Publications

development of species-specific hybridization probes for marine luminous bacteria by using in vitro dna amplification.	by using two highly conserved region of the luxa gene as primers, polymerase chain reaction amplification methods were used to prepare species-specific probes against the luciferase gene from four major groups of marine luminous bacteria. laboratory studies with test strains indicated that three of the four probes cross-reacted with themselves and with one or more of the other species at low stringencies but were specific for members of their own species at high stringencies. the fourth probe, g ...	1991	1854194
nucleotide sequences of 5s ribosomal rnas from three marine eubacteria: shewanella hanedai, alteromonas colwelliana and vibrio mediterranei.		1989	2473444
differentiation of shewanella putrefaciens and shewanella alga on the basis of whole-cell protein profiles, ribotyping, phenotypic characterization, and 16s rrna gene sequence analysis.	seventy-six presumed shewanella putrefaciens isolates from fish, oil drillings, and clinical specimens, the type strain of shewanella putrefaciens (atcc 8071), the type strain of shewanella alga (iam 14159), and the type strain of shewanella hanedai (atcc 33224) were compared by several typing methods. numerical analysis of sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole-cell protein and ribotyping patterns showed that the strains were separated into two distinct clusters with ...	1997	9172338
shewanella woodyi sp. nov., an exclusively respiratory luminous bacterium isolated from the alboran sea.	thirty-four strains of nonfermentative, respiratory, luminous bacteria were isolated from samples of squid ink and seawater from depths of 200 to 300 m in the alboran sea. although these strains had a few properties similar to properties of shewanella (alteromonas) hanedai, they did not cluster phenotypically with any previously described bacterium. the nucleotide sequence of a 740-bp segment of luxa was not homologous with other known luxa sequences but clustered with the luxa sequences of shew ...	1997	9336902
shewanella gelidimarina sp. nov. and shewanella frigidimarina sp. nov., novel antarctic species with the ability to produce eicosapentaenoic acid (20:5 omega 3) and grow anaerobically by dissimilatory fe(iii) reduction.	a polyphasic taxonomic study was performed to characterize dissimilatory iron-reducing strains mostly isolated from antarctic sea ice. the strains were isolated from samples of congelated (land-fast) sea ice, grease ice, and ice algal biomass collected from the coastal areas of the vestfold hills in eastern antarctica (68 degrees s 78 degrees e). the strains were facultatively anaerobic, motile, and rod shaped, were capable of anaerobic growth either by fermentation of carbohydrates or by anaero ...	1997	9336903
cloning and nucleotide sequence of the gyrb gene of vibrio parahaemolyticus and its application in detection of this pathogen in shrimp.	because biochemical testing and 16s rrna sequence analysis have proven inadequate for the differentiation of vibrio parahaemolyticus from closely related species, we employed the gyrase b gene (gyrb) as a molecular diagnostic probe. the gyrb genes of v. parahaemolyticus and closely related vibrio alginolyticus were cloned and sequenced. oligonucleotide pcr primers were designed for the amplification of a 285-bp fragment from within gyrb specific for v. parahaemolyticus. these primers recognized ...	1998	9464408
kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rrna gene pcr amplicon length heterogeneity	marine bacterioplankton diversity was examined by quantifying natural length variation in the 5' domain of small-subunit (ssu) rrna genes (rdna) amplified by pcr from a dna sample from the oregon coast. this new technique, length heterogeneity analysis by pcr (lh-pcr), determines the relative proportions of amplicons originating from different organisms by measuring the fluorescence emission of a labeled primer used in the amplification reaction. relationships between the sizes of amplicons and ...	1998	9797317
isolation and identification of photobacterium phosphoreum from an unexpected niche: migrating salmon.	six luminous bacteria were isolated from migrating salmon in the yukon river, alaska. all isolates were identified as photobacterium phosphoreum. previous studies suggest that p. phosphoreum is an exclusively marine bacterium, while our alaskan isolates are from salmon which migrated up to 1,228 km from the marine environment.	2003	14602659
shewanella sediminis sp. nov., a novel na+-requiring and hexahydro-1,3,5-trinitro-1,3,5-triazine-degrading bacterium from marine sediment.	previously, a psychrophilic rod-shaped marine bacterium (strain haw-eb3(t)) isolated from halifax harbour sediment was noted for its ability to degrade hexahydro-1,3,5-trinitro-1,3,5-triazine (rdx). in the present study phenotypic, chemotaxonomic and genotypic characterization showed that strain haw-eb3(t) represents a novel species of shewanella. strain haw-eb3(t) contained lysine decarboxylase, which is absent in other known shewanella species, and distinguished itself from most other species ...	2005	16014474
suspension array analysis of 16s rrna from fe- and so(4)2- reducing bacteria in uranium-contaminated sediments undergoing bioremediation.	a 16s rrna-targeted tunable bead array was developed and used in a retrospective analysis of metal- and sulfate-reducing bacteria in contaminated subsurface sediments undergoing in situ u(vi) bioremediation. total rna was extracted from subsurface sediments and interrogated directly, without a pcr step. bead array validation studies with total rna derived from 24 isolates indicated that the behavior and response of the 16s rrna-targeted oligonucleotide probes could not be predicted based on the ...	2006	16820459
lateral transfer of the lux gene cluster.	the lux operon is an uncommon gene cluster. to find the pathway through which the operon has been transferred, we sequenced the operon and both flanking regions in four typical luminous species. in vibrio cholerae ncimb 41, a five-gene cluster, most genes of which were highly similar to orthologues present in gram-positive bacteria, along with the lux operon, is inserted between vc1560 and vc1563, on chromosome 1. because this entire five-gene cluster is present in photorhabdus luminescens tt01, ...	2007	17169972
the mycobacterium marinum mel2 locus displays similarity to bacterial bioluminescence systems and plays a role in defense against reactive oxygen and nitrogen species.	mycobacteria have developed a number of pathways that provide partial protection against both reactive oxygen species (ros) and reactive nitrogen species (rns). we recently identified a locus in mycobacterium marinum, mel2, that plays a role during infection of macrophages. the molecular mechanism of mel2 action is not well understood.	2007	17239244
phylogenetic analysis of the incidence of lux gene horizontal transfer in vibrionaceae.	horizontal gene transfer (hgt) is thought to occur frequently in bacteria in nature and to play an important role in bacterial evolution, contributing to the formation of new species. to gain insight into the frequency of hgt in vibrionaceae and its possible impact on speciation, we assessed the incidence of interspecies transfer of the lux genes (luxcdabeg), which encode proteins involved in luminescence, a distinctive phenotype. three hundred three luminous strains, most of which were recently ...	2008	18359809
a persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations.	acute exacerbations of chronic obstructive pulmonary disease (copd) are a major source of morbidity and contribute significantly to healthcare costs. although bacterial infections are implicated in nearly 50% of exacerbations, only a handful of pathogens have been consistently identified in copd airways, primarily by culture-based methods, and the bacterial microbiota in acute exacerbations remains largely uncharacterized. the aim of this study was to comprehensively profile airway bacterial com ...	2010	20141328
shewanella spp. genomic evolution for a cold marine lifestyle and in-situ explosive biodegradation.	shewanella halifaxensis and shewanella sediminis were among a few aquatic gamma-proteobacteria that were psychrophiles and the first anaerobic bacteria that degraded hexahydro-1,3,5-trinitro-1,3,5-triazine (rdx). although many mesophilic or psychrophilic strains of shewanella and gamma-proteobacteria were sequenced for their genomes, the genomic evolution pathways for temperature adaptation were poorly understood. on the other hand, the genes responsible for anaerobic rdx mineralization pathways ...	2010	20174598
probing of potential luminous bacteria in bay of bengal and its enzyme characterization.	the present study dealt with the isolation, identification and enzyme characterization of potential luminous bacteria from water, sediment, squid, and cuttle fish samples of the karaikal coast, bay of bengal, india during the study period september 2007 - august 2008. bioluminescent strains were screened in swc agar and identified using biochemical tests. as shewanella henadai was found to be the most common and abundant species with maximum light emission [69,702,240 photons per second (pps)], ...	2013	23676923
determination of the genetic diversity of different bioluminescent bacteria by pulsed-field gel electrophoresis (pfge).	there are 4 different genera (i.e. vibrio, aliivibrio, photobacterium, and shewanella) in the new classification of bioluminescent bacteria. the mechanism of bioluminescence has yet to be fully elucidated. therefore, the determination of physiological and genetic characteristics of bioluminescent bacteria isolated from different sources is very important. pulsed-field gel electrophoresis (pfge) has the highest discriminatory power among the different molecular typing methods for the investigatio ...	2015	26421141