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Standards in Genomic Sciences 2017We report here the draft genome sequences of eight bacterial strains of the genera , and . These isolates were obtained from aerosol sampling of bathrooms of five...
Draft genome sequences of eight bacteria isolated from the indoor environment: strain H36, strain H65, strain H62, strain H69, sp. strain H83, strain H39, sp. strain H53, and strain H72.
We report here the draft genome sequences of eight bacterial strains of the genera , and . These isolates were obtained from aerosol sampling of bathrooms of five residences in the San Francisco Bay area. Taxonomic classifications as well as the genome sequence and gene annotation of the isolates are described. As part of the "Built Environment Reference Genome" project, these isolates and associated genome data provide valuable resources for studying the microbiology of the built environment.
PubMed: 28163826
DOI: 10.1186/s40793-017-0223-9 -
Analytical and Bioanalytical Chemistry Mar 2017A metaproteomic approach, based on liquid chromatography-high resolution mass spectrometry (LC-HRMS) analysis, was followed to map the major bacterial metabolic...
A metaproteomic approach, based on liquid chromatography-high resolution mass spectrometry (LC-HRMS) analysis, was followed to map the major bacterial metabolic functions associated with the rhizosphere of metal-tolerant and metal hyperaccumulator plants, growing in a serpentine soil naturally contaminated by heavy metals such as Ni, Co and Cr. In particular, an "in-house" bacterial protein database was built based on the genera recognised by 16S rDNA profiling, then it was used for protein identification from LC-MS data. The combination of the information arising from three different extraction protocols, applied to each soil sample, permitted the identification of almost 800 proteins, corresponding to functions assigned to proper Gene Ontology categories. Mainly proteins involved in response to stimulus or in transport of metals and nutrients revealed variability of bacteria responses to microenvironment conditions. As for taxonomy, Phyllobacterium, Microbacterium oxidans, Pseudomonas oryzihabitans, Stenotrophomonas rhizophila and Bacillus methylotrophicus bacterial species were more represented in the rhizosphere samples of the metal-tolerant Biscutella laevigata and of the Ni hyperaccumulator Noccaea caerulescens with respect to bulk soil. Combining 16S rRNA gene-based sequencing and metaproteomic analysis, we get insights into microbial community functions and their interaction with plants colonising the stressful environment of serpentine soils.
Topics: Bacteria; Bacterial Physiological Phenomena; Bacterial Proteins; Chromatography, Liquid; DNA, Bacterial; Mass Spectrometry; Proteome; RNA, Ribosomal, 16S; Rhizosphere; Soil; Soil Microbiology
PubMed: 28083663
DOI: 10.1007/s00216-016-0175-8 -
Applied Biochemistry and Biotechnology Nov 2016One novel microbial esterase PHE21 was cloned from the genome of Pseudomonas oryzihabitans HUP022 identified from the deep sea of the Western Pacific. PHE21 was...
One novel microbial esterase PHE21 was cloned from the genome of Pseudomonas oryzihabitans HUP022 identified from the deep sea of the Western Pacific. PHE21 was heterologously expressed and functionally characterized to be a robust esterase which behaved high resistance to various metal ions, organic solvents, surfactants, and NaCl. Despite the fact that the two enantiomers of ethyl 3-hydroxybutyrate were hard to be enzymatically resolved before, we successfully resolved racemic ethyl 3-hydroxybutyrate through direct hydrolysis reactions and generated chiral ethyl (S)-3-hydroxybutyrate using esterase PHE21. After process optimization, the enantiomeric excess, the conversion rate, and the yield of desired product ethyl (S)-3-hydroxybutyrate could reach 99, 65, and 87 %, respectively. PHE21 is a novel marine microbial esterase with great potential in asymmetric synthesis as well as in other industries.
Topics: Enzyme Stability; Esterases; Hydrogen-Ion Concentration; Hydrolysis; Hydroxybutyrates; Ions; Kinetics; Metals; Pseudomonas; Seawater; Sequence Analysis, Protein; Sodium Chloride; Solvents; Stereoisomerism; Substrate Specificity; Surface-Active Agents; Temperature; Time Factors
PubMed: 27299920
DOI: 10.1007/s12010-016-2161-1 -
Genome Announcements Jun 2016We report the genome sequences of two double-stranded DNA siphoviruses, POR1 infective for Pseudomonas oryzihabitans and PAE1 infective for Pseudomonas aeruginosa The...
We report the genome sequences of two double-stranded DNA siphoviruses, POR1 infective for Pseudomonas oryzihabitans and PAE1 infective for Pseudomonas aeruginosa The phage POR1 genome showed no nucleotide sequence homology to any other DNA phage sequence in the GenBank database, while phage PAE1 displayed synteny to P. aeruginosa phages M6, MP1412, and YuA.
PubMed: 27313312
DOI: 10.1128/genomeA.01515-15 -
Journal of Basic Microbiology Mar 2016Glacier ice and firn cores have ecological and biotechnological importance. The present study is aimed at characterizing bacteria in crustal ice cores from Svalbard, the...
Glacier ice and firn cores have ecological and biotechnological importance. The present study is aimed at characterizing bacteria in crustal ice cores from Svalbard, the Arctic. Counts of viable isolates ranged from 10 to 7000 CFU/ml (mean 803 CFU/ml) while the total bacterial numbers ranged from 7.20 × 10(4) to 2.59 × 10(7) cells ml(-1) (mean 3.12 × 10(6) cells ml(-1) ). Based on 16S rDNA sequence data, the identified species belonged to seven species, namely Bacillus barbaricus, Pseudomonas orientalis, Pseudomonas oryzihabitans, Pseudomonas fluorescens, Pseudomonas syncyanea, Sphingomonas dokdonensis, and Sphingomonas phyllosphaerae, with a sequence similarity ranging between 93.5 and 99.9% with taxa present in the database. The isolates exhibited unique phenotypic properties, and three isolates (MLB-2, MLB-5, and MLB-9) are novel species, yet to be described. To the best of our knowledge, this is the first report on characterization of cultured bacterial communities from Svalbard ice cores. We conclude that high lipase, protease, cellulase, amylase, and urease activities expressed by most of the isolates provide a clue to the potential industrial applications of these organisms. These microbes, producing cold-adapted enzymes may provide an opportunity for biotechnological research.
Topics: Adaptation, Physiological; Antifreeze Proteins; Arctic Regions; Bacteria; Bacterial Proteins; Biodiversity; Cold Temperature; DNA, Bacterial; DNA, Ribosomal; Enzyme Activation; Enzymes; Fatty Acids; Ice Cover; Industrial Microbiology; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 26567474
DOI: 10.1002/jobm.201500298 -
Journal of Infection and Chemotherapy :... Oct 2015Pseudomonas oryzihabitans (formerly Flavimonas oryzihabitans) is a glucose non-fermentative, Gram-negative bacillus which is rarely isolated from human specimens. When...
Pseudomonas oryzihabitans (formerly Flavimonas oryzihabitans) is a glucose non-fermentative, Gram-negative bacillus which is rarely isolated from human specimens. When isolated, it is on very rare occasion as a causative pathogen of catheter-related bloodstream infection in an immunocompromised patient. Herein, we describe two hematological malignancy patients suspected to have P. oryzihabitans bacteremia. We also review cases with bacteremia due to this pathogen and its microbiological characteristics.
Topics: Antineoplastic Combined Chemotherapy Protocols; Bacteremia; Catheter-Related Infections; Catheters, Indwelling; Child, Preschool; Equipment Contamination; Humans; Immunocompromised Host; Lymphoma, T-Cell; Male; Middle Aged; Precursor B-Cell Lymphoblastic Leukemia-Lymphoma; Pseudomonas; Pseudomonas Infections
PubMed: 26184853
DOI: 10.1016/j.jiac.2015.06.005 -
Infectious Diseases (London, England) 2015Skin and soft tissue infections (SSTIs) due to Pseudomonas oryzihabitans are very rare. The aim of the present study was to investigate the clinical and microbiological...
Skin and soft tissue infections (SSTIs) due to Pseudomonas oryzihabitans are very rare. The aim of the present study was to investigate the clinical and microbiological characteristics of this infection. We performed a retrospective review of six cases that occurred in our area over a period of 6 years, and six cases previously reported in the literature. Predisposing factors were recognized in 76.9% of patients, including previous surgery, immunosuppression, diabetes mellitus, trauma, bites and lactation. The source of infection was probably environmental in most cases. Our study shows that P. oryzihabitans should be considered a potential pathogen, especially in patients with surgical site infections, mastitis and wound infections after bites or trauma. Clinical outcome is usually favourable and treatment is not difficult due to the low level of resistance to commonly used antibiotics.
Topics: Adult; Aged; Aged, 80 and over; Anti-Bacterial Agents; Female; Humans; Male; Middle Aged; Pseudomonas; Pseudomonas Infections; Retrospective Studies; Skin Diseases; Soft Tissue Infections; Young Adult
PubMed: 26179756
DOI: 10.3109/23744235.2015.1034170 -
Genome Announcements Apr 2015Here, we report the genome sequences of Bacillus safensis RIT372 and Pseudomonas oryzihabitans RIT370 from Capsicum spp. Annotation revealed gene clusters for the...
Whole-Genome Sequencing and Annotation of Bacillus safensis RIT372 and Pseudomonas oryzihabitans RIT370 from Capsicum annuum (Bird's Eye Chili) and Capsicum chinense (Yellow Lantern Chili), Respectively.
Here, we report the genome sequences of Bacillus safensis RIT372 and Pseudomonas oryzihabitans RIT370 from Capsicum spp. Annotation revealed gene clusters for the synthesis of bacilysin, lichensin, and bacillibactin and sporulation killing factor (skfA) in Bacillus safensis RIT372 and turnerbactin and carotenoid in Pseudomonas oryzihabitans RIT370.
PubMed: 25883290
DOI: 10.1128/genomeA.00288-15 -
Infection & Chemotherapy Mar 2014Pseudomonas oryzihabitans is frequently found in various sites within hospital settings, including sink drains and respiratory therapy equipment. Although it rarely...
Pseudomonas oryzihabitans is frequently found in various sites within hospital settings, including sink drains and respiratory therapy equipment. Although it rarely causes human infections, P. oryzihabitans has recently been considered a potential nosocomial pathogen, especially in immunocompromised hosts. We report our experience of an outbreak of P. oryzihabitans pseudobacteremia, presumably due to faulty aseptic preparation of a saline gauze canister.
PubMed: 24693469
DOI: 10.3947/ic.2014.46.1.42 -
Hemodialysis International.... Jul 2014Pseudomonas oryzihabitans (P. orizyhabitans) has already been reported both as a human and a zoonotic pathogen. A few cases of P. orizyhabitans bacteremia have...
Pseudomonas oryzihabitans (P. orizyhabitans) has already been reported both as a human and a zoonotic pathogen. A few cases of P. orizyhabitans bacteremia have been reported among patients who underwent peritoneal dialysis. P. orizyhabitans bacteremia has never been reported among patients on hemodialysis. We report the first case of P. orizyhabitans bacteremia in a chronic hemodialysis patient; this patient did not have a central venous catheter angioaccess as a potential portal of entry.
Topics: Adult; Bacteremia; Catheters, Indwelling; Female; Humans; Pseudomonas; Pseudomonas Infections; Renal Dialysis
PubMed: 24612459
DOI: 10.1111/hdi.12150