Publications

crispr-cas systems: new players in gene regulation and bacterial physiology.	crispr-cas systems are bacterial defenses against foreign nucleic acids derived from bacteriophages, plasmids or other sources. these systems are targeted in an rna-dependent, sequence-specific manner, and are also adaptive, providing protection against previously encountered foreign elements. in addition to their canonical function in defense against foreign nucleic acid, their roles in various aspects of bacterial physiology are now being uncovered. we recently revealed a role for a cas9-based ...	2014	24772391
the reduced genome of the francisella tularensis live vaccine strain (lvs) encodes two iron acquisition systems essential for optimal growth and virulence.	bacterial pathogens require multiple iron-specific acquisition systems for survival within the iron-limiting environment of the host. francisella tularensis is a virulent intracellular pathogen that can replicate in multiple cell-types. to study the interrelationship of iron acquisition capability and virulence potential of this organism, we generated single and double deletion mutants within the ferrous iron (feo) and ferric-siderophore (fsl) uptake systems of the live vaccine strain (lvs). the ...	2014	24695402
prevalence of yersinia species in traditional and commercial dairy products in isfahan province, iran.	yersinia species, especially yersinia enterocolitica, are considered as the most prevalent milk-borne pathogens. several serological and molecular techniques have been developed for rapid and safe diagnosis of yersiniosis.	2014	25147698
a retrospective analysis of acute gastroenteritis agents in children admitted to a university hospital pediatric emergency unit.	acute gastroenteritis is responsible observed in all age groups, especially infants and children. the etiology and clinical course of acute gastroenteritis may vary with age and etiological agents. in developing countries, the morbidity and mortality associated with infectious diarrhea is higher in children younger than five-years-of-age.	2014	25147694
seasonal and monthly trends in the occurrence of guillain-barre syndrome over a 5-year period: a tertiary care hospital-based study from south india.		2014	25024587
sialic acids in the brain: gangliosides and polysialic acid in nervous system development, stability, disease, and regeneration.	every cell in nature carries a rich surface coat of glycans, its glycocalyx, which constitutes the cell's interface with its environment. in eukaryotes, the glycocalyx is composed of glycolipids, glycoproteins, and proteoglycans, the compositions of which vary among different tissues and cell types. many of the linear and branched glycans on cell surface glycoproteins and glycolipids of vertebrates are terminated with sialic acids, nine-carbon sugars with a carboxylic acid, a glycerol side-chain ...	2014	24692354
oxidative stress: an essential factor in the pathogenesis of gastrointestinal mucosal diseases.	reactive oxygen species (ros) are generated as by-products of normal cellular metabolic activities. superoxide dismutase, glutathione peroxidase, and catalase are the enzymes involved in protecting cells from the damaging effects of ros. ros are produced in response to ultraviolet radiation, cigarette smoking, alcohol, nonsteroidal anti-inflammatory drugs, ischemia-reperfusion injury, chronic infections, and inflammatory disorders. disruption of normal cellular homeostasis by redox signaling may ...	2014	24692350
prevalence of shigella, salmonella and campylobacter species and their susceptibility patters among under five children with diarrhea in hawassa town, south ethiopia.	diarrhea is the leading cause of morbidity and mortality in under-five children in developing countries including ethiopia. therefore, up-to-date data on etiologic agent and susceptibility pattern are important for the management of bacterial diarrhea in under-five children, which was the main objective of this study.	2014	24795510
bacterial mechanosensitive channels: progress towards an understanding of their roles in cell physiology.	bacterial mechanosensitive channels sense the changes in lateral tension in the bilayer of the cytoplasmic membrane generated by rapid water flow into the cell. two major structural families are found widely distributed across bacteria and archaea: mscl and mscs. our understanding of the mechanisms of gating has advanced rapidly through genetic analysis, structural biology and electrophysiology. it is only recently that the analysis of the physiological roles of the channels has kept pace with m ...	2014	24607989
simultaneous detection of five enteric viruses associated with gastroenteritis by use of a pcr assay: a single real-time multiplex reaction and its clinical application.	we developed a highly sensitive reverse transcription and multiplex real-time pcr (rtpcr) assay that can identify five viruses, including six genogroups, in a single reaction: norovirus genogroups i and ii; sapovirus genogroups i, ii, iv, and v; human rotavirus a; adenovirus serotypes 40 and 41; and human astrovirus. in comparison to monoplex rtpcr assays, the sensitivities and specificities of the multiplex rtpcr ranged from 75% to 100% and from 99% to 100%, respectively, evaluated on 812 clini ...	2014	24478418
incorporation of phosphorylcholine into the lipooligosaccharide of nontypeable haemophilus influenzae does not correlate with the level of biofilm formation in vitro.	nontypeable haemophilus influenzae (nthi) is an opportunistic pathogen that causes otitis media in children and community-acquired pneumonia or exacerbations of chronic obstructive pulmonary disease in adults. a large variety of studies suggest that biofilm formation by nthi may be an important step in the pathogenesis of this bacterium. the objective of this report was to determine the relationship between the presence of phosphorylcholine in the lipooligosaccharide of nthi and the level of bio ...	2014	24452688
natural competence and the evolution of dna uptake specificity.	many bacteria are naturally competent, able to actively transport environmental dna fragments across their cell envelope and into their cytoplasm. because incoming dna fragments can recombine with and replace homologous segments of the chromosome, competence provides cells with a potent mechanism of horizontal gene transfer as well as access to the nutrients in extracellular dna. this review starts with an introductory overview of competence and continues with a detailed consideration of the dna ...	2014	24488316
a new subfamily of polyphosphate kinase 2 (class iii ppk2) catalyzes both nucleoside monophosphate phosphorylation and nucleoside diphosphate phosphorylation.	inorganic polyphosphate (polyp) is a linear polymer of tens to hundreds of phosphate (pi) residues linked by "high-energy" phosphoanhydride bonds as in atp. polyp kinases, responsible for the synthesis and utilization of polyp, are divided into two families (ppk1 and ppk2) due to differences in amino acid sequence and kinetic properties. ppk2 catalyzes preferentially polyp-driven nucleotide phosphorylation (utilization of polyp), which is important for the survival of microbial cells under condi ...	2014	24532069
refined nrfa phylogeny improves pcr-based nrfa gene detection.	dissimilatory nitrate reduction to ammonium (dnra) and denitrification are contrasting microbial processes in the terrestrial nitrogen (n) cycle, in that the former promotes n retention and the latter leads to n loss (i.e., the formation of gaseous products). the nitrite reductase nrfa catalyzes nitrite reduction to ammonium, the enzyme associated with respiratory nitrite ammonification and the key step in dnra. although well studied biochemically, the diversity and phylogeny of this enzyme had ...	2014	24463965
anti-infective activities of lactobacillus strains in the human intestinal microbiota: from probiotics to gastrointestinal anti-infectious biotherapeutic agents.	a vast and diverse array of microbial species displaying great phylogenic, genomic, and metabolic diversity have colonized the gastrointestinal tract. resident microbes play a beneficial role by regulating the intestinal immune system, stimulating the maturation of host tissues, and playing a variety of roles in nutrition and in host resistance to gastric and enteric bacterial pathogens. the mechanisms by which the resident microbial species combat gastrointestinal pathogens are complex and incl ...	2014	24696432
unnatural amino acid incorporation in e. coli: current and future applications in the design of therapeutic proteins.	unnatural amino acid (uaa) incorporation by amber codon suppression offers scientists a powerful tool to modify the properties of proteins at will. uaa incorporation has been used for a plethora of fundamental research applications and, more recently, also for the selective modification of therapeutic proteins. in this review most recent developments in escherichia coli codon expansion and, unnatural amino acid incorporation are discussed together with some remarkable recent developments in impr ...	2014	24790983
mnsod in oxidative stress response-potential regulation via mitochondrial protein influx.	the mitochondrial antioxidant manganese superoxide dismutase (mnsod) is encoded by genomic dna and its dismutase function is fully activated in the mitochondria to detoxify free radical o2(•-) generated by mitochondrial respiration. accumulating evidence shows an extensive communication between the mitochondria and cytoplasm under oxidative stress. not only is the mnsod gene upregulated by oxidative stress, but mnsod activity can be enhanced via the mitochondrial protein influx (mpi).	2014	23581847
idiopathic non cirrhotic portal hypertension and spleno-portal axis abnormalities in patients with severe primary antibody deficiencies.	portal hypertension has been reported in association with acquired and primary immune deficiencies without a comprehensive description of associated spleno-portal axis abnormalities. pathological mechanisms are poorly defined.	2014	24741616
the science behind the probiotic strain bifidobacterium animalis subsp. lactis bb-12(®).	this review presents selected data on the probiotic strain bifidobacterium animalis subsp. lactis bb-12(®) (bb-12(®)), which is the world's most documented probiotic bifidobacterium. it is described in more than 300 scientific publications out of which more than 130 are publications of human clinical studies. the complete genome sequence of bb-12(®) has been determined and published. bb-12(®) originates from chr. hansen's collection of dairy cultures and has high stability in foods and as freeze ...	2014	27682233
tssar: tss annotation regime for drna-seq data.	differential rna sequencing (drna-seq) is a high-throughput screening technique designed to examine the architecture of bacterial operons in general and the precise position of transcription start sites (tss) in particular. hitherto, drna-seq data were analyzed by visualizing the sequencing reads mapped to the reference genome and manually annotating reliable positions. this is very labor intensive and, due to the subjectivity, biased.	2014	24674136
a qpcr assay to detect and quantify shiga toxin-producing e. coli (stec) in cattle and on farms: a potential predictive tool for stec culture-positive farms.	shiga toxin-producing e. coli (stec), of various serogroups harboring the intimin gene, form a serious threat to human health. they are asymptomatically carried by cattle. in this study, a quantitative real-time pcr (qpcr) method was developed as a molecular method to detect and quantify shiga toxin genes stx1 and stx2 and the intimin gene eae. subsequently, 59 fecal samples from six farms were tested using qpcr and a culture method as a reference. three farms had contaminated animals as demonst ...	2014	24681714
enteroaggregative coli: a pathogen bridging the north and south.	enteroaggregative escherichia coli (eaec) is a heterogeneous emerging enteric pathogen. identified during the 1980's when eaec strains where isolated from cases of acute and persistent diarrhea among infants from developing countries and of traveler's diarrhea. subsequently, eaec strains were linked with foodborne outbreaks and diarrhea illness in adults and children from industrialized countries, hiv-infected subjects and stunting of malnourished poor children. nowadays, eaec is increasingly re ...	2014	24892007
mechanisms of post-transcriptional gene regulation in bacterial biofilms.	biofilms are characterized by a dense multicellular community of microorganisms that can be formed by the attachment of bacteria to an inert surface and to each other. the development of biofilm involves the initial attachment of planktonic bacteria to a surface, followed by replication, cell-to-cell adhesion to form microcolonies, maturation, and detachment. mature biofilms are embedded in a self-produced extracellular polymeric matrix composed primarily of bacterial-derived exopolysaccharides, ...	2014	24724055
chemotactic chemokines are important in the pathogenesis of irritable bowel syndrome.	irritable bowel syndrome (ibs) is one of the most frequently diagnosed disorders, affecting about 20% of the general population in western countries. this syndrome poses an enormous socio-economic burden, impairs the quality of life substantially, and increases healthcare costs. ibs can be classified as either idiopathic (id-ibs) with unknown etiology or post-infectious (pi-ibs), which develops after a bout of acute diarrhea or gastroenteritis. little is known about the immunopathogenesis of the ...	2014	24667736
shiga toxin production and translocation during microaerobic human colonic infection with shiga toxin-producing e. coli o157:h7 and o104:h4.	haemolytic uraemic syndrome caused by shiga toxin-producing e. coli (stec) is dependent on release of shiga toxins (stxs) during intestinal infection and subsequent absorption into the bloodstream. an understanding of stx-related events in the human gut is limited due to lack of suitable experimental models. in this study, we have used a vertical diffusion chamber system with polarized human colon carcinoma cells to simulate the microaerobic (ma) environment in the human intestine and investigat ...	2014	24612002
extensive microbial and functional diversity within the chicken cecal microbiome.	chickens are major source of food and protein worldwide. feed conversion and the health of chickens relies on the largely unexplored complex microbial community that inhabits the chicken gut, including the ceca. we have carried out deep microbial community profiling of the microbiota in twenty cecal samples via 16s rrna gene sequences and an in-depth metagenomics analysis of a single cecal microbiota. we recovered 699 phylotypes, over half of which appear to represent previously unknown species. ...	2014	24657972
the arable ecosystem as battleground for emergence of new human pathogens.	disease incidences related to escherichia coli and salmonella enterica infections by consumption of (fresh) vegetables, sprouts, and occasionally fruits made clear that these pathogens are not only transmitted to humans via the "classical" routes of meat, eggs, and dairy products, but also can be transmitted to humans via plants or products derived from plants. nowadays, it is of major concern that these human pathogens, especially the ones belonging to the taxonomical family of enterobacteriace ...	2014	24688484
the role of autophagy in the intracellular survival of campylobacter concisus.	campylobacter concisus is an emerging pathogen that has been associated with gastrointestinal diseases. given the importance of autophagy for the elimination of intracellular bacteria and the subversion of this process by pathogenic bacteria, we investigated the role of autophagy in c. concisus intracellular survival. gentamicin protection assays were employed to assess intracellular levels of c. concisus within caco-2 cells, following autophagy induction and inhibition. to assess the interactio ...	2014	24918042
cholera toxin production during anaerobic trimethylamine n-oxide respiration is mediated by stringent response in vibrio cholerae.	as a facultative anaerobe, vibrio cholerae can grow by anaerobic respiration. production of cholera toxin (ct), a major virulence factor of v. cholerae, is highly promoted during anaerobic growth using trimethylamine n-oxide (tmao) as an alternative electron acceptor. here, we investigated the molecular mechanisms of tmao-stimulated ct production and uncovered the crucial involvement of stringent response in this process. v. cholerae 7th pandemic strain n16961 produced a significantly elevated l ...	2014	24648517
the cjie1 prophage of campylobacter jejuni affects protein expression in growth media with and without bile salts.	the presence of campylobacter jejuni temperate bacteriophages has increasingly been associated with specific biological effects. it has recently been demonstrated that the presence of the prophage cjie1 is associated with increased adherence and invasion of c. jejuni isolates in cell culture assays.	2014	24641125
pan-genome analyses identify lineage- and niche-specific markers of evolution and adaptation in epsilonproteobacteria.	the rapidly increasing availability of complete bacterial genomes has created new opportunities for reconstructing bacterial evolution, but it has also highlighted the difficulty to fully understand the genomic and functional variations occurring among different lineages. using the class epsilonproteobacteria as a case study, we investigated the composition, flexibility, and function of its pan-genomes. models were constructed to extrapolate the expansion of pan-genomes at three different taxono ...	2014	24678308
fever management in intensive care patients with infections.	with great interest we read the article by dr schoeneberg and colleagues regarding gender-specific differences with respect to outcome in patients with severe traumatic injury. the authors show that, apart from the acute phase after trauma, women have a more favorable trauma severity-adjusted outcome, with shorter icu and hospital stay and lower sepsis rates. however, a possible mechanism of action behind this difference was not suggested. we hypothesize that, in view of the fact that morbidity ...	2014	25029624
fosfomycin: uses and potentialities in veterinary medicine.	fosfomycin (fos) is a natural bactericidal broad-spectrum antibiotic which acts on proliferating bacteria by inhibiting cell wall and early murein/peptidoglycan synthesis. bactericidal activity is evident against gram positive and gram negative bacteria and can also act synergistically with other antibiotics. bacterial resistance to fos may be natural or acquired. other properties of this drug include inhibition of bacterial adhesion to epithelial cells, exopolysaccharide biofilm penetration, im ...	2014	26623336
the role of maternal breast milk in preventing infantile diarrhea in the developing world.	multiple interventions have been designed to decrease mortality and disability in children. among these, breastfeeding is the most cost effective intervention for protecting children against diarrhea and all causes of mortality. human milk is uniquely suited to the human infant, both in its nutritional composition and in the nonnutritive bioactive factors that promote survival and healthy development. suboptimal breastfeeding has been linked with numerous adverse child health outcomes including ...	2014	24883263
ordering microbial diversity into ecologically and genetically cohesive units.	we propose that microbial diversity must be viewed in light of gene flow and selection, which define units of genetic similarity, and of phenotype and ecological function, respectively. we discuss to what extent ecological and genetic units overlap to form cohesive populations in the wild, based on recent evolutionary modeling and on evidence from some of the first microbial populations studied with genomics. these show that if recombination is frequent and selection moderate, ecologically adapt ...	2014	24630527
what's the damage? the impact of pathogens on pathways that maintain host genome integrity.	maintaining genome integrity and transmission of intact genomes is critical for cellular, organismal, and species survival. cells can detect damaged dna, activate checkpoints, and either enable dna repair or trigger apoptosis to eliminate the damaged cell. aberrations in these mechanisms lead to somatic mutations and genetic instability, which are hallmarks of cancer. considering the long history of host-microbe coevolution, an impact of microbial infection on host genome integrity is not unexpe ...	2014	24629335
complete posttranslational modification mapping of pathogenic neisseria meningitidis pilins requires top-down mass spectrometry.	in pathogenic bacteria, posttranslationally modified proteins have been found to promote bacterial survival, replication, and evasion from the host immune system. in the human pathogen neisseria meningitidis, the protein pile (15-18 kda) is the major building block of type iv pili, extracellular filamentous organelles that play a major role in mediating pathogenesis. previous reports have shown that pile can be expressed as a number of different proteoforms, each harboring its own set of ptms an ...	2014	24459079
nucleotide-binding oligomerization domain-containing protein 2 controls host response to campylobacter jejuni in il10-/- mice.	innate signaling-induced antimicrobial response represents a key protective host feature against infectious microorganisms such as campylobacter species. in this study, we investigated the role of nucleotide-binding oligomerization domain-containing protein 2 (nod2) in campylobacter jejuni-induced intestinal inflammation. specific-pathogen-free il10(-/-), nod2(-/-), and il10(-/-); nod2(-/-) mice were infected with c. jejuni (10(9) colony-forming units/mouse) 24 hours after a 7-day course of anti ...	2014	24620022
preferential packing of acidic glycosidases and proteases into bacteroides outer membrane vesicles.	outer membrane vesicles (omv) are spherical membranous structures released from the outer membrane (om) of gram-negative bacteria. omv have been proposed to play several different roles during both pathogenesis and symbiosis. despite the fact that omv were described several decades ago, their biogenesis is a poorly characterized process. whether omv are produced by an active mechanism or by passive disintegration of the om is a still matter of controversy. bacteroides fragilis and bacteroides th ...	2014	24618254
a two-tube multiplex reverse transcription pcr assay for simultaneous detection of viral and bacterial pathogens of infectious diarrhea.	diarrhea caused by viral and bacterial infections is a major health problem in developing countries. the purpose of this study is to develop a two-tube multiplex pcr assay using automatic electrophoresis for simultaneous detection of 13 diarrhea-causative viruses or bacteria, with an intended application in provincial centers for diseases control and prevention, china. the assay was designed to detect rotavirus a, norovirus genogroups gi and gii, human astrovirus, enteric adenoviruses, and human ...	2014	24711998
species-specific viability analysis of pseudomonas aeruginosa, burkholderia cepacia and staphylococcus aureus in mixed culture by flow cytometry.	bacterial species coexist commonly in mixed communities, for instance those occurring in microbial infections of humans. interspecies effects contribute to alterations in composition of communities with respect to species and thus, to the course and severity of infection. therefore, knowledge concerning growth and viability of single species in medically-relevant mixed communities is of high interest to resolve complexity of interspecies dynamics and to support development of treatment strategie ...	2014	24606608
metabolomic analysis of the food-borne pathogen campylobacter jejuni: application of direct injection mass spectrometry for mutant characterisation.	campylobacter jejuni is the most frequent cause of human food-borne bacterial gastroenteritis but its physiology and biochemistry are poorly understood. only a few amino-acids can be catabolised and these are known to be important for host colonization. here we have established methods for rapid high throughput analyses of global metabolism in c. jejuni using direct injection mass spectrometry (dims) to compare metabolite fingerprints of wild-type and mutant strains. principal component analyses ...	2014	25177231
immune and genetic gardening of the intestinal microbiome.	the mucosal immune system - consisting of adaptive and innate immune cells as well as the epithelium - is profoundly influenced by its microbial environment. there is now growing evidence that the converse is also true, that the immune system shapes the composition of the intestinal microbiome. during conditions of health, this bidirectional interaction achieves a homeostasis in which inappropriate immune responses to non-pathogenic microbes are averted and immune activity suppresses blooms of p ...	2014	24613921
lactobacillus brevis strains from fermented aloe vera survive gastroduodenal environment and suppress common food borne enteropathogens.	five novel lactobacillus brevis strains were isolated from naturally fermented aloe vera leaf flesh. each strain was identified by random amplified polymorphic dna (rapd) analysis and 16s rrna sequence comparison. these strains were highly tolerant to acid, surviving in ph2.5 for up to 4 hours, and resistant to 5% bile salts at 37°c for 18 hours. due to its tolerance to acid and bile salts, one strain passed through the gastric barrier and colonised the intestine after oral administration. all f ...	2014	24598940
maf-dependent bacterial flagellin glycosylation occurs before chaperone binding and flagellar t3ss export.	bacterial swimming is mediated by rotation of a filament that is assembled via polymerization of flagellin monomers after secretion via a dedicated flagellar type iii secretion system. several bacteria decorate their flagellin with sialic acid related sugars that is essential for motility. aeromonas caviae is a model organism for this process as it contains a genetically simple glycosylation system and decorates its flagellin with pseudaminic acid (pse). the link between flagellin glycosylation ...	2014	24527847
passive immunization to reduce campylobacter jejuni colonization and transmission in broiler chickens.	campylobacter jejuni is the most common cause of bacterium-mediated diarrheal disease in humans worldwide. poultry products are considered the most important source of c. jejuni infections in humans but to date no effective strategy exists to eradicate this zoonotic pathogen from poultry production. here, the potential use of passive immunization to reduce campylobacter colonization in broiler chicks was examined. for this purpose, laying hens were immunized with either a whole-cell lysate or th ...	2014	24589217
efficacy of three light technologies for reducing microbial populations in liquid suspensions.	the aim of the current study was to evaluate the effectiveness of three nonthermal light technologies (nuv-vis, continuous uv, and hilp) on their ability to inactivate escherichia coli k12 and listeria innocua. e. coli k12 was selected as a representative microorganism for the enterohaemorrhagic foodborne pathogen e. coli o157:h7 and l. innocua as a surrogate microorganism for the common foodborne pathogen listeria monocytogenes, respectively. the liquid matrix used for the disinfection experim ...	2014	24724092
enterocolitis without diarrhoea in an adult patient: a clinical dilemma.	campylobacter jejuni is one of the most common causes of bloody diarrhoea in the usa. we report a case of a young woman who presented with a clinical picture reminiscent of acute appendicitis. ultrasonography and ct of the abdomen performed subsequently revealed evidence of colitis. quite unexpectedly, she had no symptoms of diarrhoea and the stool gram stain and culture were negative. nevertheless, due to high clinical suspicion of infectious colitis, appendectomy was deferred. blood culture wa ...	2014	24596412
total phenolic content and antibacterial activity of five plants of labiatae against four foodborne and some other bacteria.	the aim of this study was to evaluate the antibacterial effects of thymus vulgaris, thymus caramanicus, zataria multiflora, ziziphora clinopodioides and ziziphora tenuior against four foodborne and four other bacteria including staphylococcus aureus, shigella dysenteriae, salmonella typhimurium, escherichia coli, staphylococcus epidermidis, bacillus subtilis, mrsa and pseudomona aeruginosa and measuring the amount of total phenolics of the plants. the extracts were prepared by maceration method. ...	2014	25237351
a report of guillain-barré syndrome with myalgia and mild weakness.	we report a rare case that revealed severe myalgia as the chief complaint that is not mentioned in the list of frequent symptoms of guillain barré. guillain-barré syndrome (gbs) is an acute inflammatory demyelinating polyneuropathy (aidp).required features for diagnosis of gbs are progressive motor weakness of more than one limb and areflexia. we report an 11-yearold boy who was referred to the emergency department with complaints of generalized body pain and gate problem. it seems that if myalg ...	2014	24949056
irritable bowel syndrome: the role of food in pathogenesis and management.	irritable bowel syndrome (ibs) is a common functional gastrointestinal disorder that affects approximately 10% to 20% of the general adult population in europe and the americas and is characterized by abdominal pain and altered bowel habits in the absence of reliable biomarkers. the pathophysiology of ibs is poorly understood and is currently thought to represent a complex interplay among the gut microbiota, low-grade inflammation, impaired mucosal barrier function, visceral hypersensitivity, gu ...	2014	24829543
the nod1, nod2, and rip2 axis contributes to host immune defense against intracellular acinetobacter baumannii infection.	acinetobacter baumannii is a major extensively drug-resistant lethal human nosocomial bacterium. however, the host innate immune mechanisms controlling a. baumannii are not well understood. although viewed as an extracellular pathogen, a. baumannii can also invade and survive intracellularly. however, whether host innate immune pathways sensing intracellular bacteria contribute to immunity against a. baumannii is not known. here, we provide evidence for the first time that intracellular antibact ...	2014	24366254
real-time pcr threshold cycle cutoffs help to identify agents causing acute childhood diarrhea in zanzibar.	molecular assays might improve the identification of causes of acute diarrheal disease but might lead to more frequent detection of asymptomatic infections. in the present study, real-time pcr targeting 14 pathogens was applied to rectal swabs from 330 children aged 2 to 59 months in zanzibar, including 165 patients with acute diarrhea and 165 asymptomatic control subjects. at least one pathogen was detected for 94% of the patients and 84% of the controls, with higher rates among patients for no ...	2014	24403298
flagellin a toll-like receptor 5 agonist as an adjuvant in chicken vaccines.	chicken raised under commercial conditions are vulnerable to environmental exposure to a number of pathogens. therefore, regular vaccination of the flock is an absolute requirement to prevent the occurrence of infectious diseases. to combat infectious diseases, vaccines require inclusion of effective adjuvants that promote enhanced protection and do not cause any undesired adverse reaction when administered to birds along with the vaccine. with this perspective in mind, there is an increased nee ...	2014	24451328
prevalence in bulk tank milk and epidemiology of campylobacter jejuni in dairy herds in northern italy.	thermotolerant campylobacter spp. are frequently the cause of human gastroenteritis and have assumed more importance in italy following the increased consumption of raw milk. our objectives were to determine the prevalence and genotypes of campylobacter spp. in dairy herds and to investigate the possible sources of bulk milk contamination. bulk milk from dairy herds (n = 282) was cultured for campylobacter spp. and enterobacteriaceae. at three campylobacter jejuni-positive farms, bovine feces, p ...	2014	24413598
cas9-based tools for targeted genome editing and transcriptional control.	development of tools for targeted genome editing and regulation of gene expression has significantly expanded our ability to elucidate the mechanisms of interesting biological phenomena and to engineer desirable biological systems. recent rapid progress in the study of a clustered, regularly interspaced short palindromic repeat (crispr)/crispr-associated (cas) protein system in bacteria has facilitated the development of newly facile and programmable platforms for genome editing and transcriptio ...	2014	24389925
age-related shifts in the density and distribution of genetic marker water quality indicators in cow and calf feces.	calves make up about 16% of the current bovine population in the united states and can excrete high levels of human pathogens in their feces. we describe the density and distribution of genetic markers from 9 pcr- and real-time quantitative pcr-based assays, including cf128, cf193, cowm2, cowm3, genbac3, entero1, ec23s857, campf2, and ttr-6, commonly used to help assess ambient surface water quality. each assay was tested against a collection of 381 individual bovine fecal samples representing 3 ...	2014	24362434
cov2html: a visualization and analysis tool of bacterial next generation sequencing (ngs) data for postgenomics life scientists.	cov2html is an interactive web interface, which is addressed to biologists, and allows performing both coverage visualization and analysis of ngs alignments performed on prokaryotic organisms (bacteria and phages). it combines two processes: a tool that converts the huge ngs mapping or coverage files into light specific coverage files containing information on genetic elements; and a visualization interface allowing a real-time analysis of data with optional integration of statistical results. t ...	2014	24512253
brain-gut microbiome interactions and functional bowel disorders.	alterations in the bidirectional interactions between the intestine and the nervous system have important roles in the pathogenesis of irritable bowel syndrome (ibs). a body of largely preclinical evidence suggests that the gut microbiota can modulate these interactions. a small and poorly defined role for dysbiosis in the development of ibs symptoms has been established through characterization of altered intestinal microbiota in ibs patients and reported improvement of subjective symptoms afte ...	2014	24583088
chlamydia exploit the mammalian tryptophan-depletion defense strategy as a counter-defensive cue to trigger a survival state of persistence.	we previously proposed that in chlamydiaceae rapid vegetative growth and a quiescent state of survival (persistence) depend upon alternative protein translational profiles dictated by host tryptophan (trp) availability. these alternative profiles correspond, respectively, with a set of chlamydial proteins having higher-than-predicted contents of trp ("up-trp" selection), or with another set exhibiting lower-than-predicted contents of trp ("down-trp" selection). a comparative evaluation of chlamy ...	2014	24616884
efficient inference of recombination hot regions in bacterial genomes.	in eukaryotes, detailed surveys of recombination rates have shown variation at multiple genomic scales and the presence of "hotspots" of highly elevated recombination. in bacteria, studies of recombination rate variation are less developed, in part because there are few analysis methods that take into account the clonal context within which bacterial evolution occurs. here, we focus in particular on identifying "hot regions" of the genome where dna is transferred frequently between isolates. we ...	2014	24586045
avian antimicrobial host defense peptides: from biology to therapeutic applications.	host defense peptides (hdps) are an important first line of defense with antimicrobial and immunomoduatory properties. because they act on the microbial membranes or host immune cells, hdps pose a low risk of triggering microbial resistance and therefore, are being actively investigated as a novel class of antimicrobials and vaccine adjuvants. cathelicidins and β-defensins are two major families of hdps in avian species. more than a dozen hdps exist in birds, with the genes in each hdp family cl ...	2014	24583933
functional characterization of exopolyphosphatase/guanosine pentaphosphate phosphohydrolase (ppx/gppa) of campylobacter jejuni.	the inorganic polyphosphate (poly-p) is a key regulator of stress responses and virulence in many bacterial pathogens including campylobacter jejuni. the role of exopolyphosphatases/guanosine pentaphosphate (pppgpp) phosphohydrolases (ppx/gppa) in poly-p homeostasis and c. jejuni pathobiology remains unexplored. here, we analyzed deletion mutants (∆ppx1, ∆ppx2) and the double knockout mutant (dkppx), all ∆ppx mutants exhibited increased capacity to accumulate poly-p; however only ∆ppx1 and dkppx ...	2014	24569519
disulfide bond formation in prokaryotes: history, diversity and design.	the formation of structural disulfide bonds is essential for the function and stability of a great number of proteins, particularly those that are secreted. there exists a variety of dedicated cellular catalysts and pathways from archaea to humans that ensure the formation of native disulfide bonds. in this review we describe the initial discoveries of these pathways and report progress in recent years in our understanding of the diversity of these pathways in prokaryotes, including those newly ...	2014	24576574
impact of campylobacter jejuni cj0268c knockout mutation on intestinal colonization, translocation, and induction of immunopathology in gnotobiotic il-10 deficient mice.	although campylobacter jejuni infections have a high prevalence worldwide and represent a significant socioeconomic burden, the underlying molecular mechanisms of induced intestinal immunopathology are still not well understood. we have recently generated a c. jejuni mutant strain nctc11168::cj0268c, which has been shown to be involved in cellular adhesion and invasion. the immunopathological impact of this gene, however, has not been investigated in vivo so far.	2014	24587249
high detection rates of enteropathogens in asymptomatic children attending day care.	gastroenteritis morbidity is high among children under the age of four, especially amongst those who attend day care.	2014	24586825
omics approaches in food safety: fulfilling the promise?	genomics, transcriptomics, and proteomics are rapidly transforming our approaches to the detection, prevention, and treatment of foodborne pathogens. microbial genome sequencing in particular has evolved from a research tool into an approach that can be used to characterize foodborne pathogen isolates as part of routine surveillance systems. genome sequencing efforts will not only improve outbreak detection and source tracking, but will also create large amounts of foodborne pathogen genome sequ ...	2014	24572764
antibacterial efficacy testing of a bioelectric wound dressing against clinical wound pathogens.	silver-based wound dressings have been developed for the control of bioburden in wounds. however, the popularity and extensive use of silver-based dressings has been associated with emerging microbial resistances to silver. in this study we examined in vitro antibacterial efficacy of a bioelectric dressing containing silver and zinc against various wound pathogens. antibiotic-sensitive clinical wound isolates showed a 100% reduction in bacterial growth, except that enterococcus faecalis isolate ...	2014	24627730
noroviral p-particles as an in vitro model to assess the interactions of noroviruses with probiotics.	noroviruses (novs) are the main etiologic agents of acute epidemic gastroenteritis and probiotic bacteria have been reported to exert a positive effect on viral diarrhea. the protruding (p) domain from novs vp1 capsid protein has the ability to assemble into the so-called p-particles, which retain the binding ability to host receptors. we purified the p-domains from novs genotypes gi.1 and gii.4 as 6x(his)-tagged proteins and determined that, similar to native domains, they were structured into ...	2014	24586892
aeromonas hydrophila flagella glycosylation: involvement of a lipid carrier.	polar flagellin proteins from aeromonas hydrophila strain ah-3 (serotype o34) were found to be o-glycosylated with a heterogeneous glycan. mutants unable to produce wecp or gne enzymes showed altered motility, and the study of their polar flagellin glycosylation showed that the patterns of glycosylation differed from that observed with wild type polar flagellin. this suggested the involvement of a lipid carrier in glycosylation. a gene coding for an enzyme linking sugar to a lipid carrier was id ...	2014	24586923
mycobacterium tuberculosis exploits asparagine to assimilate nitrogen and resist acid stress during infection.	mycobacterium tuberculosis is an intracellular pathogen. within macrophages, m. tuberculosis thrives in a specialized membrane-bound vacuole, the phagosome, whose ph is slightly acidic, and where access to nutrients is limited. understanding how the bacillus extracts and incorporates nutrients from its host may help develop novel strategies to combat tuberculosis. here we show that m. tuberculosis employs the asparagine transporter ansp2 and the secreted asparaginase ansa to assimilate nitrogen ...	2014	24586151
the relation between helicobacter pylori infection and acute bacterial diarrhea in children.	background. h. pylori infection leads to chronic gastritis in both children and adults. but recently, there are arising theories of its protective effect in diarrheal diseases. aim. to explore the prevalence of h. pylori infection in children with bacterial diarrhea and compare it with healthy controls. patients and methods. two matched groups consisted of 122 consecutive children, aged 24-72 months old, with acute bacterial diarrhea, who had shigellosis (n = 68) and salmonellosis (n = 54) as pa ...	2014	24696690
prediction of ctl epitope, in silico modeling and functional analysis of cytolethal distending toxin (cdt) protein of campylobacter jejuni.	campylobacter jejuni is a potent bacterial pathogen culpable for diarrheal disease called campylobacteriosis. it is realized as a major health issue attributable to unavailability of appropriate vaccines and clinical treatment options. as other pathogens, c. jejuni entails host cellular components of an infected individual to disseminate this disease. these host-pathogen interfaces during c. jejuni infection are complex, vibrant and involved in the nicking of host cell environment, enzymes and p ...	2014	24552167
helicobacter pylori: expect the unexpected.	helicobacter pylori is one of the most common bacterial infections worldwide, and virtually all infected persons develop coexisting gastritis, a signature feature of which is the capacity to persist for decades. in support of its lifestyle, h. pylori has evolved to express an array of diverse phenotypes, including enzyme functional diversity, that help to subvert obstacles presented by the human host, which permits long-term microbial colonization. the versatility of the newly discovered enzyme ...	2014	24471732
small distances can keep bacteria at bay for days.	transmission of pathogens between spatially separated hosts, i.e., indirect transmission, is a commonly encountered phenomenon important for epidemic pathogen spread. the routes of indirect transmission often remain untraced, making it difficult to develop control strategies. here we used a tailor-made design to study indirect transmission experimentally, using two different zoonotic bacteria in broilers. previous experiments using a single bacterial species yielded a delay in the onset of trans ...	2014	24550476
high frequency, spontaneous mota mutations in campylobacter jejuni strain 81-176.	campylobacter jejuni is an important cause of bacterial diarrhea worldwide. the pathogenesis of c. jejuni is poorly understood and complicated by phase variation of multiple surface structures including lipooligosaccharide, capsule, and flagellum. when c. jejuni strain 81-176 was plated on blood agar for single colonies, the presence of translucent, non-motile colonial variants was noted among the majority of opaque, motile colonies. high-throughput genomic sequencing of two flagellated transluc ...	2014	24558375
regulation of intestinal immune responses through tlr activation: implications for pro- and prebiotics.	the intestinal mucosa is constantly facing a high load of antigens including bacterial antigens derived from the microbiota and food. despite this, the immune cells present in the gastrointestinal tract do not initiate a pro-inflammatory immune response. toll-like receptors (tlrs) are pattern recognition receptors expressed by various cells in the gastrointestinal tract, including intestinal epithelial cells (iec) and resident immune cells in the lamina propria. many diseases, including chronic ...	2014	24600450
crystal structure and putative substrate identification for the entamoeba histolytica low molecular weight tyrosine phosphatase.	entamoeba histolytica is a eukaryotic intestinal parasite of humans, and is endemic in developing countries. we have characterized the e. histolytica putative low molecular weight protein tyrosine phosphatase (lmw-ptp). the structure for this amebic tyrosine phosphatase was solved, showing the ligand-induced conformational changes necessary for binding of substrate. in amebae, it was expressed at low but detectable levels as detected by immunoprecipitation followed by immunoblotting. a mutant lm ...	2014	24548880
producing proficient methyl donors from alternative substrates of s-adenosylmethionine synthetase.	bacteria use quorum sensing to probe and respond to population densities in their external environment. the detection of quorum signaling molecules causes a virulence response in many pathogenic bacteria. blocking this signaling pathway, without interfering with critical metabolic functions, would produce compounds that can disarm pathogens without killing them. by not blocking growth per se, this therapeutic approach would have a lower associated risk for the development of bacterial resistance ...	2014	24528526
structural and functional aspects of the helicobacter pylori secretome.	proteins secreted by helicobacter pylori (h. pylori), an important human pathogen responsible for severe gastric diseases, are reviewed from the point of view of their biochemical characterization, both functional and structural. despite the vast amount of experimental data available on the proteins secreted by this bacterium, the precise size of the secretome remains unknown. in this review, we consider as secreted both proteins that contain a secretion signal for the periplasm and proteins tha ...	2014	24587618
norspermidine is not a self-produced trigger for biofilm disassembly.	formation of bacillus subtilis biofilms, consisting of cells encapsulated within an extracellular matrix of exopolysaccharide and protein, requires the polyamine spermidine. a recent study reported that (1) related polyamine norspermidine is synthesized by b. subtilis using the equivalent of the vibrio cholerae biosynthetic pathway, (2) exogenous norspermidine at 25 μm prevents b. subtilis biofilm formation, (3) endogenous norspermidine is present in biofilms at 50-80 μm, and (4) norspermidine p ...	2014	24529384
starvation induces phenotypic diversification and convergent evolution in vibrio vulnificus.	starvation is a common stress experienced by bacteria living in natural environments and the ability to adapt to and survive intense stress is of paramount importance for any bacterial population. a series of starvation experiments were conducted using v. vulnificus 93u204 in phosphate-buffered saline and seawater. the starved population entered the death phase during the first week and approximately 1% of cells survived. after that the population entered a long-term stationary phase, and could ...	2014	24551129
recent advances in human milk glycobiology.		2014	24522101
genotypes, antibiotic resistance, and st-8 genetic clone in campylobacter isolates from sheep and goats in grenada.	rectal swabs from 155 sheep and 252 goats from grenada were evaluated to determine the prevalence of campylobacter spp., antibiotic resistance, and multilocus sequence types. fifteen campylobacter isolates were obtained (14 c. jejuni and 1 c. coli). the prevalence (3.7%) did not differ significantly between sheep (4.5%) and goats (3.2%). among the seven antimicrobials tested, resistance was only detected for tetracycline (30.8%) and metronidazole (38.5%). campylobacter isolates showed no signifi ...	2014	24693459
a metabolomic perspective on coeliac disease.	metabolomics is an "omic" science that is now emerging with the purpose of elaborating a comprehensive analysis of the metabolome, which is the complete set of metabolites (i.e., small molecules intermediates) in an organism, tissue, cell, or biofluid. in the past decade, metabolomics has already proved to be useful for the characterization of several pathological conditions and offers promises as a clinical tool. a metabolomics investigation of coeliac disease (cd) revealed that a metabolic fin ...	2014	24665364
emra1 membrane fusion protein of francisella tularensis lvs is required for resistance to oxidative stress, intramacrophage survival and virulence in mice.	francisella tularensis is a category a biodefence agent that causes a fatal human disease known as tularaemia. the pathogenicity of f. tularensis depends on its ability to persist inside host immune cells primarily by resisting an attack from host-generated reactive oxygen and nitrogen species (ros/rns). based on the ability of f. tularensis to resist high ros/rns levels, we have hypothesized that additional unknown factors act in conjunction with known antioxidant defences to render ros resista ...	2014	24397487
origin and evolution of the peptidyl transferase center from proto-trnas.	we tested the hypothesis of tamura (2011) [3] that molecules of trna gave origin to ribosomes, particularly to the peptidyl transferase center (ptc) of the 23s ribosomal rna. we reconstructed the ancestral sequences from all types of trna and compared them in their sequences with the current ptc of 23s ribosomal rna from different organisms. we built an ancestral sequence of proto-trnas that showed a remarkable overall identity of 50.53% with the catalytic site of ptc. we conclude that the pepti ...	2014	24649398
the impairment of methylmenaquinol:fumarate reductase affects hydrogen peroxide susceptibility and accumulation in campylobacter jejuni.	the methylmenaquinol:fumarate reductase (mfr) of campylobacter jejuni is a periplasmic respiratory (redox) protein that contributes to the metabolism of fumarate and displays homology to succinate dehydrogenase (sdh). since chemically oxidized redox-enzymes, including fumarate reductase and sdh, contribute to the generation of oxidative stress in escherichia coli, we assessed the role of mfr in c. jejuni after exposure to hydrogen peroxide (h2 o2 ). our results show that a mfr mutant (∆mfra) str ...	2014	24515965
campylobacter concisus and inflammatory bowel disease.	investigation of the possible role of campylobacter concisus (c. concisus) in inflammatory bowel disease (ibd) is an emerging research area. despite the association found between c. concisus and ibd, it has been difficult to explain how c. concisus, a bacterium that is commonly present in the human oral cavity, may contribute to the development of enteric diseases. the evidence presented in this review shows that some c. concisus strains in the oral cavity acquired zonula occludens toxin (zot) g ...	2014	24574800
role of the gut microbiota in inflammatory bowel disease pathogenesis: what have we learnt in the past 10 years?	our understanding of the microbial involvement in inflammatory bowel disease (ibd) pathogenesis has increased exponentially over the past decade. the development of newer molecular tools for the global assessment of the gut microbiome and the identification of nucleotide-binding oligomerization domain-containing protein 2 in 2001 and other susceptibility genes for crohn's disease in particular has led to better understanding of the aetiopathogenesis of ibd. the microbial studies have elaborated ...	2014	24574795
comparative variation within the genome of campylobacter jejuni nctc 11168 in human and murine hosts.	campylobacteriosis incited by c. jejuni is a significant enteric disease of human beings. a person working with two reference strains of c. jejuni national collection of type cultures (nctc) 11168 developed symptoms of severe enteritis including bloody diarrhea. the worker was determined to be infected by c. jejuni. in excess of 50 isolates were recovered from the worker's stool. all of the recovered isolates and the two reference strains were indistinguishable from each other based on comparati ...	2014	24516617
genome sequences of campylobacter jejuni 81-176 variants with enhanced fitness relative to the parental strain in the chicken gastrointestinal tract.	campylobacter jejuni is a major cause of food-borne infections in the united states due to its ability to asymptomatically colonize the gastrointestinal tracts of chickens. using competition assays with parental c. jejuni 81-176, variants with consistently improved fitness in chicken ceca relative to the parental strain were identified and sequenced.	2014	24503981
mining locus tags in pubmed central to improve microbial gene annotation.	the scientific literature contains millions of microbial gene identifiers within the full text and tables, but these annotations rarely get incorporated into public sequence databases. we propose to utilize the open access (oa) subset of pubmed central (pmc) as a gene annotation database and have developed an r package called pmcxml to automatically mine and extract locus tags from full text, tables and supplements.	2014	24499370
a loop-mediated isothermal amplification (lamp) assay for strongyloides stercoralis in stool that uses a visual detection method with syto-82 fluorescent dye.	an assay to detect strongyloides stercoralis in stool specimens was developed using the loop-mediated isothermal amplification (lamp) method. primers were based on the 28s ribosomal subunit gene. the reaction conditions were optimized and syto-82 fluorescent dye was used to allow real-time and visual detection of the product. the product identity was confirmed with restriction enzyme digestion, cloning, and sequence analysis. the assay was specific when tested against dna from bacteria, fungi an ...	2014	24323513
helicobacter pylori rna polymerase α-subunit c-terminal domain shows features unique to ɛ-proteobacteria and binds nikr/dna complexes.	bacterial rna polymerase is a large, multi-subunit enzyme responsible for transcription of genomic information. the c-terminal domain of the α subunit of rna polymerase (αctd) functions as a dna and protein recognition element localizing the polymerase on certain promoter sequences and is essential in all bacteria. although αctd is part of rna polymerase, it is thought to have once been a separate transcription factor, and its primary role is the recruitment of rna polymerase to various promoter ...	2014	24442709
mycobacterium tuberculosis cyclophilin a uses novel signal sequence for secretion and mimics eukaryotic cyclophilins for interaction with host protein repertoire.	cyclophilins are prolyl isomerases with multitude of functions in different cellular processes and pathological conditions. cyclophilin a (ppia) of mycobacterium tuberculosis is secreted during infection in intraphagosomal niche. however, our understanding about the evolutionary origin, secretory mechanism or the interactome of m. tuberculosis ppia is limited. this study demonstrates through phylogenetic and structural analyses that ppia has more proximity to human cyclophilins than the prokaryo ...	2014	24505389
genotyping of clostridium perfringens isolated from healthy and diseased ostriches (struthio camelus).	clostridium perfringens is more prevalent type of clostridia genus isolated from the intestinal tract of ostrich (struthio camelus). necrotic enteritis (ne) is a potentially fatal gastrointestinal (gi) disease of poultry and other avian species, which produces marked destruction of intestinal lining in digestive tract caused by c. perfringens. pathogenicity and lesions are correlated with the toxins produced, thus toxin typing of the bacterium has diagnostic and epidemiological significance. the ...	2014	25954489
combined effects of high pressure processing and addition of soy sauce and olive oil on safety and quality characteristics of chicken breast meat.	this study was conducted to evaluate the combined effect of high pressure (hp) with the addition of soy sauce and/or olive oil on the quality and safety of chicken breast meats. samples were cut into 100 g pieces and 10% (w/w) of soy sauce (ss), 10% (w/w) of olive oil (oo), and a mixture of both 5% of soy sauce and 5% olive oil (w/w) (so) were pressurized into meat with high pressure at 300 or 600 mpa. cooking loss was lower in oo samples than ss samples. with increased pressure to 600 mpa, the ...	2014	25049950
dietary supplementation of benzoic acid and essential oil compounds affects buffering capacity of the feeds, performance of turkey poults and their antioxidant status, ph in the digestive tract, intestinal microbiota and morphology.	three trials were conducted to evaluate the effect of supplementation of a basal diet with benzoic acid or thymol or a mixture of essential oil blends (meo) or a combination of benzoic acid with meo (bmeo) on growth performance of turkey poults. control groups were fed a basal diet. in trial 1, benzoic acid was supplied at levels of 300 and 1,000 mg/kg. in trial 2, thymol or the meo were supplied at levels of 30 mg/kg. in trial 3, the combination of benzoic acid with meo was evaluated. benzoic a ...	2014	25049947
pathogens of bovine respiratory disease in north american feedlots conferring multidrug resistance via integrative conjugative elements.	in this study, we determined the prevalence of bovine respiratory disease (brd)-associated viral and bacterial pathogens in cattle and characterized the genetic profiles, antimicrobial susceptibilities, and nature of antimicrobial resistance determinants in collected bacteria. nasopharyngeal swab and lung tissue samples from 68 brd mortalities in alberta, canada (n = 42), texas (n = 6), and nebraska (n = 20) were screened using pcr for bovine viral diarrhea virus (bvdv), bovine respiratory syncy ...	2014	24478472