Publications

clear distinction between burkholderia mallei and burkholderia pseudomallei using fluorescent motb primers.	a frame-shift mutation in the flagellum motor gene motb coding for the chemotaxis motb protein of burkholderia mallei has been utilized to design a conventional duplex pcr assay with fluorescent labelled primers.	2015	25887130
shifts in bacterial communities of eggshells and antimicrobial activities in eggs during incubation in a ground-nesting passerine.	microbial invasion of egg contents is a cause of embryonic death. to counter infection risks, the embryo is protected physically by the eggshell and chemically by antimicrobial proteins. if microbial pressure drives embryo mortality, then females may have evolved, through natural selection, to adapt their immune investment into eggs. although frequently hypothesized, this match between immune allocation and microorganisms has not been explored yet. to examine if correlations between microbes on ...	2015	25880684
draft genome sequence of ochrobactrum anthropi strain ml7 isolated from soil samples in vinhphuc province, vietnam.	ochrobactrum species are widespread in the environment and can colonize a wide variety of habitats. here, we describe the sequencing of a new environmental isolate of ochrobactrum anthropi isolated from northern vietnam.	2015	25838481
3-way networks: application of hypergraphs for modelling increased complexity in comparative genomics.	we present and develop the theory of 3-way networks, a type of hypergraph in which each edge models relationships between triplets of objects as opposed to pairs of objects as done by standard network models. we explore approaches of how to prune these 3-way networks, illustrate their utility in comparative genomics and demonstrate how they find relationships which would be missed by standard 2-way network models using a phylogenomic dataset of 211 bacterial genomes.	2015	25815802
improved detection of extended spectrum beta-lactamase (esbl)-producing escherichia coli in input and output samples of german biogas plants by a selective pre-enrichment procedure.	the presence of extended-spectrum beta-lactamase (esbl)-producing escherichia coli was investigated in input (manure from livestock husbandry) and output samples of six german biogas plants in 2012 (one sampling per biogas plant) and two german biogas plants investigated in an annual cycle four times in 2013/2014. esbl-producing escherichia coli were cultured by direct plating on chromagar esbl from input samples in the range of 100 to 104 colony forming units (cfu) per g dry weight but not from ...	2015	25799434
thermodynamic matchers for the construction of the cuckoo rna family.	rna family models describe classes of functionally related, non-coding rnas based on sequence and structure conservation. the most important method for modeling rna families is the use of covariance models, which are stochastic models that serve in the discovery of yet unknown, homologous rnas. however, the performance of covariance models in finding remote homologs is poor for rna families with high sequence conservation, while for families with high structure but low sequence conservation, the ...	2015	25779873
antibacterial properties of silver nanoparticles synthesized by marine ochrobactrum sp.	metal nanoparticle synthesis is an interesting area in nanotechnology due to their remarkable optical, magnetic, electrical, catalytic and biomedical properties, but there needs to develop clean, non-toxic and environmental friendly methods for the synthesis and assembly of nanoparticles. biological agents in the form of microbes have emerged up as efficient candidates for nanoparticle synthesis due to their extreme versatility to synthesize diverse nanoparticles with varying size and shape. in ...	2014	25763025
antibacterial properties of silver nanoparticles synthesized by marine ochrobactrum sp.	metal nanoparticle synthesis is an interesting area in nanotechnology due to their remarkable optical, magnetic, electrical, catalytic and biomedical properties, but there needs to develop clean, non-toxic and environmental friendly methods for the synthesis and assembly of nanoparticles. biological agents in the form of microbes have emerged up as efficient candidates for nanoparticle synthesis due to their extreme versatility to synthesize diverse nanoparticles with varying size and shape. in ...	2014	25763025
higher diversity and abundance of denitrifying microorganisms in environments than considered previously.	denitrification is an important process in the global nitrogen cycle. the genes encoding nirk and nirs (nirk and nirs), which catalyze the reduction of nitrite to nitric oxide, have been used as marker genes to study the ecological behavior of denitrifiers in environments. however, conventional polymerase chain reaction (pcr) primers can only detect a limited range of the phylogenetically diverse nirk and nirs. thus, we developed new pcr primers covering the diverse nirk and nirs. clone library ...	2015	25756678
concordance and discordance of sequence survey methods for molecular epidemiology.	the post-genomic era is characterized by the direct acquisition and analysis of genomic data with many applications, including the enhancement of the understanding of microbial epidemiology and pathology. however, there are a number of molecular approaches to survey pathogen diversity, and the impact of these different approaches on parameter estimation and inference are not entirely clear. we sequenced whole genomes of bacterial pathogens, burkholderia pseudomallei, yersinia pestis, and brucell ...	2015	25737810
characterization and evaluation of an arbitrary primed polymerase chain reaction (pcr) product for the specific detection of brucella species.	laboratory detection of brucella is based largely on bacterial isolation and phenotypic characterization. these methods are lengthy and labor-intensive and have been associated with a heightened risk of laboratory-acquired infection. antibody based indirect detection methods also suffer from limitations in proper diagnosis of the organism. to overcome these problems, nucleic acid amplification has been explored for rapid detection and confirmation of the presence of brucella spp. pcr-based diagn ...	2014	25737656
characterization and evaluation of an arbitrary primed polymerase chain reaction (pcr) product for the specific detection of brucella species.	laboratory detection of brucella is based largely on bacterial isolation and phenotypic characterization. these methods are lengthy and labor-intensive and have been associated with a heightened risk of laboratory-acquired infection. antibody based indirect detection methods also suffer from limitations in proper diagnosis of the organism. to overcome these problems, nucleic acid amplification has been explored for rapid detection and confirmation of the presence of brucella spp. pcr-based diagn ...	2014	25737656
diversity of bacteria nesting the plant cover of north sinai deserts, egypt.	north sinai deserts were surveyed for the predominant plant cover and for the culturable bacteria nesting their roots and shoots. among 43 plant species reported, 13 are perennial (e.g. fagonia spp., pancratium spp.) and 30 annuals (e.g. bromus spp., erodium spp.). eleven species possessed rhizo-sheath, e.g. cyperus capitatus, panicum turgidum and trisetaria koelerioides. microbiological analyses demonstrated: the great diversity and richness of associated culturable bacteria, in particular nitr ...	2012	25685397
diversity of bacteria nesting the plant cover of north sinai deserts, egypt.	north sinai deserts were surveyed for the predominant plant cover and for the culturable bacteria nesting their roots and shoots. among 43 plant species reported, 13 are perennial (e.g. fagonia spp., pancratium spp.) and 30 annuals (e.g. bromus spp., erodium spp.). eleven species possessed rhizo-sheath, e.g. cyperus capitatus, panicum turgidum and trisetaria koelerioides. microbiological analyses demonstrated: the great diversity and richness of associated culturable bacteria, in particular nitr ...	2012	25685397
bacterial community analysis of cypermethrin enrichment cultures and bioremediation of cypermethrin contaminated soils.	cypermethrin is widely used for insect control; however, its toxicity toward aquatic life requires its complete removal from contaminated areas where the natural degradation ability of microbes can be utilized. agricultural soil with extensive history of cm application was used to prepare enrichment cultures using cypermethrin as sole carbon source for isolation of cypermethrin degrading bacteria and bacterial community analysis using pcr-dgge of 16 s rrna gene. dgge analysis revealed that domin ...	2015	25656248
the microbiome of the upper airways: focus on chronic rhinosinusitis.	upper airway diseases including allergic rhinitis, chronic rhinosinusitis with or without polyps, and cystic fibrosis are characterized by substantially different inflammatory profiles. traditionally, studies on the association of specific bacterial patterns with inflammatory profiles of diseases had been dependent on bacterial culturing. in the past 30 years, molecular biology methods have allowed bacterial culture free studies of microbial communities, revealing microbiota much more diverse th ...	2015	25624972
whole-genome sequence of chryseobacterium oranimense, a colistin-resistant bacterium isolated from a cystic fibrosis patient in france.	for the first time, we report the whole-genome sequence analysis of chryseobacterium oranimense g311, a multidrug-resistant bacterium, from a cystic fibrosis patient in france, including resistance to colistin. whole-genome sequencing of c. oranimense g311 was performed using ion torrent pgm, and rast, the embl-ebi server, and the antibiotic resistance gene-annotation (arg-annot) database were used for annotation of all genes, including antibiotic resistance (ar) genes. general features of the c ...	2015	25583710
experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.	the rate at which genome sequencing data is accruing demands enhanced methods for functional annotation and metabolism discovery. solute binding proteins (sbps) facilitate the transport of the first reactant in a metabolic pathway, thereby constraining the regions of chemical space and the chemistries that must be considered for pathway reconstruction. we describe high-throughput protein production and differential scanning fluorimetry platforms, which enabled the screening of 158 sbps against a ...	2014	25540822
experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.	the rate at which genome sequencing data is accruing demands enhanced methods for functional annotation and metabolism discovery. solute binding proteins (sbps) facilitate the transport of the first reactant in a metabolic pathway, thereby constraining the regions of chemical space and the chemistries that must be considered for pathway reconstruction. we describe high-throughput protein production and differential scanning fluorimetry platforms, which enabled the screening of 158 sbps against a ...	2014	25540822
development and assessment of multiplex high resolution melting assay as a tool for rapid single-tube identification of five brucella species.	the zoonosis brucellosis causes economically significant reproductive problems in livestock and potentially debilitating disease of humans. although the causative agent, organisms from the genus brucella, can be differentiated into a number of species based on phenotypic characteristics, there are also significant differences in genotype that are concordant with individual species. this paper describes the development of a five target multiplex assay to identify five terrestrial brucella species ...	2014	25495428
molecular modeling and computational analyses suggests that the sinorhizobium meliloti periplasmic regulator protein exor adopts a superhelical fold and is controlled by a unique mechanism of proteolysis.	the sinorhizobium meliloti periplasmic exor protein and the exos/chvi two-component system form a regulatory mechanism that directly controls the transformation of free-living to host-invading cells. in the absence of crystal structures, understanding the molecular mechanism of interaction between exor and the exos sensor, which is believed to drive the key regulatory step in the invasion process, remains a major challenge. in this study, we present a theoretical structural model of the active f ...	2014	25492513
molecular modeling and computational analyses suggests that the sinorhizobium meliloti periplasmic regulator protein exor adopts a superhelical fold and is controlled by a unique mechanism of proteolysis.	the sinorhizobium meliloti periplasmic exor protein and the exos/chvi two-component system form a regulatory mechanism that directly controls the transformation of free-living to host-invading cells. in the absence of crystal structures, understanding the molecular mechanism of interaction between exor and the exos sensor, which is believed to drive the key regulatory step in the invasion process, remains a major challenge. in this study, we present a theoretical structural model of the active f ...	2014	25492513
lessons from mother: long-term impact of antibodies in breast milk on the gut microbiota and intestinal immune system of breastfed offspring.	from birth to adulthood, the gut microbiota matures from a simple community dominated by a few major bacterial groups into a highly diverse ecosystem that provides both benefits and challenges to the host. currently there is great interest in identifying environmental and host factors that shape the development of our gut microbiota. breast milk is a rich source of maternal antibodies, which provide the first source of adaptive immunity in the newborn's intestinal tract. in this addendum, we sum ...	2014	25483336
a novel a3 group aconitase tolerates oxidation and nitric oxide.	achromobacter denitrificans yd35 is an no2 (-)-tolerant bacterium that expresses the aconitase genes acna3, acna4, and acnb, of which acna3 is essential for growth tolerance against 100 mm no2 (-). atmospheric oxygen inactivated acna3 at a rate of 1.6 × 10(-3) min(-1), which was 2.7- and 37-fold lower compared with acna4 and acnb, respectively. stoichiometric titration showed that the [4fe-4s](2+) cluster of acna3 was more stable against oxidative inactivation by ferricyanide than that of acna4. ...	2014	25477516
a novel a3 group aconitase tolerates oxidation and nitric oxide.	achromobacter denitrificans yd35 is an no2 (-)-tolerant bacterium that expresses the aconitase genes acna3, acna4, and acnb, of which acna3 is essential for growth tolerance against 100 mm no2 (-). atmospheric oxygen inactivated acna3 at a rate of 1.6 × 10(-3) min(-1), which was 2.7- and 37-fold lower compared with acna4 and acnb, respectively. stoichiometric titration showed that the [4fe-4s](2+) cluster of acna3 was more stable against oxidative inactivation by ferricyanide than that of acna4. ...	2014	25477516
the predicted abc transporter abcedcba is required for type iv secretion system expression and lysosomal evasion by brucella ovis.	brucella ovis is a major cause of reproductive failure in rams and it is one of the few well-described brucella species that is not zoonotic. previous work showed that a b. ovis mutant lacking a species-specific abc transporter (δabcba) was attenuated in mice and was unable to survive in macrophages. the aim of this study was to evaluate the role of this abc transporter during intracellular survival of b. ovis. in hela cells, b. ovis wt was able to survive and replicate at later time point (48 h ...	2014	25474545
unexpected diversity of feral genetically modified oilseed rape (brassica napus l.) despite a cultivation and import ban in switzerland.	despite cultivation and seed import bans of genetically modified (gm) oilseed rape (brassica napus l.), feral gm plants were found growing along railway lines and in port areas at four sites in switzerland in 2011 and 2012. all gm plants were identified as glyphosate-resistant gm event gt73 (roundup ready, monsanto). the most affected sites were the rhine port of basel and the st. johann freight railway station in basel. to assess the distribution and intra- and interspecific outcrossing of gm o ...	2014	25464509
erythritol feeds the pentose phosphate pathway via three new isomerases leading to d-erythrose-4-phosphate in brucella.	erythritol is an important nutrient for several α-2 proteobacteria, including n2-fixing plant endosymbionts and brucella, a worldwide pathogen that finds this four-carbon polyol in genital tissues. erythritol metabolism involves phosphorylation to l-erythritol-4-phosphate by the kinase erya and oxidation of the latter to l-3-tetrulose 4-phosphate by the dehydrogenase eryb. it is accepted that further steps involve oxidation by the putative dehydrogenase eryc and subsequent decarboxylation to yie ...	2014	25453104
characterization of exoelectrogenic bacteria enterobacter strains isolated from a microbial fuel cell exposed to copper shock load.	microorganisms capable of generating electricity in microbial fuel cells (mfcs) have gained increasing interest. here fourteen exoelectrogenic bacterial strains were isolated from the anodic biofilm in an mfc before and after copper (cu) shock load by hungate roll-tube technique with solid ferric (iii) oxide as an electron acceptor and acetate as an electron donor. phylogenetic analysis of the 16s rrna gene sequences revealed that they were all closely related to enterobacter ludwigii dsm 16688t ...	2014	25412475
a marine inducible prophage vb_cibm-p1 isolated from the aerobic anoxygenic phototrophic bacterium citromicrobium bathyomarinum jl354.	a prophage vb_cibm-p1 was induced by mitomycin c from the epipelagic strain citromicrobium bathyomarinum jl354, a member of the alpha-iv subcluster of marine aerobic anoxygenic phototrophic bacteria (aapb). the induced bacteriophage vb_cibm-p1 had myoviridae-like morphology and polyhedral heads (approximately capsid 60-100 nm) with tail fibers. the vb_cibm-p1 genome is ~38 kb in size, with 66.0% gc content. the genome contains 58 proposed open reading frames that are involved in integration, dna ...	2014	25406510
bacterial bloodstream infections and antimicrobial susceptibility pattern in pediatric hematology/oncology patients after anticancer chemotherapy.	bloodstream infections in pediatric hematology and oncology represent a major problem worldwide, but this has not been studied in qatar. in this study, we investigated the burden of infection and the resistance pattern in the bacterial etiology, in the only tertiary pediatric hematology and oncology center in qatar.	2014	25395866
kocuria rhizophila misidentified as corynebacterium jeikeium and other errors caused by the vitek ms system call for maintained microbiological competence in the era of matrix-assisted laser desorption ionization-time of flight mass spectrometry.		2014	25392349
kocuria rhizophila misidentified as corynebacterium jeikeium and other errors caused by the vitek ms system call for maintained microbiological competence in the era of matrix-assisted laser desorption ionization-time of flight mass spectrometry.		2014	25392349
evaluation of the removal of pyrene and fluoranthene by ochrobactrum anthropi, fusarium sp. and their coculture.	fluoranthene and pyrene are polycyclic aromatic hydrocarbons of high molecular weight that are recalcitrant and toxic to humans; therefore, their removal from the environment is crucial. from hydrocarbon-contaminated soil, 25 bacteria and 12 filamentous fungi capable of growth on pyrene and fluoranthene as the sole carbon and energy source were isolated. from these isolates, ochrobactrum anthropi bpyf3 and fusarium sp. fpyf1 were selected and identified because they grew quickly and abundantly i ...	2015	25369894
enterovirus-71 virus-like particles induce the activation and maturation of human monocyte-derived dendritic cells through tlr4 signaling.	enterovirus 71 (ev71) causes seasonal epidemics of hand-foot-and-mouth disease and has a high mortality rate among young children. we recently demonstrated potent induction of the humoral and cell-mediated immune response in monkeys immunized with ev71 virus-like particles (vlps), with a morphology resembling that of infectious ev71 virions but not containing a viral genome, which could potentially be safe as a vaccine for ev71. to elucidate the mechanisms through which ev71 vlps induce cell-med ...	2014	25360749
pandoraea pulmonicola chronic colonization in a cystic fibrosis patient, france.	pandoraea are considered emerging multidrug resistant pathogens in the context of cystic fibrosis. we report herein for the first time the case of a 30-year-old woman with cystic fibrosis, living in france, who was chronically infected with pandoraea pulmonicola and who died of pseudomonas aeruginosa sepsis 3 weeks after bilateral lung transplantation.	2013	25356323
biochemical characteristics, adhesion, and cytotoxicity of environmental and clinical isolates of herbaspirillum spp.	herbaspirillum bacteria are best known as plant growth-promoting rhizobacteria but have also been recovered from clinical samples. here, biochemical tests, matrix-assisted laser deionization-time of flight (maldi-tof) mass spectrometry, adherence, and cytotoxicity to eukaryotic cells were used to compare clinical and environmental isolates of herbaspirillum spp. discrete biochemical differences were observed between human and environmental strains. all strains adhered to hela cells at low densit ...	2014	25355763
biochemical characteristics, adhesion, and cytotoxicity of environmental and clinical isolates of herbaspirillum spp.	herbaspirillum bacteria are best known as plant growth-promoting rhizobacteria but have also been recovered from clinical samples. here, biochemical tests, matrix-assisted laser deionization-time of flight (maldi-tof) mass spectrometry, adherence, and cytotoxicity to eukaryotic cells were used to compare clinical and environmental isolates of herbaspirillum spp. discrete biochemical differences were observed between human and environmental strains. all strains adhered to hela cells at low densit ...	2014	25355763
lethal septic shock after dental scaling in a healthy dog due to ochrobactrum anthropi-contaminated propofol.	a 10-year-old, 6-kg male yorkshire terrier dog was scheduled for routine dental cleaning. no significant problem was observed either during anaesthesia, which was induced with propofol, or during recovery. however, 2 hours after discharge, the dog's owner returned to the clinic, complaining that the animal was lethargic and had had bloody diarrhoea. on physical examination the dog was depressed, dyspnoeic, tachycardic and hypoglycaemic. despite supportive treatment, the dog deteriorated and died ...	2015	25354910
molecular mechanism of nicotine degradation by a newly isolated strain, ochrobactrum sp. strain sjy1.	a newly isolated strain, sjy1, identified as ochrobactrum sp., utilizes nicotine as a sole source of carbon, nitrogen, and energy. strain sjy1 could efficiently degrade nicotine via a variant of the pyridine and pyrrolidine pathways (the vpp pathway), which highlights bacterial metabolic diversity in relation to nicotine degradation. a 97-kbp dna fragment containing six nicotine degradation-related genes was obtained by gap closing from the genome sequence of strain sjy1. three genes, designated ...	2014	25344232
molecular mechanism of nicotine degradation by a newly isolated strain, ochrobactrum sp. strain sjy1.	a newly isolated strain, sjy1, identified as ochrobactrum sp., utilizes nicotine as a sole source of carbon, nitrogen, and energy. strain sjy1 could efficiently degrade nicotine via a variant of the pyridine and pyrrolidine pathways (the vpp pathway), which highlights bacterial metabolic diversity in relation to nicotine degradation. a 97-kbp dna fragment containing six nicotine degradation-related genes was obtained by gap closing from the genome sequence of strain sjy1. three genes, designated ...	2014	25344232
effects of hexavalent chromium on performance and microbial community of an aerobic granular sequencing batch reactor.	the performance and microbial community of an aerobic granular sequencing batch reactor (gsbr) were investigated at different hexavalent chromium (cr(vi)) concentrations. the cod and nh4 (+)-n removal efficiencies decreased with the increase in cr(vi) concentration from 0 to 30 mg/l. the specific oxygen utilization rate (sour) decreased from 34.86 to 12.18 mg/(g mixed liquor suspended sludge (mlss)·h) with the increase in cr(vi) concentration from 0 to 30 mg/l. the specific ammonium oxidation ra ...	2015	25318421
complete genome assembly of reference strain ochrobactrum anthropi atcc 49687.	ochrobactrum anthropi is an occasional cause of nosocomial infections; however, interest in the organism lies in its phylogenetic proximity to the genus brucella. here, we present the 4.9-mb finished genome of ochrobactrum anthropi atcc 49687, most commonly used as an exclusionary reference organism.	2014	25291772
bloodstream infections in patients with hematological malignancies: which is more fatal - cancer or resistant pathogens?	the primary objective of this study was to report the incidence of bloodstream infections (bsis) and clinically or microbiologically proven bacterial or fungal bsis during neutropenic episodes in patients with hematological malignancies.	2014	25258539
ochrobactrum anthropi bacteremia in a preterm infant with cystic fibrosis.	ochrobactrum anthropi infection in newborn patients is rare, and the treatment is challenging because of its widespread and unpredictable resistance to antimicrobial agents and discrepancies between in vitro susceptibility and in vivo efficacy. we report the clinical and microbiological characteristics of ochrobactrum anthropi bacteremia in a preterm patient.	2014	25242942
the still mysterious roles of cysteine-containing glutathione transferases in plants.	glutathione transferases (gsts) represent a widespread multigenic enzyme family able to modify a broad range of molecules. these notably include secondary metabolites and exogenous substrates often referred to as xenobiotics, usually for their detoxification, subsequent transport or export. to achieve this, these enzymes can bind non-substrate ligands (ligandin function) and/or catalyze the conjugation of glutathione onto the targeted molecules, the latter activity being exhibited by gsts having ...	2014	25191271
isolation, identification and characterization of burkholderia pseudomallei from soil of coastal region of india.	melioidosis is an emerging infectious disease caused by a free living soil dwelling gram-negative bacterium burkholderia pseudomallei. the disease is endemic to most parts of southeast asia and northern australia and the organism has been isolated from moist soil and water. in india clinical cases are recently reported from the states of tamilnadu, kerala, karnataka, maharashtra, orissa, assam, west bengal, pondicherry and tripura. this study is aimed to confirm the prevalence of this important ...	2014	25187882
colonization by endophytic ochrobactrum anthropi mn1 promotes growth of jerusalem artichoke.	the ochrobactrum anthropi mn1 strain, taxonomically identified using 16s ribosomal dna sequence, was isolated from roots of jerusalem artichoke. its endophytic colonization was investigated microscopically using green fluorescent protein introduced by vector phc60. the strain entered jerusalem artichoke tissues through the root, and was localized in the roots and stems. the plant growth-promoting (pgp) effects of o. anthropi mn1 were assessed in greenhouse as well as field trials with different ...	2014	25073416
response mechanisms of bacterial degraders to environmental contaminants on the level of cell walls and cytoplasmic membrane.	bacterial strains living in the environment must cope with the toxic compounds originating from humans production. surface bacterial structures, cell wall and cytoplasmic membrane, surround each bacterial cell and create selective barriers between the cell interior and the outside world. they are a first site of contact between the cell and toxic compounds. organic pollutants are able to penetrate into cytoplasmic membrane and affect membrane physiological functions. bacteria had to evolve adapt ...	2014	25057269
a novel function of controlled-release nitrogen fertilizers.		2014	25047661
culturable aerobic and facultative anaerobic intestinal bacterial flora of black cobra (naja naja karachiensis) in southern pakistan.	using morphological analysis and biochemical testing, here for the first time, we determined the culturable gut bacterial flora (aerobes and facultative anaerobes) in the venomous black cobra (naja naja karachiensis) from south asia. the findings revealed that these snakes inhabit potentially pathogenic bacteria including serratia marcescens, pseudomonas aeruginosa, shewanella putrefaciens, aeromonas hydrophila, salmonella sp., moraxella sp., bacillus sp., ochrobactrum anthropi, and providencia ...	2014	25002979
anatomical localization of commensal bacteria in immune cell homeostasis and disease.	the mammalian gastrointestinal (gi) tract is colonized by trillions of beneficial commensal bacteria that are essential for promoting normal intestinal physiology. while the majority of commensal bacteria are found in the intestinal lumen, many species have also adapted to colonize different anatomical locations in the intestine, including the surface of intestinal epithelial cells (iecs) and the interior of gut-associated lymphoid tissues. these distinct tissue localization patterns permit uniq ...	2014	24942680
immune response varies with rate of dispersal in invasive cane toads (rhinella marina).	what level of immunocompetence should an animal maintain while undertaking long-distance dispersal? immune function (surveillance and response) might be down-regulated during prolonged physical exertion due to energy depletion, and/or to avoid autoimmune reactions arising from damaged tissue. on the other hand, heightened immune vigilance might be favored if the organism encounters novel pathogens as it enters novel environments. we assessed the links between immune defense and long-distance mov ...	2014	24936876
brucella abortus depends on pyruvate phosphate dikinase and malic enzyme but not on fbp and glpx fructose-1,6-bisphosphatases for full virulence in laboratory models.	the brucellae are the etiological agents of brucellosis, a worldwide-distributed zoonosis. these bacteria are facultative intracellular parasites and thus are able to adjust their metabolism to the extra- and intracellular environments encountered during an infectious cycle. however, this aspect of brucella biology is imperfectly understood, and the nutrients available in the intracellular niche are unknown. here, we investigated the central pathways of c metabolism used by brucella abortus by d ...	2014	24936050
outbreaks of infections associated with drug diversion by us health care personnel.	to summarize available information about outbreaks of infections stemming from drug diversion in us health care settings and describe recommended protocols and public health actions.	2014	24933292
16s rrna gene phylogeny and tfda gene analysis of 2,4-d-degrading bacteria isolated in china.	twenty-two 2,4-dichlorophenoxyacetic acid (2,4-d)-degrading bacterial isolates were collected from agricultural soils at three sites in china. sequence analysis of the 16s rrna genes indicated that the isolates were phylogenetically grouped into four categories: ochrobactrum anthropi, in the alpha- class of the phylum proteobacteria (3 out of 22 isolates), cupriavidus sp., of the betaproteobacteria (3 out of 22), pseudomonas sp. and stenotrophomonas sp., which are gammaproteobacteria (7 out of 2 ...	2014	24898178
cooperativity among secretory iga, the polymeric immunoglobulin receptor, and the gut microbiota promotes host-microbial mutualism.	secretory iga (siga) antibodies in the intestinal tract form the first line of antigen-specific immune defense, preventing access of pathogens as well as commensal microbes to the body proper. siga is transported into external secretions by the polymeric immunoglobulin receptor (pigr). evidence is reported here that the gut microbiota regulates production of siga and pigr, which act together to regulate the composition and activity of the microbiota. siga in the intestinal mucus layer helps to m ...	2014	24877874
16s ribosomal dna sequence-based identification of bacteria in laboratory rodents: a practical approach in laboratory animal bacteriology diagnostics.	correct identification of bacteria is crucial for the management of rodent colonies. some bacteria are difficult to identify phenotypically outside reference laboratories. in this study, we evaluated the utility of 16s ribosomal dna (rdna) sequencing as a means of identifying a collection of 30 isolates of rodent origin which are conventionally difficult to identify. sequence analysis of the first approximate 720 to 880 bp of the 5'- end of 16s rdna identified 25 isolates (83.33%) with ≥ 99% sim ...	2014	24876090
the effect of spent bleaching earth ageing process on its physicochemical and microbial composition and its potential use as a source of fatty acids and triterpenes.	this study was aimed at investigating the physicochemical and microbiological changes that took place during the ageing process of spent bleaching earth in the presence of autochthonous microorganisms. research material included fresh spent bleaching earth (sbe0) and the same material after 3 years of storage at the constant temperature of 20 °c, without aeration and moistening (sbe3). changes in the chemical composition of analysed waste material were observed during its ageing process point to ...	2014	24875308
late-onset ochrobactrum anthropi sepsis in a preterm neonate with congenital urinary tract abnormalities.	recent trends in late-onset neonatal sepsis have revealed an increase in gram-negative organisms as causative agents. ochrobactrum anthropi is an emerging human pathogen that has been reported primarily in immunocompromised hosts, especially those with indwelling catheters or other medical devices. we report the occurrence of late-onset urosepsis secondary to o. anthropi in a preterm neonate with posterior urethral valves and review the salient features of the pathogen and its management.	2014	24872126
mechanisms and regulation of surface interactions and biofilm formation in agrobacterium.	for many pathogenic bacteria surface attachment is a required first step during host interactions. attachment can proceed to invasion of host tissue or cells or to establishment of a multicellular bacterial community known as a biofilm. the transition from a unicellular, often motile, state to a sessile, multicellular, biofilm-associated state is one of the most important developmental decisions for bacteria. agrobacterium tumefaciens genetically transforms plant cells by transfer and integratio ...	2014	24834068
the value of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in identifying clinically relevant bacteria: a comparison with automated microbiology system.	matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms) has been developed as a new-type soft ionization mass spectrometry in the recent year. increasing number of clinical microbiological laboratories consider it as an innovate approach for bacterial identification.	2014	24822117
the more, the merrier: heterotroph richness stimulates methanotrophic activity.	although microorganisms coexist in the same environment, it is still unclear how their interaction regulates ecosystem functioning. using a methanotroph as a model microorganism, we determined how methane oxidation responds to heterotroph diversity. artificial communities comprising of a methanotroph and increasing heterotroph richness, while holding equal starting cell numbers were assembled. we considered methane oxidation rate as a functional response variable. our results showed a significan ...	2014	24785289
composition and diversity analysis of the gut bacterial community of the oriental armyworm, mythimna separata, determined by culture-independent and culture-dependent techniques.	the intestinal bacteria community structure and diversity of the oriental armyworm, mythimna separata (walker) (lepidoptera: noctuidae), was studied by analysis of a 16s rdna clone library, denaturing gradient gel electrophoresis,and culture-dependent techniques. the 16s rdna clone library revealed a bacterial community diversity comprising cyanobacteria, firmicutes, actinobacteria, gracilicutes and proteobacteria, among which escherichia coli (migula) (enterobacteriales: enterobacteriaceae) was ...	2013	24773514
pediatric multicenter evaluation of the verigene gram-negative blood culture test for rapid detection of inpatient bacteremia involving gram-negative organisms, extended-spectrum beta-lactamases, and carbapenemases.	we evaluated the investigational use only (iuo) version of the rapid verigene gram-negative blood culture test (bc-gn), a microarray that detects 9 genus/species targets (acinetobacter spp., citrobacter spp., enterobacter spp., escherichia coli/shigella spp., klebsiella oxytoca, klebsiella pneumoniae, proteus spp., pseudomonas aeruginosa, and serratia marcescens) and 6 antimicrobial resistance determinants (blactx-m, blakpc, blandm, blavim, blaimp, and blaoxa) directly from positive blood cultur ...	2014	24759724
diagnostic yield of bronchial washing fluid analysis for hemoptysis in patients with bronchiectasis.	bronchiectasis is the main cause of hemoptysis. when patients with bronchiectasis develop hemoptysis, clinicians often perform bronchoscopy and bronchial washing to obtain samples for microbiological and cytological examinations. bronchial washing fluids were analyzed from patients with bronchiectasis who developed hemoptysis, and the clinical impacts of these analyses were examined.	2014	24719142
influenza viral vectors expressing the brucella omp16 or l7/l12 proteins as vaccines against b. abortus infection.	we generated novel, effective candidate vaccine against brucella abortus based on recombinant influenza viruses expressing the brucella ribosomal protein l7/l12 or outer membrane protein (omp)-16 from the ns1 open reading frame. the main purpose of this work was to evaluate the safety, immunogenicity and protectiveness of vaccine candidate in laboratory animals.	2014	24716528
annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms.	the functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. the molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden markov models of structural recognition. here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. we find ...	2011	24710297
regen: ancestral genome reconstruction for bacteria.	ancestral genome reconstruction can be understood as a phylogenetic study with more details than a traditional phylogenetic tree reconstruction. we present a new computational system called regen for ancestral bacterial genome reconstruction at both the gene and replicon levels. regen reconstructs gene content, contiguous gene runs, and replicon structure for each ancestral genome. along each branch of the phylogenetic tree, regen infers evolutionary events, including gene creation and deletion ...	2012	24704978
from environment to man: genome evolution and adaptation of human opportunistic bacterial pathogens.	environment is recognized as a huge reservoir for bacterial species and a source of human pathogens. some environmental bacteria have an extraordinary range of activities that include promotion of plant growth or disease, breakdown of pollutants, production of original biomolecules, but also multidrug resistance and human pathogenicity. the versatility of bacterial life-style involves adaptation to various niches. adaptation to both open environment and human specific niches is a major challenge ...	2012	24704914
precipitation of phosphate minerals by microorganisms isolated from a fixed-biofilm reactor used for the treatment of domestic wastewater.	the ability of bacteria isolated from a fixed-film bioreactor to precipitate phosphate crystals for the treatment of domestic wastewater in both artificial and natural media was studied. when this was demonstrated in artificial solid media for crystal formation, precipitation took place rapidly, and crystal formation began 3 days after inoculation. the percentage of phosphate-forming bacteria was slightly higher than 75%. twelve major colonies with phosphate precipitation capacity were the domin ...	2014	24699031
physical, chemical, and biological methods for the removal of arsenic compounds.	arsenic is a toxic metalloid which is widely distributed in nature. it is normally present as arsenate under oxic conditions while arsenite is predominant under reducing condition. the major discharges of arsenic in the environment are mainly due to natural sources such as aquifers and anthropogenic sources. it is known that arsenite salts are more toxic than arsenate as it binds with vicinal thiols in pyruvate dehydrogenase while arsenate inhibits the oxidative phosphorylation process. the comm ...	2014	24696853
typing of ochrobactrum anthropi clinical isolates using automated repetitive extragenic palindromic-polymerase chain reaction dna fingerprinting and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry.	ochrobactrum anthropi (o. anthropi), is a non-fermenting gram-negative bacillus usually found in the environment. nevertheless, during the past decade it has been identified as pathogenic to immunocompromised patients. in this study, we assessed the usefulness of the automated repetitive extragenic palindromic-polymerase chain reaction (rep-pcr-based diversilab™ system, biomèrieux, france) and of matrix-assisted laser desorption/ionization-time-of-flight (maldi-tof ms) for typing of twentythree ...	2014	24655432
microbial metabolism and community structure in response to bioelectrochemically enhanced remediation of petroleum hydrocarbon-contaminated soil.	this study demonstrates that electrodes in a bioelectrochemical system (bes) can potentially serve as a nonexhaustible electron acceptor for in situ bioremediation of hydrocarbon contaminated soil. the deployment of bes not only eliminates aeration or supplement of electron acceptors as in contemporary bioremediation but also significantly shortens the remediation period and produces sustainable electricity. more interestingly, the study reveals that microbial metabolism and community structure ...	2014	24628095
utilization of glyphosate as phosphate source: biochemistry and genetics of bacterial carbon-phosphorus lyase.	after several decades of use of glyphosate, the active ingredient in weed killers such as roundup, in fields, forests, and gardens, the biochemical pathway of transformation of glyphosate phosphorus to a useful phosphorus source for microorganisms has been disclosed. glyphosate is a member of a large group of chemicals, phosphonic acids or phosphonates, which are characterized by a carbon-phosphorus bond. this is in contrast to the general phosphorus compounds utilized and metabolized by microor ...	2014	24600043
semiquantitative analysis of clinical heat stress in clostridium difficile strain 630 using a gelc/ms workflow with empai quantitation.	clostridium difficile is considered to be the most frequent cause of infectious bacterial diarrhoea in hospitals worldwide yet its adaptive ability remains relatively uncharacterised. here, we used gelc/ms and the exponentially modified protein abundance index (empai) calculation to determine proteomic changes in response to a clinically relevant heat stress. reproducibility between both biological and technical replicates was good, and a 37°c proteome of 224 proteins was complemented by a 41°c ...	2014	24586458
secretory antibodies in breast milk promote long-term intestinal homeostasis by regulating the gut microbiota and host gene expression.	maintenance of intestinal homeostasis requires a healthy relationship between the commensal gut microbiota and the host immune system. breast milk supplies the first source of antigen-specific immune protection in the gastrointestinal tract of suckling mammals, in the form of secretory iga (siga). siga is transported across glandular and mucosal epithelial cells into external secretions by the polymeric ig receptor (pigr). here, a breeding scheme with polymeric ig receptor-sufficient and -defici ...	2014	24569806
brain empyema due to ochrobactrum anthropi.		2014	24534092
catheter-associated bacteremia caused by ochrobactrum anthropi in a patient on parenteral nutrition.		2014	24533972
specific microbial attachment to root knot nematodes in suppressive soil.	understanding the interactions of plant-parasitic nematodes with antagonistic soil microbes could provide opportunities for novel crop protection strategies. three arable soils were investigated for their suppressiveness against the root knot nematode meloidogyne hapla. for all three soils, m. hapla developed significantly fewer galls, egg masses, and eggs on tomato plants in unsterilized than in sterilized infested soil. egg numbers were reduced by up to 93%. this suggested suppression by soil ...	2014	24532076
ochrobactrum anthropi septic arthritis: case report and implications in orthopedic infections.	ochrobactrum anthropi is a rare cause of orthopedic infections. we report the second case of ochrobactrum anthropi septic arthritis in the literature. our case highlights the ability of ochrobactrum anthropi to cause septic arthritis and its relevance in the field of orthopedic infections.	2010	24470885
niches, population structure and genome reduction in ochrobactrum intermedium: clues to technology-driven emergence of pathogens.	ochrobactrum intermedium is considered as an emerging human environmental opportunistic pathogen with mild virulence. the distribution of isolates and sequences described in literature and databases showed frequent association with human beings and polluted environments. as population structures are related to bacterial lifestyles, we investigated by multi-locus approach the genetic structure of a population of 65 isolates representative of the known natural distribution of o. intermedium. the p ...	2014	24465379
correction of sequence-dependent ambiguous bases (ns) from the 454 pyrosequencing system.	pyrosequencing of the 16s ribosomal rna gene (16s) has become one of the most popular methods to assess microbial diversity. pyrosequencing reads containing ambiguous bases (ns) are generally discarded based on the assumptions of their non-sequence-dependent formation and high error rates. however, taxonomic composition differed by removal of reads with ns. we determined whether ns from pyrosequencing occur in a sequence-dependent manner. our reads and the corresponding flow value data revealed ...	2014	24464999
sloth hair as a novel source of fungi with potent anti-parasitic, anti-cancer and anti-bacterial bioactivity.	the extraordinary biological diversity of tropical forests harbors a rich chemical diversity with enormous potential as a source of novel bioactive compounds. of particular interest are new environments for microbial discovery. sloths--arboreal mammals commonly found in the lowland forests of panama--carry a wide variety of micro- and macro-organisms on their coarse outer hair. here we report for the first time the isolation of diverse and bioactive strains of fungi from sloth hair, and their ta ...	2014	24454729
achromobacter denitrificans strain yd35 pyruvate dehydrogenase controls nadh production to allow tolerance to extremely high nitrite levels.	we identified the extremely nitrite-tolerant bacterium achromobacter denitrificans yd35 that can grow in complex medium containing 100 mm nitrite (no2(-)) under aerobic conditions. nitrite induced global proteomic changes and upregulated tricarboxylate (tca) cycle enzymes as well as antioxidant proteins in yd35. transposon mutagenesis generated no2(-)-hypersensitive mutants of yd35 that had mutations at genes for aconitate hydratase and α-ketoglutarate dehydrogenase in the tca cycle and a pyruva ...	2014	24413603
microbial degradation of acetamiprid by ochrobactrum sp. d-12 isolated from contaminated soil.	neonicotinoid insecticides are one of the most important commercial insecticides used worldwide. the potential toxicity of the residues present in environment to humans has received considerable attention. in this study, a novel ochrobactrum sp. strain d-12 capable of using acetamiprid as the sole carbon source as well as energy, nitrogen source for growth was isolated and identified from polluted agricultural soil. strain d-12 was able to completely degrade acetamiprid with initial concentratio ...	2013	24386105
comparative clinical study of different multiplex real time pcr strategies for the simultaneous differential diagnosis between extrapulmonary tuberculosis and focal complications of brucellosis.	both brucellosis and tuberculosis are chronic-debilitating systemic granulomatous diseases with a high incidence in many countries in africa, central and south america, the middle east and the indian subcontinent. certain focal complications of brucellosis and extrapulmonary tuberculosis are very difficult to differentiate clinically, biologically and radiologically. as the conventional microbiological methods for the diagnosis of the two diseases have many limitations, as well as being time-con ...	2013	24349599
quorum sensing and self-quorum quenching in the intracellular pathogen brucellamelitensis.	brucella quorum sensing has been described as an important regulatory system controlling crucial virulence determinants such as the virb type iv secretion system and the flagellar genes. however, the basis of quorum sensing, namely the production of autoinducers in brucella has been questioned. here, we report data obtained from the use of a genetic tool allowing the in situ detection of long-chain n-acyl-homoserine lactones (ahl) activity at single bacterium level in brucella melitensis. these ...	2013	24349302
comparative phylogenomics and evolution of the brucellae reveal a path to virulence.	brucella species include important zoonotic pathogens that have a substantial impact on both agriculture and human health throughout the world. brucellae are thought of as "stealth pathogens" that escape recognition by the host innate immune response, modulate the acquired immune response, and evade intracellular destruction. we analyzed the genome sequences of members of the family brucellaceae to assess its evolutionary history from likely free-living soil-based progenitors into highly success ...	2014	24336939
a review of 11 years of stenotrophomonas maltophilia blood isolates at a tertiary care institute in canada.	stenotrophomonas maltophilia has emerged as a significant nosocomial pathogen with increasing resistance to trimethoprim/sulphamethoxazole (tmp/smx), the current drug of choice for treatment.	2012	24294268
the outcome of non-carbapenem-based empirical antibacterial therapy and vre colonisation in patients with hematological malignancies.	febrile neutropenia (fn) is generally a complication of cancer chemotherapy.	2013	24235937
improving glyphosate oxidation activity of glycine oxidase from bacillus cereus by directed evolution.	glyphosate, a broad spectrum herbicide widely used in agriculture all over the world, inhibits 5-enolpyruvylshikimate-3-phosphate synthase in the shikimate pathway, and glycine oxidase (go) has been reported to be able to catalyze the oxidative deamination of various amines and cleave the c-n bond in glyphosate. here, in an effort to improve the catalytic activity of the glycine oxidase that was cloned from a glyphosate-degrading marine strain of bacillus cereus (bcego), we used a bacteriophage ...	2013	24223901
merops: the database of proteolytic enzymes, their substrates and inhibitors.	peptidases, their substrates and inhibitors are of great relevance to biology, medicine and biotechnology. the merops database (http://merops.sanger.ac.uk) aims to fulfill the need for an integrated source of information about these. the database has hierarchical classifications in which homologous sets of peptidases and protein inhibitors are grouped into protein species, which are grouped into families, which are in turn grouped into clans. recent developments include the following. a communit ...	2013	24157837
merops: the database of proteolytic enzymes, their substrates and inhibitors.	peptidases, their substrates and inhibitors are of great relevance to biology, medicine and biotechnology. the merops database (http://merops.sanger.ac.uk) aims to fulfill the need for an integrated source of information about these. the database has hierarchical classifications in which homologous sets of peptidases and protein inhibitors are grouped into protein species, which are grouped into families, which are in turn grouped into clans. recent developments include the following. a communit ...	2013	24157837
molecular cloning and characterization of a newly isolated pyrethroid-degrading esterase gene from a genomic library of ochrobactrum anthropi yz-1.	a novel pyrethroid-degrading esterase gene pyty was isolated from the genomic library of ochrobactrum anthropi yz-1. it possesses an open reading frame (orf) of 897 bp. blast search showed that its deduced amino acid sequence shares moderate identities (30% to 46%) with most homologous esterases. phylogenetic analysis revealed that pyty is a member of the esterase vi family. pyty showed very low sequence similarity compared with reported pyrethroid-degrading genes. pyty was expressed, purified, ...	2013	24155944
ochrobactrum anthropi septicemia and pneumonia in a preterm, small for gestational age infant with multiple congenital anomalies.		2013	24152523
brucella melitensis t cell epitope recognition in humans with brucellosis in peru.	brucella melitensis, one of the causative agents of human brucellosis, causes acute, chronic, and relapsing infection. while t cell immunity in brucellosis has been extensively studied in mice, no recognized human t cell epitopes that might provide new approaches to classifying and prognosticating b. melitensis infection have ever been delineated. twenty-seven pools of 500 major histocompatibility complex class ii (mhc-ii) restricted peptides were created by computational prediction of promiscuo ...	2014	24126518
molecular diagnosis of actinomadura madurae infection by 16s rrna deep sequencing.	next-generation dna sequencing can be used to catalog individual organisms within complex, polymicrobial specimens. here, we utilized deep sequencing of 16s rrna to implicate actinomadura madurae as the cause of mycetoma in a diabetic patient when culture and conventional molecular methods were overwhelmed by overgrowth of other organisms.	2013	24108607
central line maintenance bundles and clabsis in ambulatory oncology patients.	pediatric oncology patients are frequently managed with central lines as outpatients, and these lines confer significant morbidity in this immune-compromised population. we aimed to investigate whether a multidisciplinary, central line maintenance care bundle reduces central line-associated bloodstream infections (clabsis) and bacteremias in ambulatory pediatric oncology patients.	2013	24101764
monooxygenase, a novel beta-cypermethrin degrading enzyme from streptomyces sp.	the widely used insecticide beta-cypermethrin has become a public concern because of its environmental contamination and toxic effects on mammals. in this study, a novel beta-cypermethrin degrading enzyme designated as cmo was purified to apparent homogeneity from a streptomyces sp. isolate capable of utilizing beta-cypermethrin as a growth substrate. the native enzyme showed a monomeric structure with a molecular mass of 41 kda and pi of 5.4. the enzyme exhibited the maximal activity at ph 7.5 ...	2013	24098697