC 1H00415T = KCTC 72796T).


Assuntos
Flavobacteriaceae/classificação , Sedimentos Geológicos/microbiologia , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , Ácidos Graxos/química , Flavobacteriaceae/química , Flavobacteriaceae/genética , Flavobacteriaceae/isolamento & purificação , Genoma Bacteriano/genética , Pigmentação , RNA Ribossômico 16S/genética , Água do Mar/microbiologia , Especificidade da Espécie
4.
Arch Microbiol ; 202(6): 1295-1300, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32125451

RESUMO

A novel Gram-stain-negative, orange, rod or curved rod, facultatively anaerobic, gliding bacterial strain, designated strain W255T, was isolated from Xiaoshi Island, Weihai, China. The strain W255T grows optimally at a 28 °C, pH 7.5, and 3.0% (w/v) NaCl environment. Its colonies are circular, orange, non-transparent, smooth, and approximately 0.2-0.8 mm in diameter, after being cultured for 72 h on marine agar 2216. Cells of the strain W255T are 0.3-0.8 µm wide and 1.0-4.0 µm long, catalase-positive and oxidase-positive. The major cellular fatty acids are iso-C15:0, iso-C15:1 G, and iso-C15:0 3-OH. The sole respiratory quinone is MK-6. The major polar lipids include phosphatidylethanolamine, one unidentified amino lipid, one amino glycolipid, and two unidentified lipids (L1 and L2). The phylogenetic analysis based on 16S rRNA gene sequences indicated that strain W255T has the highest similarities with the type strain of the type species of the genus Seonamhaeicola, S. aphaedonensis KCTC 32578T (97.2%), and moderate with 'S. acroporae' KCTC 62713T (96.5%), S. algicola Gy8T (95.4%) and S. marinus B011T (94.5%). The ANI and dDDH values between strain W255T and S. aphaedonensis KCTC 32578T are 86.6% and 31.3%, respectively. The genomic DNA G + C content is 33.5 mol%. On the basis of gene annotation, it was observed that strain W255T have the abilities of nitrate reduction and utilizing various carbon sources, suggesting that this strain might be an important participant in the nitrogen cycle and carbon cycle in the marine environment. Based on the phenotypic, chemotaxonomic and phylogenetic analysis, strain W255T has been considered as a novel species of the genus Seonamhaeicola, for which the name Seonamhaeicola sediminis sp. nov. is proposed. The type strain is W255T (= MCCC 1H00377T = KCTC 72085T).


Assuntos
Flavobacteriaceae/classificação , Sedimentos Geológicos/microbiologia , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/análise , Flavobacteriaceae/genética , Lipídeos/análise , Fosfatidiletanolaminas/análise , RNA Ribossômico 16S/genética , Água do Mar/microbiologia , Especificidade da Espécie , Vitamina K 2/química
5.
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
6.
ISME J ; 14(6): 1369-1383, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32071394

RESUMO

Massive releases of organic substrates during marine algal blooms trigger growth of many clades of heterotrophic bacteria. Algal polysaccharides represent the most diverse and structurally complex class of these substrates, yet their role in shaping the microbial community composition is poorly understood. We investigated, whether polysaccharide utilization capabilities contribute to niche differentiation of Polaribacter spp. (class Flavobacteriia; known to include relevant polysaccharide-degraders) that were abundant during 2009-2012 spring algal blooms in the southern North Sea. We identified six distinct Polaribacter clades using phylogenetic and phylogenomic analyses, quantified their abundances via fluorescence in situ hybridization, compared metagenome-assembled genomes, and assessed in situ gene expression using metaproteomics. Four clades with distinct polysaccharide niches were dominating. Polaribacter 2-a comprised typical first responders featuring small genomes with limited polysaccharide utilization capacities. Polaribacter 3-a were abundant only in 2010 and possessed a distinct sulfated α-glucoronomannan degradation potential. Polaribacter 3-b responded late in blooms and had the capacity to utilize sulfated xylan. Polaribacter 1-a featured high numbers of glycan degradation genes and were particularly abundant following Chattonella algae blooms. These results support the hypothesis that sympatric Polaribacter clades occupy distinct glycan niches during North Sea spring algal blooms.


Assuntos
Clorófitas/metabolismo , Clorófitas/microbiologia , Flavobacteriaceae/metabolismo , Polissacarídeos/metabolismo , Clorófitas/crescimento & desenvolvimento , Eutrofização , Flavobacteriaceae/classificação , Flavobacteriaceae/genética , Flavobacteriaceae/isolamento & purificação , Hibridização in Situ Fluorescente , Metagenoma , Mar do Norte , Filogenia , Estações do Ano
7.
Mar Drugs ; 18(2)2020 Feb 24.
Artigo em Inglês | MEDLINE | ID: mdl-32102373

RESUMO

A bifunctional alginate lyase (ALFA3) and mannuronate-specific alginate lyase (ALFA4) genes were found in the genome of polysaccharide-degrading marine bacterium Formosa algae KMM 3553T. They were classified to PL7 and PL6 polysaccharide lyases families and expressed in E. coli. The recombinant ALFA3 appeared to be active both on mannuronate- and guluronate-enriched alginates, as well as pure sodium mannuronate. For all substrates, optimum conditions were pH 6.0 and 35 °C; Km was 0.12 ± 0.01 mg/ml, and half-inactivation time was 30 min at 42 °C. Recombinant ALFA4 was active predominately on pure sodium mannuronate, with optimum pH 8.0 and temperature 30 °C, Km was 3.01 ± 0.05 mg/ml. It was stable up to 30 °C; half-inactivation time was 1h 40 min at 37 °C. 1H NMR analysis showed that ALFA3 degraded mannuronate and mannuronate-guluronate blocks, while ALFA4 degraded only mannuronate blocks, producing mainly disaccharides. Products of digestion of pure sodium mannuronate by ALFA3 at 200 µg/ml inhibited anchorage-independent colony formation of human melanoma cells SK-MEL-5, SK-MEL-28, and RPMI-7951 up to 17% stronger compared to native polymannuronate. This fact supports previous data and suggests that mannuronate oligosaccharides may be useful for synergic tumor therapy.


Assuntos
Flavobacteriaceae/enzimologia , Polissacarídeo-Liase/metabolismo , Clonagem Molecular , Flavobacteriaceae/genética , Flavobacteriaceae/metabolismo , Regulação Bacteriana da Expressão Gênica , Regulação Enzimológica da Expressão Gênica , Polissacarídeo-Liase/química , Polissacarídeo-Liase/genética , Conformação Proteica
8.
Molecules ; 25(1)2020 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-31906348

RESUMO

The synthesis of bioplastic from marine microbes has a great attendance in the realm of biotechnological applications for sustainable eco-management. This study aims to isolate novel strains of poly-ß-hydroxybutyrate (PHB)-producing bacteria from the mangrove rhizosphere, Red Sea, Saudi Arabia, and to characterize the extracted polymer. The efficient marine bacterial isolates were identified by the phylogenetic analysis of the 16S rRNA genes as Tamlana crocina, Bacillus aquimaris, Erythrobacter aquimaris, and Halomonas halophila. The optimization of PHB accumulation by E. aquimaris was achieved at 120 h, pH 8.0, 35 °C, and 2% NaCl, using glucose and peptone as the best carbon and nitrogen sources at a C:N ratio of 9.2:1. The characterization of the extracted biopolymer by Fourier-transform infrared spectroscopy (FTIR), Nuclear magnetic resonance (NMR), and Gas chromatography-mass spectrometry (GC-MS) proves the presence of hydroxyl, methyl, methylene, methine, and ester carbonyl groups, as well as derivative products of butanoic acid, that confirmed the structure of the polymer as PHB. This is the first report on E. aquimaris as a PHB producer, which promoted the hypothesis that marine rhizospheric bacteria were a new area of research for the production of biopolymers of commercial value.


Assuntos
Biopolímeros/biossíntese , Biopolímeros/química , Hidroxibutiratos/química , Hidroxibutiratos/metabolismo , Poliésteres/química , Poliésteres/metabolismo , Sphingomonadaceae/química , Sphingomonadaceae/metabolismo , Avicennia/microbiologia , Bacillus/química , Bacillus/genética , Bacillus/metabolismo , Biopolímeros/análise , Carbono/química , Carbono/metabolismo , Fermentação , Flavobacteriaceae/química , Flavobacteriaceae/genética , Flavobacteriaceae/metabolismo , Cromatografia Gasosa-Espectrometria de Massas , Halomonas/química , Halomonas/genética , Halomonas/metabolismo , Hidroxibutiratos/análise , Espectroscopia de Ressonância Magnética , Nitrogênio/química , Nitrogênio/metabolismo , Filogenia , Poliésteres/análise , RNA Ribossômico 16S/genética , Rizosfera , Salinidade , Arábia Saudita , Água do Mar/microbiologia , Espectroscopia de Infravermelho com Transformada de Fourier , Sphingomonadaceae/genética , Sphingomonadaceae/isolamento & purificação , Temperatura
9.
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
10.
Curr Microbiol ; 77(2): 294-299, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31776653

RESUMO

A Gram-stain-negative, strictly aerobic and moderately halophilic bacterium, designated strain AsT0115T, was isolated from a red marine alga, Asparagopsis taxiformis. Cells were non-motile rods showing oxidase-positive and catalase-negative activities. Growth was observed at 15-37 C (optimum, 25 C) and pH 6.5-7.5 (optimum, pH 7.0) and in the presence of 0-11.0% (w/v) NaCl (optimum, 2.0-3.0%). Strain AsT0115T contained iso-C15:0 and iso-C15:1 G as the predominant fatty acids. Menaquinone-6 was identified as the sole isoprenoid quinone. Major polar lipids consisted of phosphatidylethanolamine, an identified aminolipid and three unidentified polar lipids. The G+C content of the genomic DNA calculated from the whole genome sequence was 41.7 mol%. Strain AsT0115T was most closely related to Flagellimonas pacifica sw169T and Flagellimonas flava DSM 22638T with 96.5% and 95.6% 16S rRNA gene sequence similarities, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AsT0115T formed a phyletic lineage with F. pacifica sw169T within the genus Flagellimonas. Phenotypic, chemotaxonomic, and phylogenetic features clearly suggested that strain AsT0115T represents a novel species of the genus Flagellimonas, for which the name Flagellimonas algicola sp. nov. is proposed. The type strain is AsT0115T (= KACC 19790T = JCM 32942T).


Assuntos
Flavobacteriaceae/classificação , Flavobacteriaceae/genética , Filogenia , Rodófitas/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Flavobacteriaceae/química , Flavobacteriaceae/isolamento & purificação , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
11.
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
12.
Genomics ; 112(1): 952-960, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31201854

RESUMO

The genus Meridianimaribacter is one of the least-studied genera within Cytophaga-Flavobacteria. To date, no genomic analysis of Meridianimaribacter has been reported. In this study, Meridianimaribacter sp. strain CL38, a lignocellulose degrading halophile was isolated from mangrove soil. The genome of strain CL38 was sequenced and analyzed. The assembled genome contains 17 contigs with 3.33 Mbp, a GC content of 33.13% and a total of 2982 genes predicted. Lignocellulose degrading enzymes such as cellulases (GH3, 5, 9, 16, 74 and 144), xylanases (GH43 and CE4) and mannanases (GH5, 26, 27 and 130) are encoded in the genome. Furthermore, strain CL38 demonstrated its ability to decompose empty fruit bunch, a lignocellulosic waste residue arising from palm oil industry. The genome information coupled with experimental studies confirmed the ability of strain CL38 to degrade lignocellulosic biomass. Therefore, Meridianimaribacter sp. strain CL38, with its halotolerance, could be useful for seawater based lignocellulosic biorefining.


Assuntos
Flavobacteriaceae/genética , Genoma Bacteriano , Lignina/metabolismo , Flavobacteriaceae/classificação , Flavobacteriaceae/enzimologia , Genômica , Redes e Vias Metabólicas/genética , Filogenia , Polissacarídeos/metabolismo
13.
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
14.
Antonie Van Leeuwenhoek ; 113(3): 407-415, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31628626

RESUMO

A Gram-stain negative, non-motile, asporogenous, aerobic and rod-shaped bacterial strain, designated ZY113T, was isolated from the surface of a marine red alga collected from the coast in Weihai, Shandong Province, China. Strain ZY113T was found to grow at 4-37 °C (optimum at 28-30 °C), with 1.0-7.0% (w/v) NaCl (optimum 2.0-3.0%) and at pH 6.0-9.0 (optimum 7.0-8.0). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ZY113T is a member of the genus Polaribacter, with Polaribacter dokdonensis KCTC 12392T as a close relative (97.4% similarity). The sole respiratory quinone was found to be menaquinone 6 (MK-6) and the major fatty acids were identified as iso-C15:0, iso-C15:0 3-OH and iso-C13:0. The polar lipids were found to consist of phosphatidylethanolamine, two unidentified aminolipids and three unidentified lipids. The G + C content of the genomic DNA was determined to be 30.1 mol%. On the basis of phenotypic, genotypic and phylogenetic analysis, strain ZY113T is considered to represent a novel species of the genus Polaribacter, for which the name Polaribacter aquimarinus sp. nov. is proposed. The type strain is ZY113T (= KCTC 62374T = MCCC 1H00296T).


Assuntos
Organismos Aquáticos , Flavobacteriaceae/classificação , Flavobacteriaceae/isolamento & purificação , Rodófitas/microbiologia , Técnicas de Tipagem Bacteriana , Flavobacteriaceae/genética , Genoma Bacteriano , Genômica/métodos , Genótipo , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
15.
Sci Rep ; 9(1): 19167, 2019 12 16.
Artigo em Inglês | MEDLINE | ID: mdl-31844108

RESUMO

Bacteria of the genus Elizabethkingia are emerging infectious agents that can cause infection in humans. The number of published whole-genome sequences of Elizabethkingia is rapidly increasing. In this study, we used comparative genomics to investigate the genomes of the six species in the Elizabethkingia genus, namely E. meningoseptica, E. anophelis, E. miricola, E. bruuniana, E. ursingii, and E. occulta. In silico DNA-DNA hybridization, whole-genome sequence-based phylogeny, pan genome analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed, and clusters of orthologous groups were evaluated. Of the 86 whole-genome sequences available in GenBank, 21 were complete genome sequences and 65 were shotgun sequences. In silico DNA-DNA hybridization clearly delineated the six Elizabethkingia species. Phylogenetic analysis confirmed that E. bruuniana, E. ursingii, and E. occulta were closer to E. miricola than to E. meningoseptica and E. anophelis. A total of 2,609 clusters of orthologous groups were identified among the six type strains of the Elizabethkingia genus. Metabolism-related clusters of orthologous groups accounted for the majority of gene families in KEGG analysis. New genes were identified that substantially increased the total repertoire of the pan genome after the addition of 86 Elizabethkingia genomes, which suggests that Elizabethkingia has shown adaptive evolution to environmental change. This study presents a comparative genomic analysis of Elizabethkingia, and the results of this study provide knowledge that facilitates a better understanding of this microorganism.


Assuntos
Flavobacteriaceae/genética , Variação Genética , Genoma Bacteriano , Genômica , Sequenciamento Completo do Genoma , Sequência de Bases , Simulação por Computador , Farmacorresistência Bacteriana/genética , Evolução Molecular , Flavobacteriaceae/patogenicidade , Filogenia , Especificidade da Espécie , Fatores de Virulência/genética
16.
Mar Drugs ; 17(12)2019 Nov 24.
Artigo em Inglês | MEDLINE | ID: mdl-31771309

RESUMO

We obtained two novel draft genomes of type Zobellia strains with estimated genome sizes of 5.14 Mb for Z. amurskyensis KMM 3526Т and 5.16 Mb for Z. laminariae KMM 3676Т. Comparative genomic analysis has been carried out between obtained and known genomes of Zobellia representatives. The pan-genome of Zobellia genus is composed of 4853 orthologous clusters and the core genome was estimated at 2963 clusters. The genus CAZome was represented by 775 GHs classified into 62 families, 297 GTs of 16 families, 100 PLs of 13 families, 112 CEs of 13 families, 186 CBMs of 18 families and 42 AAs of six families. A closer inspection of the carbohydrate-active enzyme (CAZyme) genomic repertoires revealed members of new putative subfamilies of GH16 and GH117, which can be biotechnologically promising for production of oligosaccharides and rare monomers with different bioactivities. We analyzed AA3s, among them putative FAD-dependent glycoside oxidoreductases (FAD-GOs) being of particular interest as promising biocatalysts for glycoside deglycosylation in food and pharmaceutical industries.


Assuntos
Organismos Aquáticos/genética , Proteínas de Bactérias/genética , Flavobacteriaceae/genética , Genoma Bacteriano/genética , Genômica , Organismos Aquáticos/enzimologia , Proteínas de Bactérias/metabolismo , Biotecnologia/métodos , Metabolismo dos Carboidratos , Flavobacteriaceae/enzimologia , Filogenia , Polissacarídeos/metabolismo , Alga Marinha/química , Alga Marinha/metabolismo , Análise de Sequência de DNA
17.
PLoS One ; 14(10): e0222648, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31600234

RESUMO

Three human clinical isolates of bacteria (designated strains Em1, Em2 and Em3) had high average nucleotide identity (ANI) to Elizabethkingia meningoseptica. Their genome sizes (3.89, 4.04 and 4.04 Mb) were comparable to those of other Elizabethkingia species and strains, and exhibited open pan-genome characteristics, with two strains being nearly identical and the third divergent. These strains were susceptible only to trimethoprim/sulfamethoxazole and ciprofloxacin amongst 16 antibiotics in minimum inhibitory tests. The resistome exhibited a high diversity of resistance genes, including 5 different lactamase- and 18 efflux protein- encoding genes. Forty-four genes encoding virulence factors were conserved among the strains. Sialic acid transporters and curli synthesis genes were well conserved in E. meningoseptica but absent in E. anophelis and E. miricola. E. meningoseptica carried several genes contributing to biofilm formation. 58 glycoside hydrolases (GH) and 25 putative polysaccharide utilization loci (PULs) were found. The strains carried numerous genes encoding two-component system proteins (56), transcription factor proteins (187~191), and DNA-binding proteins (6~7). Several prophages and CRISPR/Cas elements were uniquely present in the genomes.


Assuntos
Farmacorresistência Bacteriana/genética , Infecções por Flavobacteriaceae/genética , Flavobacteriaceae/genética , Genoma Bacteriano/genética , Antibacterianos/uso terapêutico , Biofilmes/crescimento & desenvolvimento , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas/genética , Hibridização Genômica Comparativa , Proteínas de Ligação a DNA/genética , Flavobacteriaceae/patogenicidade , Infecções por Flavobacteriaceae/tratamento farmacológico , Infecções por Flavobacteriaceae/epidemiologia , Infecções por Flavobacteriaceae/microbiologia , Genômica/métodos , Humanos , Filogenia , Fatores de Transcrição/genética , Fatores de Virulência/genética
18.
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
19.
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
20.
Zoonoses Public Health ; 66(8): 936-942, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31464049

RESUMO

Bergeyella zoohelcum causes rare but severe human clinical diseases, which mostly arise from animal bites. Notably, Bergeyella infections can also occur in older people after prolonged exposure to dogs or cats without biting. We detected B. zoohelcum in oral cavities of therapy dogs in close contact with older people residing in nursing homes. Twenty-two bacterial isolates were identified as B. zoohelcum by using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing. Our results showed that MALDI-TOF MS is an effective tool for rapid identification of rarely isolated, difficult-to-identify microorganisms, such as B. zoohelcum, derived from not only human clinical samples but also animal samples. To our knowledge, this is the first report on detection of B. zoohelcum from therapy dogs. We have provided information on dog-assisted therapy to improve the relationship between humans and animals in ageing societies, particularly for preventive healthcare of older people living in nursing care facilities.


Assuntos
Infecções por Flavobacteriaceae/veterinária , Flavobacteriaceae/isolamento & purificação , Boca/microbiologia , Animais , Doenças do Cão/microbiologia , Cães , Flavobacteriaceae/genética , Infecções por Flavobacteriaceae/transmissão , Instituição de Longa Permanência para Idosos , Humanos , Japão , RNA Ribossômico 16S/genética , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz
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