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1.
mSphere ; 4(3)2019 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-31043518

RESUMO

Laryngotracheal stenosis is an obstructive respiratory disease that leads to voicing difficulties and dyspnea with potential life-threatening consequences. The majority of incidences are due to iatrogenic etiology from endotracheal tube intubation; however, airway scarring also has idiopathic causes. While recent evidence suggests a microbial contribution to mucosal inflammation, the microbiota associated with different types of stenosis has not been characterized. High-throughput sequencing of the V4 region of the16S rRNA gene was performed to characterize the microbial communities of 61 swab samples from 17 iatrogenic and 10 adult idiopathic stenosis patients. Nonscar swabs from stenosis patients were internal controls, and eight swabs from four patients without stenosis represented external controls. Significant differences in diversity were observed between scar and nonscar samples and among sample sites, with decreased diversity detected in scar samples and the glottis region. Permutational analysis of variance (PERMANOVA) results revealed significant differences in community composition for scar versus nonscar samples, etiology type, sample site, groups (iatrogenic, idiopathic, and internal and external controls), and individual patients. Pairwise Spearman's correlation revealed a strong inverse correlation between Prevotella and Streptococcus among all samples. Finally, bacteria in the family Moraxellaceae were found to be distinctly associated with idiopathic stenosis samples in comparison with external controls. Our findings suggest that specific microbiota and community shifts are present with laryngotracheal stenosis in adults, with members of the family Moraxellaceae, including the known pathogens Moraxella and Acinetobacter, identified in idiopathic scar. Further work is warranted to elucidate the contributing role of bacteria on the pathogenesis of laryngotracheal stenosis.IMPORTANCE The laryngotracheal region resides at the intersection between the heavily studied nasal cavity and lungs; however, examination of the microbiome in chronic inflammatory conditions of the subglottis and trachea remains scarce. To date, studies have focused on the microbiota of the vocal folds, or the glottis, for laryngeal carcinoma, as well as healthy larynges, benign vocal fold lesions, and larynges exposed to smoking and refluxate. In this study, we seek to examine the structure and composition of the microbial community in adult laryngotracheal stenosis of various etiologies. Due to the heterogeneity among the underlying pathogenesis mechanisms and clinical outcomes seen in laryngotracheal stenosis disease, we hypothesized that different microbial profiles will be detected among various stenosis etiology types. Understanding differences in the microbiota for subglottic stenosis subtypes may shed light upon etiology-specific biomarker identification and offer novel insights into management approaches for this debilitating disease.


Assuntos
Bactérias/classificação , Laringoestenose/microbiologia , Microbiota , Traqueia/microbiologia , Estenose Traqueal/microbiologia , Acinetobacter/genética , Acinetobacter/isolamento & purificação , Adolescente , Adulto , Idoso , Bactérias/isolamento & purificação , Cicatriz/microbiologia , Constrição Patológica , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Laringoestenose/patologia , Masculino , Pessoa de Meia-Idade , Moraxellaceae/genética , Moraxellaceae/isolamento & purificação , Traqueia/patologia , Estenose Traqueal/patologia
2.
mSphere ; 4(1)2019 02 20.
Artigo em Inglês | MEDLINE | ID: mdl-30787115

RESUMO

Insertion sequences (IS) are fundamental mediators of genome plasticity with the potential to generate phenotypic variation with significant evolutionary outcomes. Here, a recently active miniature inverted-repeat transposon element (MITE) was identified in a derivative of Acinetobacter baumannii ATCC 17978 after being subjected to stress conditions. Transposition of the novel element led to the disruption of the hns gene, resulting in a characteristic hypermotile phenotype. DNA identity shared between the terminal inverted repeats of this MITE and coresident ISAba12 elements, together with the generation of 9-bp target site duplications, provides strong evidence that ISAba12 elements were responsible for mobilization of the MITE (designated MITE Aba12 ) within this strain. A wider genome-level survey identified MITE Aba12 in 30 additional Acinetobacter genomes at various frequencies and one Moraxella osloensis genome. Ninety MITE Aba12 copies could be identified, of which 40% had target site duplications, indicating recent transposition events. Elements ranged between 111 and 114 bp; 90% were 113 bp in length. Using the MITE Aba12 consensus sequence, putative outward-facing Escherichia coli σ70 promoter sequences in both orientations were identified. The identification of transcripts originating from the promoter in one direction supports the proposal that the element can influence neighboring host gene transcription. The location of MITE Aba12 varied significantly between and within genomes, preferentially integrating into AT-rich regions. Additionally, a copy of MITE Aba12 was identified in a novel 8.5-kb composite transposon, Tn6645, in the M. osloensis CCUG 350 chromosome. Overall, this study shows that MITE Aba12 is the most abundant nonautonomous element currently found in Acinetobacter IMPORTANCE One of the most important weapons in the armory of Acinetobacter is its impressive genetic plasticity, facilitating rapid genetic mutations and rearrangements as well as integration of foreign determinants carried by mobile genetic elements. Of these, IS are considered one of the key forces shaping bacterial genomes and ultimately evolution. We report the identification of a novel nonautonomous IS-derived element present in multiple bacterial species from the Moraxellaceae family and its recent translocation into the hns locus in the A. baumannii ATCC 17978 genome. The latter finding adds new knowledge to only a limited number of documented examples of MITEs in the literature and underscores the plastic nature of the hns locus in A. baumannii MITE Aba12 , and its predicted parent(s), may be a source of substantial adaptive evolution within environmental and clinically relevant bacterial pathogens and, thus, have broad implications for niche-specific adaptation.


Assuntos
Acinetobacter baumannii/genética , Elementos de DNA Transponíveis , Genoma Bacteriano , Sequências Repetidas Invertidas , Moraxellaceae/genética , Evolução Molecular
3.
Curr Microbiol ; 76(4): 478-484, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30783797

RESUMO

A gram-stain-negative and strictly aerobic bacterium, designated strain HR-ET, was isolated from a water sample of the Han River in South Korea. Cells were catalase-negative and oxidase-positive motile rods with a flagellum. The strain grew at 10-37 °C and pH 7-8 and in the presence of 0-2% (w/v) NaCl. Ubiquinone-8 and summed features 3 (comprising C16:1ω7c and/or C16:1ω6c) and 8 (comprising C18:1ω7c and/or C18:1ω6c), C16:0, iso-C10:0 and C12:0 3-OH were identified as the major respiratory quinone and fatty acids (>5%), respectively. The 16S rRNA gene sequence of strain HR-ET shared the highest similarities with Perlucidibaca piscinae IMCC 1704T (98.1%), Perlucidibaca aquatica BK296T (96.8%), Paraperlucidibaca baekdonensis RL-2T (95.8%) and Paraperlucidibaca wandonensis WT-RY4T (95.7%). However, strain HR-ET formed a phylogenetic lineage distinct from members of the family Moraxellaceae, and a taxonomic analysis by RDP Naïve Bayesian rRNA Classifier classified strain HR-ET as a new genus of the family Moraxellaceae. In addition, analyses based on rpoD, secA and gyrB gene sequences also showed that strain HR-ET formed a lineage distinct from those of the genera Perlucidibaca and Paraperlucidibaca. Average nucleotide identity and in silico DNA-DNA hybridization values between strain HR-ET and the type strains of P. piscinae and P. aquatica were very low with 80.1 and 23.6% and 75.7 and 21.2%, respectively. The DNA G+C content was 67.0 mol%. Based on the phenotypic, genotypic and chemotaxonomic analyses, strain HR-ET represents a novel genus of the family Moraxellaceae, for which the name Amnimonas aquatica gen. nov., sp. nov. is proposed. The type strain of the type species is HR-ET (=KACC 19408T=JCM 32266T).


Assuntos
Moraxellaceae/classificação , Moraxellaceae/fisiologia , Filogenia , Rios/microbiologia , Microbiologia da Água , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Genes Bacterianos/genética , Moraxellaceae/química , Moraxellaceae/genética , Hibridização de Ácido Nucleico , Fenótipo , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Especificidade da Espécie , Ubiquinona/química
4.
Talanta ; 182: 536-543, 2018 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-29501189

RESUMO

The identification of microorganisms is very important in different fields and alternative methods are necessary for a rapid and simple identification. The use of fatty acids for bacterial identification is gaining attention as phenotypic characteristics are reflective of the genotype and are more easily analyzed. In this work, gas chromatography-vacuum ultraviolet spectroscopy (GC-VUV) was used to determine bacteria fatty acid methyl esters (FAMEs), to identify and discriminate different environmental bacteria based on their fatty acid profile. Microorganisms were grown in agar and their fatty acids extracted, saponified, and esterified before analysis. Unique FAME profiles were obtained for each microorganism mainly composed of branched, cyclopropane, hydroxy, saturated, and unsaturated fatty acid methyl esters. S. maltophilia showed a higher diversity of fatty acids while Bacillus species showed higher complexity in terms of branched-chain FAMEs, with several iso and anteiso forms. 12 different bacteria genera and 15 species were successfully differentiated based on their fatty acid profiles after performing PCA and cluster analysis. Some difficult to differentiate species, such as Bacillus sp., which are genetically very similar, were differentiated with the developed method.


Assuntos
Bactérias/isolamento & purificação , Cromatografia Gasosa/métodos , Ácidos Graxos/isolamento & purificação , Água Subterrânea/microbiologia , Espectroscopia Fotoeletrônica/métodos , Aeromonadaceae/classificação , Aeromonadaceae/isolamento & purificação , Aeromonadaceae/metabolismo , Alcaligenaceae/classificação , Alcaligenaceae/isolamento & purificação , Alcaligenaceae/metabolismo , Bacillaceae/classificação , Bacillaceae/isolamento & purificação , Bacillaceae/metabolismo , Bactérias/classificação , Bactérias/metabolismo , Análise por Conglomerados , Comamonadaceae/classificação , Comamonadaceae/isolamento & purificação , Comamonadaceae/metabolismo , Enterobacteriaceae/classificação , Enterobacteriaceae/isolamento & purificação , Enterobacteriaceae/metabolismo , Ésteres , Ácidos Graxos/química , Ácidos Graxos/classificação , Moraxellaceae/classificação , Moraxellaceae/isolamento & purificação , Moraxellaceae/metabolismo , Análise de Componente Principal , Pseudomonadaceae/classificação , Pseudomonadaceae/isolamento & purificação , Pseudomonadaceae/metabolismo , Vácuo , Microbiologia da Água , Xanthomonadaceae/classificação , Xanthomonadaceae/isolamento & purificação , Xanthomonadaceae/metabolismo
5.
Eur J Mass Spectrom (Chichester) ; 24(3): 261-268, 2018 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-29392979

RESUMO

The detection of post-translational modifications of proteins is an important comprehensive research area. Over the years, proteomic studies involving protein acetylation have attracted a great deal of attention. In the present study, we have focussed on the acetylation of histidine and the intrinsic stability of b1-ion of oxazolone ring and/or with side chain imidazole bicyclic product. The formation of oxazolone structure may occur when an amino moiety undergoes acetylation reaction and when it is present in the vicinity of the side chain imidazole moiety. Tryptic peptides generated from the proteins of Acenitobacter radioresistens MMC5-containing N-terminal histidine were explored in a standard proteomic workflow. Formation of [Formula: see text] ion with an oxazolone ring in these peptides has been supported by a tandem mass spectrometric study of a synthetic peptide and density functional theory calculations. The results obtained from this study have implications in understanding the fragmentation of the peptides generated in the proteomic workflows.


Assuntos
Proteínas de Bactérias/química , Histidina/química , Imidazóis/química , Moraxellaceae/química , Oxazolona/química , Acetilação , Íons/química , Estrutura Molecular , Peptídeos/química , Processamento de Proteína Pós-Traducional , Proteômica , Espectrometria de Massas em Tandem
6.
PLoS Negl Trop Dis ; 11(10): e0005975, 2017 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-28968382

RESUMO

A longitudinal study was undertaken in infants living in the Maela refugee camp on the Thailand-Myanmar border between 2007 and 2010. Nasopharyngeal swabs were collected monthly, from birth to 24 months of age, with additional swabs taken if the infant was diagnosed with pneumonia according to WHO clinical criteria. At the time of collection, swabs were cultured for Streptococcus pneumoniae and multiple serotype carriage was assessed. The bacterial 16S rRNA gene profiles of 544 swabs from 21 infants were analysed to see how the microbiota changes with age, respiratory infection, antibiotic consumption and pneumococcal acquisition. The nasopharyngeal microbiota is a somewhat homogenous community compared to that of other body sites. In this cohort it is dominated by five taxa: Moraxella, Streptococcus, Haemophilus, Corynebacterium and an uncharacterized Flavobacteriaceae taxon of 93% nucleotide similarity to Ornithobacterium. Infant age correlates with certain changes in the microbiota across the cohort: Staphylococcus and Corynebacterium are associated with the first few months of life while Moraxella and the uncharacterised Flavobacteriaceae increase in proportional abundance with age. Respiratory illness and antibiotic use often coincide with an unpredictable perturbation of the microbiota that differs from infant to infant and in different illness episodes. The previously described interaction between Dolosigranulum and Streptococcus was observed in these data. Monthly sampling demonstrates that the nasopharyngeal microbiota is in flux throughout the first two years of life, and that in this refugee camp population the pool of potential bacterial colonisers may be limited.


Assuntos
Antibacterianos/uso terapêutico , Bactérias/isolamento & purificação , Microbiota , Nasofaringe/microbiologia , Infecções Respiratórias/epidemiologia , Fatores Etários , Antibacterianos/efeitos adversos , Bactérias/classificação , Bactérias/genética , Portador Sadio/epidemiologia , Portador Sadio/microbiologia , Estudos de Coortes , Feminino , Humanos , Lactente , Recém-Nascido , Estudos Longitudinais , Masculino , Moraxellaceae/genética , Moraxellaceae/isolamento & purificação , Pneumonia/epidemiologia , RNA Ribossômico 16S/genética , Refugiados , Infecções Respiratórias/microbiologia , Streptococcus pneumoniae/genética , Streptococcus pneumoniae/isolamento & purificação
7.
Int J Syst Evol Microbiol ; 67(7): 2296-2300, 2017 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-28741994

RESUMO

A Gram-staining-negative, non-motile, non-pigmented, strictly aerobic and rod-shape bacterium, designated BK296T, was isolated from stream water originating from a limestone cave in Samcheok, Korea. Optimal growth of strain BK296T was observed at 30 °C, pH 7.0-8.0 and without NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BK296T belonged to the genus Perlucidibaca, forming a robust clade with a member of the genus, and was most closely related to Perlucidibaca piscinae (97.8 %). The average nucleotide identity value between strain BK296T and Perlucidibacapiscinae IMCC1704T was 79.8 %, and the genome-to-genome distance was 17.5 % on mean. The G+C content of the DNA of strain BK296T was 55.7 mol%. The major fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0, C12 : 0 3-OH and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The major isoprenoid quinone was ubiquinone Q-8. On the basis of phenotypic, genotypic and phylogenetic analyses, strain BK296T (=KCTC 52162T=JCM 31377T) represents a novel species of the genus Perlucidibaca, for which the name Perlucidibaca aquatica sp. nov. is proposed.


Assuntos
Água Doce/microbiologia , Moraxellaceae/classificação , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , Cavernas , DNA Bacteriano/genética , Ácidos Graxos/química , Moraxellaceae/genética , Moraxellaceae/isolamento & purificação , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Ubiquinona/química
8.
Res Microbiol ; 167(9-10): 731-744, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27475037

RESUMO

Uncultivable microorganisms account for over 99% of all species on the planet, but their functions are yet not well characterized. Though many cultivable degraders for n-alkanes have been intensively investigated, the roles of functional n-alkane degraders remain hidden in the natural environment. This study introduces the novel magnetic nanoparticle-mediated isolation (MMI) technology in Nigerian soils and successfully separates functional microbes belonging to the families Oxalobacteraceae and Moraxellaceae, which are dominant and responsible for alkane metabolism in situ. The alkR-type n-alkane monooxygenase genes, instead of alkA- or alkP-type, were the key functional genes involved in the n-alkane degradation process. Further physiological investigation via a BIOLOG PM plate revealed some carbon (Tween 20, Tween 40 and Tween 80) and nitrogen (tyramine, l-glutamine and d-aspartic acid) sources promoting microbial respiration and n-alkane degradation. With further addition of promoter carbon or nitrogen sources, the separated functional alkane degraders significantly improved n-alkane biodegradation rates. This suggests that MMI is a promising technology for separating functional microbes from complex microbiota, with deeper insight into their ecological functions and influencing factors. The technique also broadens the application of the BIOLOG PM plate for physiological research on functional yet uncultivable microorganisms.


Assuntos
Alcanos/metabolismo , Técnicas Bacteriológicas/métodos , Moraxellaceae/isolamento & purificação , Oxalobacteraceae/isolamento & purificação , Petróleo/metabolismo , Microbiologia do Solo , Poluentes do Solo/metabolismo , Biotransformação , Carbono/metabolismo , Magnetismo , Metaboloma , Análise em Microsséries , Nanopartículas , Nitrogênio/metabolismo , Fenótipo
10.
Carbohydr Res ; 422: 5-12, 2016 Mar 03.
Artigo em Inglês | MEDLINE | ID: mdl-26795079

RESUMO

The heptose-deficient inner core of the lipopolysaccharide of several pathogenic strains of the Moraxellaceae family (Moraxella, Acinetobacter) and of Bartonella henselae, respectively, comprises an α-D-glucopyranose attached to position 5 of Kdo. In continuation of the synthesis of fragments of Acinetobacter haemolyticus LPS, the branched α-Glcp-(1 → 5)[α-Kdo-(2 → 4)]-α-Kdo trisaccharide motif was elaborated. The glycosylation of a suitably protected, α-(2 → 4)-interlinked Kdo-disaccharide was achieved in high yield and fair anomeric selectivity using a 4,6-O-benzylidene N-phenyltrifluoroacetimidate glucosyl donor. Subsequent regioselective reductive benzylidene opening afforded a trisaccharide acceptor, which was extended with ß-D-glucopyranosyl and isomaltosyl residues. Global deprotection provided tri- to pentasaccharide structures corresponding to the inner core region of A. haemolyticus lipopolysaccharide.


Assuntos
Dissacarídeos/química , Dissacarídeos/síntese química , Glucose/química , Lipopolissacarídeos/química , Moraxellaceae/química , Técnicas de Química Sintética , Estereoisomerismo , Trissacarídeos/química
11.
Int J Syst Evol Microbiol ; 66(1): 201-205, 2016 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-26498187

RESUMO

A Gram-stain-negative, non-spore-forming and coccus-shaped bacterial strain, designated 4DR5T, was isolated from freshwater and its taxonomic position was investigated using a polyphasic approach. Growth occurred at 10-40 °C (optimum 30 °C), at pH 6-9 (optimum pH 7) and in the presence of 0-0.4 % (w/v) NaCl (optimum 0 %) on R2A agar. On the basis of 16S rRNA gene sequence similarity, strain 4DR5T was assigned to the family Moraxellaceae of the class Gammaproteobacteria, and its closest related taxa were species of the genera Perlucidibaca (93.67 % sequence similarity), Agitococcus (93.07 %), Paraperlucidibaca (92.31-92.38 %), Alkanindiges (91.79 %) and Acinetobacter (90.24-91.23 %). The predominant isoprenoid quinone detected in strain 4DR5T was Q-10. The major cellular fatty acids were a summed feature consisting of C16 : 1ω7c and/or C16 : 1ω6c, one consisting of C18 : 1ω7c and/or C18 : 1ω6c, and C16 : 0. The major polar lipid was phosphatidylethanolamine. The genomic DNA G+C content of the strain was 61.2 mol%. The phylogenetic, chemotaxonomic and biochemical data not only supported the affiliation of strain 4DR5T to the family Moraxellaceae, but also separated it from other established genera within the family. Therefore, the novel isolate evidently represents a novel species of a new genus of Moraxellaceae, for which the name Fluviicoccus keumensis gen. nov., sp. nov. is proposed. The type strain of Fluviicoccus keumensis is 4DR5T ( = KCTC 32475T = JCM 19370T).


Assuntos
Água Doce/microbiologia , Moraxellaceae/classificação , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Dados de Sequência Molecular , Moraxellaceae/genética , Moraxellaceae/isolamento & purificação , Fosfatidiletanolaminas/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Ubiquinona/análogos & derivados , Ubiquinona/química
12.
Int J Syst Evol Microbiol ; 65(Pt 1): 11-14, 2015 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-25267870

RESUMO

An aerobic, Gram-stain-negative, non-motile coccus, designated strain GVCNT2(T), was isolated from the tonsils of a healthy adult female. Cells were oxidase- and catalase-positive, positive for the production of esterase (C4), esterase lipase (C8) and leucine arylamidase, and weakly positive for naphthol-AS-BI-phosphohydrolase and alkaline phosphatase. Cells were also capable of hydrolysing DNA. Growth was observed at 20-37 °C and in the presence of up to 1.5% NaCl. Phylogenetic analysis of near full-length 16S rRNA gene sequences indicated that the strain exhibited closest sequence similarity to Moraxella boevrei ATCC 700022(T) (94.68%) and an uncultured, unspeciated bacterial clone (strain S12-08; 99%). The major fatty acids were C18:1ω9c, C18 : 0, C16:0 and C16:1ω6c/C16:1ω7c. The DNA G+C content of strain GVCNT2(T) was 40.7 mol%. The major respiratory quinone identified was Q-8. Strain GVCNT2(T) exhibited a comparable phenotypic profile to other members of the genus Moraxella but could be distinguished based on its ability to produce acid (weakly) from d-glucose, melibiose, l-arabinose and rhamnose and on its ability to hydrolyse DNA. On the basis of phenotypic and phylogenetic differences from other members of the family Moraxellaceae, strain GVCNT2(T) is considered to represent a novel species of a new genus, for which the name Faucicola mancuniensis gen. nov., sp. nov. is proposed. The type strain of Faucicola mancuniensis is GVCNT2(T) ( =DSM 28411(T) =NCIMB 14946(T)).


Assuntos
Moraxellaceae/classificação , Orofaringe/microbiologia , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Feminino , Humanos , Dados de Sequência Molecular , Moraxellaceae/genética , Moraxellaceae/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
13.
J Infect Chemother ; 20(1): 61-4, 2014 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-24462428

RESUMO

We report the first case of both endocarditis and bilateral septic arthritis in a patient caused by Moraxella lacunata and successful management of the infection with antimicrobial therapy. The route of entry leading to bacteremia may have been the oral cavity given the poor oral hygiene of the patient as evidenced by bleeding gums. We hypothesize that the bacteremia led to septic arthritis and mitral valve infective endocarditis. In this case report, we also review the literature on M. lacunata infections and conclude that this organism should be considered in bilateral septic arthritis in a patient with underlying heart abnormalities and/or with renal failure.


Assuntos
Artrite Infecciosa/microbiologia , Bacteriemia/microbiologia , Endocardite Bacteriana/microbiologia , Infecções por Moraxellaceae/microbiologia , Sepse/microbiologia , Idoso , Antibacterianos/uso terapêutico , Artrite Infecciosa/tratamento farmacológico , Bacteriemia/tratamento farmacológico , Endocardite Bacteriana/tratamento farmacológico , Feminino , Humanos , Moraxellaceae/efeitos dos fármacos , Infecções por Moraxellaceae/tratamento farmacológico , Diálise Renal , Sepse/tratamento farmacológico
14.
PLoS One ; 8(10): e76177, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-24116094

RESUMO

Codon usage bias (CUB) results from the complex interplay between translational selection and mutational biases. Current methods for CUB analysis apply heuristics to integrate both components, limiting the depth and scope of CUB analysis as a technique to probe into the evolution and optimization of protein-coding genes. Here we introduce a self-consistent CUB index (scnRCA) that incorporates implicit correction for mutational biases, facilitating exploration of the translational selection component of CUB. We validate this technique using gene expression data and we apply it to a detailed analysis of CUB in the Pseudomonadales. Our results illustrate how the selective enrichment of specific codons among highly expressed genes is preserved in the context of genome-wide shifts in codon frequencies, and how the balance between mutational and translational biases leads to varying definitions of codon optimality. We extend this analysis to other moderate and fast growing bacteria and we provide unified support for the hypothesis that C- and A-ending codons of two-box amino acids, and the U-ending codons of four-box amino acids, are systematically enriched among highly expressed genes across bacteria. The use of an unbiased estimator of CUB allows us to report for the first time that the signature of translational selection is strongly conserved in the Pseudomonadales in spite of drastic changes in genome composition, and extends well beyond the core set of highly optimized genes in each genome. We generalize these results to other moderate and fast growing bacteria, hinting at selection for a universal pattern of gene expression that is conserved and detectable in conserved patterns of codon usage bias.


Assuntos
Códon , Mutação , Seleção Genética , Bases de Dados Genéticas , Genoma , Moraxellaceae/genética , Pseudomonas/genética
15.
Microbiology ; 159(Pt 9): 1900-10, 2013 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-23832000

RESUMO

Recently, we described a novel insertion element, ISPpy1, isolated from a permafrost strain of Psychrobacter maritimus. In this work, we demonstrated that ISPpy1 is a member of a novel subgroup of the IS3 family of insertion sequences (ISs) that was not identified and characterized previously. IS elements of this subgroup termed the ISPpy1 subgroup are broadly distributed among different taxa of Eubacteria, including Geobacteraceae, Chlorobiaceae, Desulfobacteraceae, Methylobacteriaceae, Nitrosomonadaceae and Cyanobacteria. While displaying characteristic features of the IS3-family elements, ISPpy1 subgroup elements exhibit some unusual features. In particular, most of them have longer terminal repeats with unconventional ends and frameshifting box with an atypical organization, and, unlike many other IS3-family elements, do not exhibit any distinct IS specificity. We studied the transposition and mutagenic properties of a representative member of this subgroup, ISPpy1 and showed that in contrast to the original P. maritimus host, in a heterologous host, Escherichia coli K-12, it is able to translocate with extremely high efficiency into the chromosome, either by itself or as a part of a composite transposon containing two ISPpy1 copies. The majority of transposants carry multiple chromosomal copies (up to 12) of ISPpy1. It was discovered that ISPpy1 is characterized by a marked mutagenic activity in E. coli: its chromosomal insertions generate various types of mutations, including auxotrophic, pleiotropic and rifampicin-resistance mutations. The distribution of IS elements of the novel subgroup among different bacteria, their role in the formation of composite transposons and the horizontal transfer of genes are examined and discussed.


Assuntos
Bactérias/genética , Elementos de DNA Transponíveis , Família Multigênica , Bactérias/classificação , Sequência de Bases , Escherichia coli/genética , Dosagem de Genes , Dados de Sequência Molecular , Moraxellaceae/classificação , Moraxellaceae/genética , Mutagênese Insercional , Filogenia
16.
Int J Syst Evol Microbiol ; 63(Pt 11): 4113-7, 2013 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-23749278

RESUMO

A Gram-stain-negative, aerobic, motile and rod-shaped bacterial strain, designated WT-RY4(T), was isolated from wood falls in the South Sea, South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain WT-RY4(T) grew optimally at 25 °C, at pH 7.0-7.5 and in the absence of NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain WT-RY4(T) clustered with the type strain of Paraperlucidibaca baekdonensis with a bootstrap resampling value of 100 %. Strain WT-RY4(T) exhibited 16S rRNA gene sequence similarity values of 98.8 % and 96.3 % to Paraperlucidibaca baekdonensis RL-2(T) and Perlucidibaca piscinae IMCC 1704(T), respectively and less than 91.5 % to the type strains of other species used in the phylogenetic analysis. The DNA G+C content of strain WT-RY4(T) was 52.4 mol% and the mean DNA-DNA relatedness value with Paraperlucidibaca baekdonensis RL-2(T) was 25 %. Strain WT-RY4(T) contained Q-11 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C12 : 0 3-OH as the major fatty acids. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, demonstrated that strain WT-RY4(T) was distinguishable from Paraperlucidibaca baekdonensis RL-2(T). On the basis of the data presented, strain WT-RY4(T) is considered to represent a novel species of the genus Paraperlucidibaca, for which the name Paraperlucidibaca wandonensis sp. nov. is proposed. The type strain is WT-RY4(T) ( = KCTC 32216(T) = CCUG 63419(T)). An emended description of the genus Paraperlucidibaca is also provided.


Assuntos
Moraxellaceae/classificação , Filogenia , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Dados de Sequência Molecular , Moraxellaceae/genética , Moraxellaceae/isolamento & purificação , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Ubiquinona/química , Microbiologia da Água
17.
J Bacteriol ; 195(8): 1680-8, 2013 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-23378507

RESUMO

Bacterial membranes serve as selective environmental barriers and contain determinants required for bacterial colonization and survival. Cell envelopes of Gram-negative bacteria consist of an outer and an inner membrane separated by a periplasmic space. Most Gram-negative bacteria display a smooth outer surface (e.g., Enterobacteriaceae), whereas members of the Pasteurellaceae and Moraxellaceae families show convoluted surfaces. Aggregatibacter actinomycetemcomitans, an oral pathogen representative of the Pasteurellaceae family, displays a convoluted membrane morphology. This phenotype is associated with the presence of morphogenesis protein C (MorC). Inactivation of the morC gene results in a smooth membrane appearance when visualized by two-dimensional (2D) electron microscopy. In this study, 3D electron microscopy and atomic force microscopy of whole-mount bacterial preparations as well as 3D electron microscopy of ultrathin sections of high-pressure frozen and freeze-substituted specimens were used to characterize the membranes of both wild-type and morC mutant strains of A. actinomycetemcomitans. Our results show that the mutant strain contains fewer convolutions than the wild-type bacterium, which exhibits a higher curvature of the outer membrane and a periplasmic space with 2-fold larger volume/area ratio than the mutant bacterium. The inner membrane of both strains has a smooth appearance and shows connections with the outer membrane, as revealed by visualization and segmentation of 3D tomograms. The present studies and the availability of genetically modified organisms with altered outer membrane morphology make A. actinomycetemcomitans a model organism for examining membrane remodeling and its implications in antibiotic resistance and virulence in the Pasteurellaceae and Moraxellaceae bacterial families.


Assuntos
Membrana Celular/ultraestrutura , Moraxellaceae/ultraestrutura , Pasteurellaceae/ultraestrutura , Antibacterianos/farmacologia , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Membrana Celular/fisiologia , Farmacorresistência Bacteriana , Regulação Bacteriana da Expressão Gênica/fisiologia , Microscopia de Força Atômica , Microscopia Eletrônica de Transmissão/métodos , Moraxellaceae/genética , Moraxellaceae/metabolismo , Moraxellaceae/patogenicidade , Mutação , Pasteurellaceae/genética , Pasteurellaceae/metabolismo , Pasteurellaceae/patogenicidade , Propriedades de Superfície , Virulência
18.
Mikrobiol Z ; 75(6): 3-9, 2013.
Artigo em Russo | MEDLINE | ID: mdl-24450178

RESUMO

The aerobic chemoorganotrophic bacteria, dominating in soils and phytocenosis of the Antarctic Region, on combination of morphological and biochemical properties belong to several taxons of Bacteria domain. Gram-negative strains 3189, 3415 (fam. Halomonadaceae, Halomonas sp.) and 3088, 3468, 3469 (fam. Moraxellaceae, Psychrobacter sp.) belong to phylum Proteobacteria, to class Gammaproteobacteria. Gram-negative strains 3294 3392 (Rhizobiales, fam. Methylobacteriaceae, Methylobacterium sp.) relate to class Alphaproteobacteria of this phylum. Gram-positive strains 3179, 3275, 3470, 3471 (fam. Microbacteriaceae, Cryobacterium sp.), 3054, 3058, 3411 (fam. Corynebacteriaceae, Corynebacterium sp.) and 3194, 3398 (fam. Micrococcaceae, Micrococcus sp.) relate to phylum Actinobacteria, class Actinobacteria. Thus, the psychrophilic and psychrotolerant Antarctic bacteria (aerobic chemoorganotrophic) isolated from phytocenosis and soils of polar region are characterized by wide taxonomic variety.


Assuntos
Actinomycetales/classificação , Halomonadaceae/classificação , Methylobacteriaceae/classificação , Moraxellaceae/classificação , Filogenia , Microbiologia do Solo , Microbiologia da Água , Actinomycetales/crescimento & desenvolvimento , Actinomycetales/metabolismo , Aerobiose , Regiões Antárticas , Temperatura Baixa , Meios de Cultura , Fermentação , Halomonadaceae/crescimento & desenvolvimento , Halomonadaceae/metabolismo , Methylobacteriaceae/crescimento & desenvolvimento , Methylobacteriaceae/metabolismo , Moraxellaceae/crescimento & desenvolvimento , Moraxellaceae/metabolismo
19.
FEBS J ; 279(20): 3776-90, 2012 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-22883393

RESUMO

Cell selective, naturally occurring, host defence cationic peptides present a good template for the design of novel peptides with the aim of achieving a short length with improved antimicrobial potency and selectivity. A novel, short peptide CS-1a (14 residues) was derived using a sequence hybridization approach on sarcotoxin I (39 residues) and cecropin B (35 residues). The sequence of CS-1a was rearranged to enhance amphipathicity with the help of a Schiffer-Edmundson diagram to obtain CS-2a. Both peptides showed good antibacterial activity in the concentration range 4-16 µg·mL(-1) against susceptible as well as drug-resistant bacterial strains, including the clinically relevant pathogens Acenatobacter sp. and methicillin-resistant Staphylococcus aureus. The major thrust of these peptides is their nonhaemolytic activity against human red blood cells up to a high concentration of 512 µg·mL(-1). Compared to CS-1a, amphipathic peptide CS-2a showed a more pronounced α-helical conformation, along with a better membrane insertion depth in bacterial mimic 1,2-dipalmitoyl-sn-glycero-3-phosphocholine/1,2-dipalmitoyl-sn-glycero-3-phospho-(1'-rac-glycerol) small unilamellar vesicles. With equivalent lipid-binding affinity, the two peptides assumed different pathways of membrane disruption, as demonstrated by calcein leakage and the results of transmission electron microscopy on model bacterial mimic large unilamellar vesicles. Extending the work from model membranes to intact Escherichia coli cells, differences in membrane perturbation were visible in microscopic images of peptide-treated E. coli. The present study describes two novel short peptides with potent activity, cell selectivity and divergent modes of action that will aid in the future design of peptides with better therapeutic potential.


Assuntos
Antibacterianos/farmacologia , Peptídeos Catiônicos Antimicrobianos/farmacologia , Bactérias/efeitos dos fármacos , Peptídeos/farmacologia , 1,2-Dipalmitoilfosfatidilcolina/análogos & derivados , 1,2-Dipalmitoilfosfatidilcolina/química , 1,2-Dipalmitoilfosfatidilcolina/metabolismo , Sequência de Aminoácidos , Antibacterianos/química , Antibacterianos/metabolismo , Peptídeos Catiônicos Antimicrobianos/química , Peptídeos Catiônicos Antimicrobianos/metabolismo , Dicroísmo Circular , Escherichia coli/química , Escherichia coli/efeitos dos fármacos , Escherichia coli/ultraestrutura , Hemólise/efeitos dos fármacos , Humanos , Proteínas de Insetos/química , Bicamadas Lipídicas/química , Bicamadas Lipídicas/metabolismo , Staphylococcus aureus Resistente à Meticilina/efeitos dos fármacos , Testes de Sensibilidade Microbiana , Microscopia Eletrônica de Varredura , Dados de Sequência Molecular , Moraxellaceae/efeitos dos fármacos , Peptídeos/química , Peptídeos/metabolismo , Fosfatidilgliceróis/química , Fosfatidilgliceróis/metabolismo , Ligação Proteica , Estrutura Secundária de Proteína , Lipossomas Unilamelares/química , Lipossomas Unilamelares/metabolismo
20.
PLoS One ; 7(12): e52241, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-23284951

RESUMO

A novel non-culture based 16S rRNA Terminal Restriction Fragment Length Polymorphism (T-RFLP) method using the restriction enzymes Tsp509I and Hpy166II was developed for the characterization of the nasopharyngeal microbiota and validated using recently published 454 pyrosequencing data. 16S rRNA gene T-RFLP for 153 clinical nasopharyngeal samples from infants with acute otitis media (AOM) revealed 5 Tsp509I and 6 Hpy166II terminal fragments (TFs) with a prevalence of >10%. Cloning and sequencing identified all TFs with a prevalence >6% allowing a sufficient description of bacterial community changes for the most important bacterial taxa. The conjugated 7-valent pneumococcal polysaccharide vaccine (PCV-7) and prior antibiotic exposure had significant effects on the bacterial composition in an additive main effects and multiplicative interaction model (AMMI) in concordance with the 16S rRNA 454 pyrosequencing data. In addition, the presented T-RFLP method is able to discriminate S. pneumoniae from other members of the Mitis group of streptococci, which therefore allows the identification of one of the most important human respiratory tract pathogens. This is usually not achieved by current high throughput sequencing protocols. In conclusion, the presented 16S rRNA gene T-RFLP method is a highly robust, easy to handle and a cheap alternative to the computationally demanding next-generation sequencing analysis. In case a lot of nasopharyngeal samples have to be characterized, it is suggested to first perform 16S rRNA T-RFLP and only use next generation sequencing if the T-RFLP nasopharyngeal patterns differ or show unknown TFs.


Assuntos
Nasofaringe/microbiologia , Polimorfismo de Fragmento de Restrição/genética , RNA Ribossômico 16S/genética , Actinomycetales/genética , Actinomycetales/isolamento & purificação , Feminino , Humanos , Lactente , Recém-Nascido , Masculino , Moraxellaceae/genética , Moraxellaceae/isolamento & purificação , Pasteurellaceae/genética , Pasteurellaceae/isolamento & purificação , Reação em Cadeia da Polimerase , Staphylococcaceae/genética , Staphylococcaceae/isolamento & purificação , Streptococcaceae/genética , Streptococcaceae/isolamento & purificação
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