Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
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| a study in entire chromosomes of violations of the intra-strand parity of complementary nucleotides (chargaff's second parity rule). | chargaff's rule of intra-strand parity (isp) between complementary mono/oligonucleotides in chromosomes is well established in the scientific literature. although a large numbers of papers have been published citing works and discussions on isp in the genomic era, scientists are yet to find all the factors responsible for such a universal phenomenon in the chromosomes. in the present work, we have tried to address the issue from a new perspective, which is a parallel feature to isp. the composit ... | 2009 | 19861381 |
| campylobacter concisus and other campylobacter species in children with newly diagnosed crohn's disease. | campylobacter concisus and other members of the campylobacter genus have recently been suggested as possible etiological agents of crohn's disease (cd). to further investigate this issue we determined the prevalence of these organisms in pediatric patients newly diagnosed with cd. | 2010 | 19885905 |
| the secretome of campylobacter concisus. | a higher prevalence of campylobacter concisus and higher levels of igg antibodies specific to c. concisus in crohn's disease patients than in controls were recently detected. in this study, 1d and 2d gel electrophoresis coupled with ltq ft-ms and qstar tandem ms, respectively, were performed to characterize the secretome of a c. concisus strain isolated from a crohn's disease patient. two hundred and one secreted proteins were identified, of which 86 were bioinformatically predicted to be secret ... | 2010 | 20148967 |
| shewanella spp. genomic evolution for a cold marine lifestyle and in-situ explosive biodegradation. | shewanella halifaxensis and shewanella sediminis were among a few aquatic gamma-proteobacteria that were psychrophiles and the first anaerobic bacteria that degraded hexahydro-1,3,5-trinitro-1,3,5-triazine (rdx). although many mesophilic or psychrophilic strains of shewanella and gamma-proteobacteria were sequenced for their genomes, the genomic evolution pathways for temperature adaptation were poorly understood. on the other hand, the genes responsible for anaerobic rdx mineralization pathways ... | 2010 | 20174598 |
| filifactor alocis--involvement in periodontal biofilms. | bacteria in periodontal pockets develop complex sessile communities that attach to the tooth surface. these highly dynamic microfloral environments challenge both clinicians and researchers alike. the exploration of structural organisation and bacterial interactions within these biofilms is critically important for a thorough understanding of periodontal disease. in recent years, filifactor alocis, a fastidious, gram-positive, obligately anaerobic rod was repeatedly identified in periodontal les ... | 2010 | 20193074 |
| twisting of the dna-binding surface by a beta-strand-bearing proline modulates dna gyrase activity. | dna gyrase is the only topoisomerase capable of introducing (-) supercoils into relaxed dna. the c-terminal domain of the gyrase a subunit (gyra-ctd) and the presence of a gyrase-specific 'gyra-box' motif within this domain are essential for this unique (-) supercoiling activity by allowing gyrase to wrap dna around itself. here we report the crystal structure of xanthomonas campestris gyra-ctd and provide the first view of a canonical gyra-box motif. this structure resembles the gyra-box-disord ... | 2010 | 20215433 |
| the internal transcribed spacer region, a new tool for use in species differentiation and delineation of systematic relationships within the campylobacter genus. | the campylobacter genus consists of a number of important human and animal pathogens. although the 16s rrna gene has been used extensively for detection and identification of campylobacter species, there is currently limited information on the 23s rrna gene and the internal transcribed spacer (its) region that lies between the 16s and 23s rrna genes. we examined the potential of the 23s rrna gene and the its region to be used in species differentiation and delineation of systematic relationships ... | 2010 | 20348308 |
| the hp0256 gene product is involved in motility and cell envelope architecture of helicobacter pylori. | helicobacter pylori is the causative agent for gastritis, and peptic and duodenal ulcers. the bacterium displays 5-6 polar sheathed flagella that are essential for colonisation and persistence in the gastric mucosa. the biochemistry and genetics of flagellar biogenesis in h. pylori has not been fully elucidated. bioinformatics analysis suggested that the gene hp0256, annotated as hypothetical, was a flij homologue. in salmonella, flij is a chaperone escort protein for flgn and flit, two proteins ... | 2010 | 20377912 |
| persistent infection of rhesus monkeys with 'helicobacter macacae' and its isolation from an animal with intestinal adenocarcinoma. | a novel helicobacter, 'helicobacter macacae', was previously isolated from a colony of rhesus and cynomolgus monkeys in which diarrhoea from chronic idiopathic colitis was enzootic. a survey performed in a second colony of rhesus monkeys without a history of chronic diarrhoea determined that 57 % were faecal-culture positive for helicobacter species. ten years after the survey, one of the animals from which 'h. macacae' had been isolated, a 23-year-old, intact male rhesus monkey (macaca mulatta) ... | 2010 | 20413623 |
| comparative analysis of sequence periodicity among prokaryotic genomes points to differences in nucleoid structure and a relationship to gene expression. | regular spacing of short runs of a or t nucleotides in dna sequences with a period close to the helical period of the dna double helix has been associated with intrinsic dna bending and nucleosome positioning in eukaryotes. analogous periodic signals were also observed in prokaryotic genomes. while the exact role of this periodicity in prokaryotes is not known, it has been proposed to facilitate the dna packaging in the prokaryotic nucleoid and/or to promote negative or positive supercoiling. we ... | 2010 | 20494989 |
| isolation and detection of campylobacter concisus from saliva of healthy individuals and patients with inflammatory bowel disease. | the presence of campylobacter concisus in the saliva of healthy individuals and patients with inflammatory bowel disease (ibd) was examined. c. concisus was detected in 97% of the healthy individuals and 100% of the patients with ibd tested. the c. concisus culture positivity rate in younger children was significantly lower than that in the other age groups. | 2010 | 20519479 |
| unusual target site disruption by the rare-cutting hnh restriction endonuclease paci. | the crystal structure of the rare-cutting hnh restriction endonuclease paci in complex with its eight-base-pair target recognition sequence 5'-ttaattaa-3' has been determined to 1.9 a resolution. the enzyme forms an extended homodimer, with each subunit containing two zinc-bound motifs surrounding a betabetaalpha-metal catalytic site. the latter is unusual in that a tyrosine residue likely initiates strand cleavage. paci dramatically distorts its target sequence from watson-crick duplex dna base ... | 2010 | 20541511 |
| characterization of n-linked protein glycosylation in helicobacter pullorum. | the first bacterial n-linked glycosylation system was discovered in campylobacter jejuni, and the key enzyme involved in the coupling of glycan to asparagine residues within the acceptor sequon of the glycoprotein is the oligosaccharyltransferase pglb. emerging genome sequence data have revealed that pglb orthologues are present in a subset of species from the deltaproteobacteria and epsilonproteobacteria, including three helicobacter species: h. pullorum, h. canadensis, and h. winghamensis. in ... | 2010 | 20581208 |
| origins and diversification of a complex signal transduction system in prokaryotes. | the molecular machinery that controls chemotaxis in bacteria is substantially more complex than any other signal transduction system in prokaryotes, and its origins and variability among living species are unknown. we found that this multiprotein "chemotaxis system" is present in most prokaryotic species and evolved from simpler two-component regulatory systems that control prokaryotic transcription. we discovered, through genomic analysis, signaling systems intermediate between two-component sy ... | 2010 | 20587806 |
| obstacles of multiplex real-time pcr for bacterial 16s rdna: primer specifity and dna decontamination of taq polymerase. | background: the detection of a broad range of bacteria by pcr is applied for the screening of blood and blood products with special attention to platelet concentrates. for practical use it is desirable that detection systems include gram-positive, gram-negative and non-gram-stainable bacteria. it is quite challenging to achieve high sensitivity along with a clear negative control with pcr reagents, because especially taq polymerase is contaminated with traces of bacterial dna. methods: bacterial ... | 2010 | 20737013 |
| bacterial 16s sequence analysis of severe caries in young permanent teeth. | previous studies have confirmed the association of the acid producers streptococcus mutans and lactobacillus spp. with childhood caries, but they also suggested these microorganisms are not sufficient to explain all cases of caries. in addition, health-associated bacterial community profiles are not well understood, including the importance of base production and acid catabolism in ph homeostasis. the bacterial community composition in health and in severe caries of the young permanent dentition ... | 2010 | 20826648 |
| what is type vi secretion doing in all those bugs? | the identification of bacterial secretion systems capable of translocating substrates into eukaryotic cells via needle-like appendages has opened fruitful and exciting areas of microbial pathogenesis research. the recent discovery of the type vi secretion system (t6ss) was met with early speculation that it too acts as a 'needle' that pathogens aim at host cells. new reports demonstrate that certain t6sss are potent mediators of interbacterial interactions. in light of these findings, we examine ... | 2010 | 20961764 |
| host attachment, invasion, and stimulation of proinflammatory cytokines by campylobacter concisus and other non-campylobacter jejuni campylobacter species. | campylobacter concisus and other non-campylobacter jejuni campylobacter species have been implicated in the initiation of gastrointestinal diseases. in the present study, we investigated the interaction between these bacteria and the human intestinal epithelium and immune cells. | 2010 | 21050118 |
| microbiota of deciduous endodontic infections analysed by mda and checkerboard dna-dna hybridization. | to evaluate the microbiota of endodontic infections in deciduous teeth by checkerboard dna-dna hybridization after uniform amplification of dna in samples by multiple displacement amplification (mda). | 2010 | 21083570 |
| microbiota of deciduous endodontic infections analysed by mda and checkerboard dna-dna hybridization. | to evaluate the microbiota of endodontic infections in deciduous teeth by checkerboard dna-dna hybridization after uniform amplification of dna in samples by multiple displacement amplification (mda). | 2010 | 21083570 |
| enteric campylobacteria and rna viruses associated with healthy and diarrheic humans in the chinook health region of southwestern alberta, canada. | the presence of campylobacter species and enteric rna viruses in stools from diarrheic (n = 442) and healthy (n = 58) humans living in southwestern alberta was examined (may to october 2005). a large number of diarrheic individuals who were culture negative for c. jejuni (n = 54) or c. coli (n = 19) were pcr positive for these taxa. overall detection rates for c. jejuni and c. coli in diarrheic stools were 29% and 5%, respectively. in contrast, 3% and 0% of stools from healthy humans were positi ... | 2010 | 21106791 |
| enteric campylobacteria and rna viruses associated with healthy and diarrheic humans in the chinook health region of southwestern alberta, canada. | the presence of campylobacter species and enteric rna viruses in stools from diarrheic (n = 442) and healthy (n = 58) humans living in southwestern alberta was examined (may to october 2005). a large number of diarrheic individuals who were culture negative for c. jejuni (n = 54) or c. coli (n = 19) were pcr positive for these taxa. overall detection rates for c. jejuni and c. coli in diarrheic stools were 29% and 5%, respectively. in contrast, 3% and 0% of stools from healthy humans were positi ... | 2010 | 21106791 |
| partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities. | cystic fibrosis (cf) patients suffer from chronic bacterial lung infections that lead to death in the majority of cases. the need to maintain lung function in these patients means that characterising these infections is vital. increasingly, culture-independent analyses are expanding the number of bacterial species associated with cf respiratory samples; however, the potential significance of these species is not known. here, we applied ecological statistical tools to such culture-independent dat ... | 2010 | 21151003 |
| partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities. | cystic fibrosis (cf) patients suffer from chronic bacterial lung infections that lead to death in the majority of cases. the need to maintain lung function in these patients means that characterising these infections is vital. increasingly, culture-independent analyses are expanding the number of bacterial species associated with cf respiratory samples; however, the potential significance of these species is not known. here, we applied ecological statistical tools to such culture-independent dat ... | 2010 | 21151003 |
| taxonomy, epidemiology, and clinical relevance of the genus arcobacter. | the genus arcobacter, defined almost 20 years ago from members of the genus campylobacter, has become increasingly important because its members are being considered emergent enteropathogens and/or potential zoonotic agents. over recent years information that is relevant for microbiologists, especially those working in the medical and veterinary fields and in the food safety sector, has accumulated. recently, the genus has been enlarged with several new species. the complete genomes of arcobacte ... | 2011 | 21233511 |
| three cases of severe invasive infections caused by campylobacter rectus and first report of fatal c. rectus infection. | we report the first fatal case of campylobacter rectus infection due to a subdural empyema and ruptured mycotic intracranial aneurysm and two cases of limb-threatening c. rectus necrotizing soft tissue and bone infection and empyema thoracis that responded to amoxicillin-clavulanate and surgical debridement and drainage. all three strains were identified by 16s rrna sequencing. | 2011 | 21270212 |
| rna-oligonucleotide quantification technique (roqt) for the enumeration of uncultivated bacterial species in subgingival biofilms. | approximately 35% of the species present in subgingival biofilms are as yet uncultivated, so their role in periodontal pathogenesis is unknown. the aim of the present study was to develop a high throughput method to quantify a wide range of cultivated and uncultivated taxa in subgingival biofilm samples associated with periodontal disease or health. oligonucleotides targeting the 16s ribosomal dna gene were designed, synthesized and labeled with digoxigenin. these probes were hybridized with the ... | 2011 | 21375703 |
| automated identification of medically important bacteria by 16s rrna gene sequencing using a novel comprehensive database, 16spathdb. | despite the increasing use of 16s rrna gene sequencing, interpretation of 16s rrna gene sequence results is one of the most difficult problems faced by clinical microbiologists and technicians. to overcome the problems we encountered in the existing databases during 16s rrna gene sequence interpretation, we built a comprehensive database, 16spathdb (http://147.8.74.24/16spathdb) based on the 16s rrna gene sequences of all medically important bacteria listed in the manual of clinical microbiology ... | 2011 | 21389154 |
| comparative genotypic and pathogenic examination of campylobacter concisus isolates from diarrheic and non-diarrheic humans. | campylobacter concisus is an emerging enteric pathogen, yet it is commonly isolated from feces and the oral cavities of healthy individuals. this genetically complex species is comprised of several distinct genomospecies which may vary in pathogenic potential. | 2011 | 21406111 |
| characterization of polybacterial clinical samples using a set of group-specific broad-range primers targeting the 16s rrna gene followed by dna sequencing and ripseq analysis. | the standard use of a single universal broad-range pcr in direct 16s rdna sequencing from polybacterial samples leaves the minor constituents at risk of remaining undetected because all bacterial dna will be competing for the same reagents. in this article we introduce a set of three broad-range group-specific 16s rdna pcrs that together cover the clinically relevant bacteria and apply them in the investigation of 25 polybacterial clinical samples. mixed dna chromatograms from samples containing ... | 2011 | 21436365 |
| emerging thermotolerant campylobacter species in healthy ruminants and swine. | campylobacters other than campylobacter jejuni or c. coli were isolated in 35% of 343 farms recently analyzed in northern spain. this study was aimed at identifying at the species level the 120 isolates collected (21 ovine, 52 beef cattle, 44 dairy cattle, and 3 porcine) by species-specific polymerase chain reaction and 16s rrna gene sequencing analysis. thus, five species were identified: campylobacter hyointestinalis (90 isolates), campylobacter lanienae (12), campylobacter fetus subsp. fetus ... | 2011 | 21438765 |
| detection of campylobacter concisus and other campylobacter species in colonic biopsies from adults with ulcerative colitis. | the critical role of bacteria in the pathogenesis of ulcerative colitis (uc) is well recognized, but an individual causative microorganism has not been singled out so far. campylobacter concisus and other non-jejuni species of campylobacter have been implicated as putative aetiological agents in inflammatory bowel disease in children, but such studies have not been addressed in adults. this study investigated the prevalence of campylobacter species in colonic biopsy samples from adults with uc a ... | 2011 | 21738679 |
| mode of birth delivery affects oral microbiota in infants. | establishment of the microbiota of the gut has been shown to differ between infants delivered by caesarian section (c-section) and those delivered vaginally. the aim of the present study was to compare the oral microbiota in infants delivered by these different routes. the oral biofilm was assayed by the human oral microbe identification microarray (homim) in healthy three-month-old infants, 38 infants born by c-section, and 25 infants delivered vaginally. among over 300 bacterial taxa targeted ... | 2011 | 21828355 |
| sequencing and validation of the genome of a campylobacter concisus reveals intra-species diversity. | campylobacter concisus is an emerging pathogen of the human gastrointestinal tract. its role in different diseases remains a subject of debate; this may be due to strain to strain genetic variation. here, we sequence and analyze the genome of a c. concisus from a biopsy of a child with crohn's disease (unswcd); the second such genome for this species. a 1.8 mb genome was assembled with paired-end reads from a next-generation sequencer. this genome is smaller than the 2.1 mb c. concisus reference ... | 2011 | 21829448 |
| microbiota of severe early childhood caries before and after therapy. | severe early childhood caries (ecc) is difficult to treat successfully. this study aimed to characterize the microbiota of severe ecc and evaluate whether baseline or follow-up microbiotas are associated with new lesions post-treatment. plaque samples from 2- to 6-year-old children were analyzed by a 16s rrna-based microarray and by pcr for selected taxa. severe-ecc children were monitored for 12 months post-therapy. by microarray, species associated with severe-ecc (n = 53) compared with caries ... | 2011 | 21868693 |
| Oral and fecal Campylobacter concisus strains perturb barrier function by apoptosis induction in HT-29/B6 intestinal epithelial cells. | Campylobacter concisus infections of the gastrointestinal tract can be accompanied by diarrhea and inflammation, whereas colonization of the human oral cavity might have a commensal nature. We focus on the pathophysiology of C. concisus and the effects of different clinical oral and fecal C. concisus strains on human HT-29/B6 colon cells. Six oral and eight fecal strains of C. concisus were isolated. Mucus-producing HT-29/B6 epithelial monolayers were infected with the C. concisus strains. Trans ... | 2011 | 21887334 |
| prevalence of campylobacter species in adult crohn's disease and the preferential colonization sites of campylobacter species in the human intestine. | crohn's disease (cd) and ulcerative colitis (uc) are the two major forms of inflammatory bowel disease (ibd). a high prevalence of campylobacter concisus was previously detected in paediatric cd and adult uc. currently, the prevalence of c. concisus in adult cd and the preferential colonization sites of campylobacter species in the human intestine are unknown. in this study, we examined the prevalence of campylobacter species in biopsies collected from multiple anatomic sites of adult patients w ... | 2011 | 21966525 |
| comparative analyses of campylobacter concisusstrains reveal the genome of the reference strain baa-1457 is not representative of the species. | abstract: | 2011 | 21992484 |
| Comparative Genomics of Helicobacter pylori and the human-derived Helicobacter bizzozeronii CIII-1 strain reveal the molecular basis of the zoonotic nature of non-pylori gastric Helicobacter infections in humans. | ABSTRACT: | 2011 | 22039924 |
| new approaches for isolation of previously uncultivated oral bacteria. | a significant number of microorganisms from the human oral cavity remain uncultivated. this is a major impediment to the study of human health since some of the uncultivated species may be involved in a variety of systemic diseases. we used a range of innovations previously developed to cultivate microorganisms from the human oral cavity, focusing on anaerobic species. these innovations include (i) in vivo cultivation to specifically enrich for species actively growing in the oral cavity (the "m ... | 2012 | 22057871 |
| a comprehensive evaluation of colonic mucosal isolates of sutterella wadsworthensis from inflammatory bowel disease. | inflammatory bowel disease (ibd) arises in genetically susceptible individuals as a result of an unidentified environmental trigger, possibly a hitherto unknown bacterial pathogen. twenty-six clinical isolates of sutterella wadsworthensis were obtained from 134 adults and 61 pediatric patients undergoing colonoscopy, of whom 69 and 29 respectively had ibd. s. wadsworthensis was initially more frequently isolated from ibd subjects, hence this comprehensive study was undertaken to elucidate its ro ... | 2011 | 22073125 |
| immunoreactive proteins of campylobacter concisus, an emergent intestinal pathogen. | campylobacter concisus is an emerging pathogen of the human gastrointestinal tract. recently, a significantly higher prevalence of c. concisus dna and higher levels of antibodies specific to c. concisus was detected in children with crohn's disease when compared with controls. the aim of this study was to identify c. concisus immunoreactive antigens. proteins from c. concisus were separated using two-dimensional gel electrophoresis, and sera from 10 c. concisus-positive children with crohn's dis ... | 2011 | 22092566 |
| pathogenic potential of campylobacter ureolyticus. | the recent detection and isolation of the aflagellate campylobacter ureolyticus (previously known as bacteroides ureolyticus) from intestinal biopsy specimens and fecal samples of children with newly diagnosed crohn's disease led us to investigate the pathogenic potential of this bacterium. adherence and gentamicin protection assays were employed to quantify the levels of adherence to and invasion into host cells. c. ureolyticus unswcd was able to adhere to the caco-2 intestinal epithelial cell ... | 2011 | 22124656 |
| correlation network analysis applied to complex biofilm communities. | the complexity of the human microbiome makes it difficult to reveal organizational principles of the community and even more challenging to generate testable hypotheses. it has been suggested that in the gut microbiome species such as bacteroides thetaiotaomicron are keystone in maintaining the stability and functional adaptability of the microbial community. in this study, we investigate the interspecies associations in a complex microbial biofilm applying systems biology principles. using corr ... | 2011 | 22163302 |
| occurrence of putative virulence genes in arcobacter species isolated from humans and animals. | interest for arcobacters in veterinary and human public health has increased since the first report of the isolation of arcobacters from food of animal origin. since then, studies worldwide have reported the occurrence of arcobacters on food and in food-production animals and have highlighted the possible transmission of especially a. butzleri to the human population. in humans, arcobacters are associated with enteritis and septicemia. to assess their clinical relevance for humans and animals, e ... | 2011 | 22170914 |
| rifaximin in the treatment of inflammatory bowel disease. | the gut microbiota plays a role in promoting and maintaining inflammation in inflammatory bowel diseases (ibd), hence the rationale for the use of antibiotics in the treatment of those disorders. antibiotics, however, may induce untoward effects, especially during long-term therapy. rifaximin α polymer is an antibacterial agent that is virtually unabsorbed after oral administration and is devoid of systemic side effects. rifaximin has provided promising results in inducing remission of crohn's d ... | 2011 | 22180705 |
| the pathogenic potential of campylobacter concisus strains associated with chronic intestinal diseases. | campylobacter concisus has garnered increasing attention due to its association with intestinal disease, thus, the pathogenic potential of strains isolated from different intestinal diseases was investigated. a method to isolate c. concisus was developed and the ability of eight strains from chronic and acute intestinal diseases to adhere to and invade intestinal epithelial cells was determined. features associated with bacterial invasion were investigated using comparative genomic analyses and ... | 2011 | 22194985 |
| gastroenteritis caused by campylobacter concisus. | we describe a case of gastroenteritis caused by campylobacter concisus. the pathogenic potential of c. concisus has yet to be elucidated. recent studies indicate an association with enteric disease in immunocompromised patients and inflammatory bowel disease in children. molecular identification methods may be necessary for identifying certain campylobacter species because of phenotypic similarity. | 2012 | 22301611 |
| the influence of iron availability on human salivary microbial community composition. | it is a well-recognized fact that the composition of human salivary microbial community is greatly affected by its nutritional environment. however, most studies are currently focused on major carbon or nitrogen sources with limited attention to trace elements like essential mineral ions. in this study, we examined the effect of iron availability on the bacterial profiles of an in vitro human salivary microbial community as iron is an essential trace element for the survival and proliferation of ... | 2012 | 22318873 |
| ibd-what role do proteobacteria play? | the gastrointestinal microbiota has come to the fore in the search for the causes of ibd. this shift has largely been driven by the finding of genetic polymorphisms involved in gastrointestinal innate immunity (particularly polymorphisms in nod2 and genes involved in autophagy) and alterations in the composition of the microbiota that might result in inflammation (so-called dysbiosis). microbial diversity studies have continually demonstrated an expansion of the proteobacteria phylum in patients ... | 2012 | 22349170 |
| characterization of the structurally diverse n-linked glycans of campylobacter species. | the gram-negative bacterium campylobacter jejuni encodes an extensively characterized n-linked protein glycosylation system that modifies many surface proteins with a heptasaccharide glycan. in c. jejuni, the genes that encode the enzymes required for glycan biosynthesis and transfer to protein are located at a single pgl gene locus. similar loci are also present in the genome sequences of all other campylobacter species, although variations in gene content and organization are evident. in this ... | 2012 | 22389484 |
| microbial community succession on developing lesions on human enamel. | dental caries is one of the most common diseases in the world. however, our understanding of how the microbial community composition changes in vivo as caries develops is lacking. | 2012 | 22432048 |
| xer recombinase and genome integrity in helicobacter pylori, a pathogen without topoisomerase iv. | in the model organism e. coli, recombination mediated by the related xerc and xerd recombinases complexed with the ftsk translocase at specialized dif sites, resolves dimeric chromosomes into free monomers to allow efficient chromosome segregation at cell division. computational genome analysis of helicobacter pylori, a slow growing gastric pathogen, identified just one chromosomal xer gene (xerh) and its cognate dif site (difh). here we show that recombination between directly repeated difh sit ... | 2012 | 22511919 |
| high incidence of campylobacter concisus in gastroenteritis in north jutland, denmark: a population-based study. | the incidence of non-thermophilic campylobacter species was assessed in an unselected population-based study in a mixed urban and rural community in north jutland, denmark. in a 2-year study period, 11,314 faecal samples from 8302 patients with gastroenteritis were cultured with supplement of the filter method. we recovered a high incidence of campylobacter concisus (annual incidence 35/100,000 inhabitants), almost as high as the common campylobacter jejuni/coli. in contrast, there was a very lo ... | 2013 | 22512739 |
| molecular characterization of the 16s rrna gene of helicobacter fennelliae isolated from stools and blood cultures from paediatric patients in south africa. | forty strains of h. fennelliae collected from paediatric blood and stool samples over an 18 year period at a children's hospital in cape town, south africa, were amplified by pcr of the 16s rrna. two distinct genotypes of h. fennelliae were identified based on the phylogenetic analysis. this was confirmed by sequencing a portion of the beta subunit of the rna polymerase (rpob) gene. all isolates from south africa clustered with a proposed novel helicobacter strain (accession number af237612) iso ... | 2010 | 22567323 |
| molecular characterization of the 16s rrna gene of helicobacter fennelliae isolated from stools and blood cultures from paediatric patients in south africa. | forty strains of h. fennelliae collected from paediatric blood and stool samples over an 18 year period at a children's hospital in cape town, south africa, were amplified by pcr of the 16s rrna. two distinct genotypes of h. fennelliae were identified based on the phylogenetic analysis. this was confirmed by sequencing a portion of the beta subunit of the rna polymerase (rpob) gene. all isolates from south africa clustered with a proposed novel helicobacter strain (accession number af237612) iso ... | 2010 | 22567323 |
| the role of bacteria in the pathogenesis of ulcerative colitis. | factors implicated in the pathophysiology of ulcerative colitis (uc) are an abnormal immune response, defect in intestinal epithelial barrier function, and gut microbiota. currently, it is unclear whether specific bacterial strains are responsible for the induction of intestinal inflammation, but increased bacterial tissue invasion has been described in affected uc patients. further, a quantitative and qualitative microbial imbalance in uc, defined as dysbiosis, has been characterized by an incr ... | 2012 | 22619714 |
| investigation of the enteric pathogenic potential of oral campylobacter concisus strains isolated from patients with inflammatory bowel disease. | campylobacter concisus, a bacterium colonizing the human oral cavity, has been shown to be associated with inflammatory bowel disease (ibd). this study investigated if patients with ibd are colonized with specific oral c. concisus strains that have potential to cause enteric diseases. | 2012 | 22666490 |
| microbial dysbiosis in pediatric patients with crohn's disease. | microbial dysbiosis has been suggested to be involved in the pathogenesis of crohn's disease (cd); however, many studies of gut microbial communities have been confounded by environmental and patient-related factors. in this study, the microbial flora of fecal samples from 19 children newly diagnosed with cd and 21 age-matched controls were analyzed using high-throughput sequencing to determine differences in the microbial composition between cd patients and controls. analysis of the microbial c ... | 2012 | 22837318 |
| evidence of an increased pathogenic footprint in the lingual microbiome of untreated hiv infected patients. | opportunistic oral infections can be found in over 80% of hiv + patients, often causing debilitating lesions that also contribute to deterioration in nutritional health. although appreciation for the role that the microbiota is likely to play in the initiation and/or enhancement of oral infections has grown considerably in recent years, little is known about the impact of hiv infection on host-microbe interactions within the oral cavity. in the current study, we characterize modulations in the b ... | 2012 | 22838383 |
| proteomics of protein secretion by aggregatibacter actinomycetemcomitans. | the extracellular proteome (secretome) of periodontitis-associated bacteria may constitute a major link between periodontitis and systemic diseases. to obtain an overview of the virulence potential of aggregatibacter actinomycetemcomitans, an oral and systemic human pathogen implicated in aggressive periodontitis, we used a combined lc-ms/ms and bioinformatics approach to characterize the secretome and protein secretion pathways of the rough-colony serotype a strain d7s. lc-ms/ms revealed 179 pr ... | 2012 | 22848560 |
| microbiological characterization in children with aggressive periodontitis. | the objective of this study was to characterize the subgingival microbiota of african-american children with localized aggressive periodontitis (lap). fifty-one children were included. subgingival plaque samples were taken from diseased (dd) and healthy sites (dh) in lap and from healthy sites in hs and hc and analyzed by 16s rrna-based microarrays. aggregatibacter actinomycetemcomitans (aa) was the only species found to be both more prevalent (or = 8.3, p = 0.0025) and abundant (p < 0.01) in dd ... | 2012 | 22863892 |
| short-term and medium-term clinical outcomes of campylobacter concisus infection. | there are only sparse data on the short-term and medium-term clinical impacts of campylobacter concisus infection. a clinical study was performed during a 2-year period to determine the clinical manifestations in c. concisus-positive adult patients. a case patient was defined as an adult patient (≥18 years) with a c. concisus-positive stool sample during the study period. clinical data were obtained with use of a questionnaire supplemented with the patients' medical records, if any. the short-te ... | 2012 | 22882347 |
| campylobacter concisus - a new player in intestinal disease. | over the last decade campylobacter concisus, a highly fastidious member of the campylobacter genus has been described as an emergent pathogen of the human intestinal tract. historically, c. concisus was associated with the human oral cavity and has been linked with periodontal lesions, including gingivitis and periodontitis, although currently its role as an oral pathogen remains contentious. evidence to support the role of c. concisus in acute intestinal disease has come from studies that have ... | 2012 | 22919596 |
| multilocus sequence typing methods for the emerging campylobacter species c. hyointestinalis, c. lanienae, c. sputorum, c. concisus, and c. curvus. | multilocus sequence typing (mlst) systems have been reported previously for multiple food- and food animal-associated campylobacter species (e.g., c. jejuni, c. coli, c. lari, and c. fetus) to both differentiate strains and identify clonal lineages. these mlst methods focused primarily on campylobacters of human clinical (e.g., c. jejuni) or veterinary (e.g., c. fetus) relevance. however, other, emerging, campylobacter species have been isolated increasingly from environmental, food animal, or h ... | 2012 | 22919636 |
| a reproducible oral microcosm biofilm model for testing dental materials. | most studies of biofilm effects on dental materials use single-species biofilms, or consortia. microcosm biofilms grown directly from saliva or plaque are much more diverse, but difficult to characterize. we used the human oral microbial identification microarray (homim) to validate a reproducible oral microcosm model. | 2012 | 22925110 |
| oral microbial profile discriminates breast-fed from formula-fed infants. | little is known about the effect of diet on the oral microbiota of infants, although diet is known to affect the gut microbiota. the aims of the present study were to compare the oral microbiota in breast-fed and formula-fed infants, and investigate growth inhibition of streptococci by infant-isolated lactobacilli. | 2013 | 22955450 |
| detection of campylobacter species and arcobacter butzleri in stool samples by use of real-time multiplex pcr. | the presence of campylobacter (or campylobacter-like) species in stools from patients suspected of infectious gastroenteritis (n = 493) was investigated using real-time pcr for detection of arcobacter butzleri (hsp60 gene), campylobacter coli (ceue gene), campylobacter jejuni (mapa), five acknowledged pathogenic campylobacter spp. (c16s_lund assay), and the campylobacter genus (c16s_lvi assay). in total, 71.4% of the samples were positive for campylobacter dna (n = 352) by a campylobacter genus- ... | 2013 | 23152553 |
| phylogenetic identification of bacterial mazf toxin protein motifs among probiotic strains and foodborne pathogens and potential implications of engineered probiotic intervention in food. | 2012 | 23186337 | |
| investigation of motility and biofilm formation by intestinal campylobacter concisus strains. | motility helps many pathogens swim through the highly viscous intestinal mucus. given the differing outcomes of campylobacter concisus infection, the motility of eight c. concisus strains isolated from patients with crohn's disease (n=3), acute (n=3) and chronic (n=1) gastroenteritis and a healthy control (n=1) were compared. following growth on solid or liquid media the eight strains formed two groups; however, the type of growth medium did not affect motility. in contrast, following growth in ... | 2012 | 23241133 |
| research advances in the study of campylobacter, helicobacter, and related organisms. | 2012 | 23267439 | |
| comparative characterization of the virulence gene clusters (lipooligosaccharide [los] and capsular polysaccharide [cps]) for campylobacter coli, campylobacter jejuni subsp. jejuni and related campylobacter species. | campylobacter jejuni subsp. jejuni and campylobacter coli are leading causes of gastroenteritis, with virulence linked to cell surface carbohydrate diversity. although the associated gene clusters are well studied for c. jejuni subsp. jejuni, c. coli has been largely neglected. here we provide comparative analysis of the lipooligosaccharide (los) and capsular polysaccharide (cps) gene clusters, using genome and cluster sequence data for 36 c. coli strains, 67 c. jejuni subsp. jejuni strains and ... | 2012 | 23279811 |
| comparative characterization of the virulence gene clusters (lipooligosaccharide [los] and capsular polysaccharide [cps]) for campylobacter coli, campylobacter jejuni subsp. jejuni and related campylobacter species. | campylobacter jejuni subsp. jejuni and campylobacter coli are leading causes of gastroenteritis, with virulence linked to cell surface carbohydrate diversity. although the associated gene clusters are well studied for c. jejuni subsp. jejuni, c. coli has been largely neglected. here we provide comparative analysis of the lipooligosaccharide (los) and capsular polysaccharide (cps) gene clusters, using genome and cluster sequence data for 36 c. coli strains, 67 c. jejuni subsp. jejuni strains and ... | 2012 | 23279811 |
| methods of combinatorial optimization to reveal factors affecting gene length. | in this paper we present a novel method for genome ranking according to gene lengths. the main outcomes described in this paper are the following: the formulation of the genome ranking problem, presentation of relevant approaches to solve it, and the demonstration of preliminary results from prokaryotic genomes ordering. using a subset of prokaryotic genomes, we attempted to uncover factors affecting gene length. we have demonstrated that hyperthermophilic species have shorter genes as compared ... | 2012 | 23300345 |
| immunoproteomics: the key to discovery of new vaccine antigens against bacterial respiratory infections. | the increase in antibiotic resistance and the shortage of new antimicrobials to prevent difficult bacterial infections underlines the importance of prophylactic therapies to prevent infection by bacterial pathogens. vaccination has reduced the incidence of many serious diseases, including respiratory bacterial infections. however, there are many pathogens for which no vaccine is available and some vaccines are not effective among all age groups or among immunocompromised individuals. immunoprote ... | 2012 | 23305366 |
| metamos: a modular and open source metagenomic assembly and analysis pipeline. | we describe metamos, an open source and modular metagenomic assembly and analysis pipeline. metamos represents an important step towards fully automated metagenomic analysis, starting with next-generation sequencing reads and producing genomic scaffolds, open-reading frames and taxonomic or functional annotations. metamos can aid in reducing assembly errors, commonly encountered when assembling metagenomic samples, and improves taxonomic assignment accuracy while also reducing computational cost ... | 2013 | 23320958 |
| bacterial protein n-glycosylation: new perspectives and applications. | protein glycosylation is widespread throughout all three domains of life. bacterial protein n-glycosylation and its application to engineering recombinant glycoproteins continue to be actively studied. here, we focus on advances made in the last 2 years, including the characterization of novel bacterial n-glycosylation pathways, examination of pathway enzymes and evolution, biological roles of protein modification in the native host, and exploitation of the n-glycosylation pathways to create nov ... | 2013 | 23329827 |
| assessment of the prevalence and diversity of emergent campylobacteria in human stool samples using a combination of traditional and molecular methods. | this study aims to assess the diversity of campylobacteria (campylobacter and arcobacter) in human fecal samples from patients with diarrhea (n = 140) and asymptomatic controls (n = 116) in chile, using a combination of traditional culture and molecular methods. the culture methods detected campylobacteria in 10.7% of the patients with diarrhea and in 1.7% of the controls. in contrast, the molecular methods detected campylobacteria more often than the traditional culture, with a prevalence of 25 ... | 2013 | 23375869 |
| the effects of oral and enteric campylobacter concisus strains on expression of tlr4, md-2, tlr2, tlr5 and cox-2 in ht-29 cells. | campylobacter concisus, a gram-negative bacterium that colonizes the human oral cavity, has been shown to be associated with inflammatory bowel diseases (ibd). the effects of different c. concisus strains on intestinal epithelial expression of toll like receptors (tlr) have not been investigated. this study examined the effects of c. concisus strains isolated from patients with ibd and controls on expression of tlr4, its co-receptor myeloid differentiation factor (md)-2; tlr2, tlr5, cyclooxygena ... | 2013 | 23437263 |
| evaluation of fecal calprotectin in campylobacter concisus and campylobacter jejuni/coli gastroenteritis. | calprotectin (cp) is a calcium-binding cytosolic neutrophil protein and the concentration in feces reflects the migration of neutrophils into the gut lumen. testing for fecal cp (f-cp) in patients with negative cultures for enteric pathogens is widely accepted as a useful screening tool for identifying patients who are most likely to benefit from endoscopy for suspected inflammatory bowel disease (ibd) with the assumption that a negative f-cp is compatible with a functional disorder. campylobact ... | 2013 | 23448294 |
| presence of campylobacter and arcobacter species in in-line milk filters of farms authorized to produce and sell raw milk and of a water buffalo dairy farm in italy. | the objectives of this study were to investigate the presence of campylobacter spp. and arcobacter spp. in dairy herds authorized for the production and sale of raw milk and in a water buffalo dairy farm, and to test the antimicrobial susceptibility of the isolates. a total of 196 in-line milk filters were collected from 14 dairy farms (13 bovine and 1 water buffalo) for detection of campylobacter spp. and arcobacter spp. by microbiological culture. for each farm investigated, 1 isolate for each ... | 2013 | 23453517 |
| immune status, antibiotic medication and ph are associated with changes in the stomach fluid microbiota. | the stomach acts as a barrier to ingested microbes, thereby influencing the microbial ecology of the entire gastrointestinal (gi) tract. the stomach microbiota and the role of human host and environmental factors, such as health status or medications, in shaping its composition remain largely unknown. we sought to characterize the bacterial and fungal microbiota in the stomach fluid in order to gain insights into the role of the stomach in gi homeostasis. gastric fluid was collected from 25 pati ... | 2013 | 23466701 |
| occurrence and characteristics of fastidious campylobacteraceae species in porcine samples. | this study investigated the prevalence and characteristics of campylobacteraceae including a range of fastidious species in porcine samples. over a thirteen month period caecal contents (n=402) and pork carcass swabs (n=401) were collected from three pork abattoirs and pork products (n=399) were purchased at point of sale in the republic of ireland. campylobacteraceae isolates were recovered by enrichment, membrane filtration and incubation in antibiotic free media under a modified atmosphere (3 ... | 2013 | 23474652 |
| the dental plaque microbiome in health and disease. | dental decay is one of the most prevalent chronic diseases worldwide. a variety of factors, including microbial, genetic, immunological, behavioral and environmental, interact to contribute to dental caries onset and development. previous studies focused on the microbial basis for dental caries have identified species associated with both dental health and disease. the purpose of the current study was to improve our knowledge of the microbial species involved in dental caries and health by perfo ... | 2013 | 23520516 |
| the microaerophilic microbiota of de-novo paediatric inflammatory bowel disease: the biscuit study. | children presenting for the first time with inflammatory bowel disease (ibd) offer a unique opportunity to study aetiological agents before the confounders of treatment. microaerophilic bacteria can exploit the ecological niche of the intestinal epithelium; helicobacter and campylobacter are previously implicated in ibd pathogenesis. we set out to study these and other microaerophilic bacteria in de-novo paediatric ibd. | 2013 | 23554935 |
| a culture-independent sequence-based metagenomics approach to the investigation of an outbreak of shiga-toxigenic escherichia coli o104:h4. | identification of the bacterium responsible for an outbreak can aid in disease management. however, traditional culture-based diagnosis can be difficult, particularly if no specific diagnostic test is available for an outbreak strain. | 2013 | 23571589 |
| oesophageal bacterial biofilm changes in gastro-oesophageal reflux disease, barrett's and oesophageal carcinoma: association or causality? | barrett's oesophagus (bo) and gastro-oesophageal reflux disease (gerd) are precursors of oesophageal adenocarcinoma (oac). there is an oesophageal biofilm, which changes in disease, but its role in aetiopathogenesis remains unclear. | 2013 | 23600758 |
| microbial biofilms and gastrointestinal diseases. | the majority of bacteria live not planktonically, but as residents of sessile biofilm communities. such populations have been defined as 'matrix-enclosed microbial accretions, which adhere to both biological and nonbiological surfaces'. bacterial formation of biofilm is implicated in many chronic disease states. growth in this mode promotes survival by increasing community recalcitrance to clearance by host immune effectors and therapeutic antimicrobials. the human gastrointestinal (gi) tract en ... | 2013 | 23620117 |
| the role of epsilonproteobacteria in children with gastroenteritis. | a polymerase chain reaction-denaturing gradient gel electrophoresis method was used to examine 50 stool samples from children in belgium with gastroenteritis for an extensive range of epsilonproteobacteria species. during the 3-month study period, campylobacter concisus was the most common species. our observations suggest that c. concisus displays similar microbiologic and clinical features as campylobacter jejuni. | 2013 | 23624432 |
| mobile microbiome: oral bacteria in extra-oral infections and inflammation. | the link between oral infections and adverse systemic conditions has attracted much attention in the research community. several mechanisms have been proposed, including spread of the oral infection due to transient bacteremia resulting in bacterial colonization in extra-oral sites, systemic injury by free toxins of oral pathogens, and systemic inflammation caused by soluble antigens of oral pathogens. mounting evidence supports a major role of the systemic spread of oral commensals and pathogen ... | 2013 | 23625375 |
| rapid 16s rrna next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections. | classifying individual bacterial species comprising complex, polymicrobial patient specimens remains a challenge for culture-based and molecular microbiology techniques in common clinical use. we therefore adapted practices from metagenomics research to rapidly catalog the bacterial composition of clinical specimens directly from patients, without need for prior culture. we have combined a semiconductor deep sequencing protocol that produces reads spanning 16s ribosomal rna gene variable regions ... | 2013 | 23734239 |
| comparison of polycarbonate and cellulose acetate membrane filters for isolation of campylobacter concisus from stool samples. | one thousand seven hundred ninety-one diarrheic stool samples were cultivated for campylobacter spp. we found a high prevalence of campylobacter concisus with use of a polycarbonate filter (n = 114) compared to a cellulose acetate filter (n = 79) (p < .0001). the polycarbonate filter is superior to the commonly used cellulose acetate filter for detection of c. concisus. | 2013 | 23743174 |
| clinical manifestations of campylobacter concisus infection in children. | there is only sparse information about the clinical impact of campylobacter concisus infections in children. | 2013 | 23743545 |
| predictive, preventive, personalised and participatory periodontology: 'the 5ps age' has already started. | an impressive progress in dentistry has been recorded in the last decades. in order to reconsider guidelines in dentistry, it is required to introduce new concepts of personalised patient treatments: the wave of predictive, preventive and personalised medicine is rapidly incoming in dentistry. worldwide dentists have to make a big cultural effort in changing the actual 'reactive' therapeutic point of view, belonging to the last century, into a futuristic 'predictive' one. the first cause of toot ... | 2013 | 23763842 |
| a consortium of aggregatibacter actinomycetemcomitans, streptococcus parasanguinis, and filifactor alocis is present in sites prior to bone loss in a longitudinal study of localized aggressive periodontitis. | aggregatibacter actinomycetemcomitans-induced localized aggressive periodontitis (lap) in african-american adolescents has been documented but is poorly understood. two thousand fifty-eight adolescents aged 11 to 17 years were screened for their periodontal status and the presence of a. actinomycetemcomitans in their oral cavity. seventy-one a. actinomycetemcomitans-negative and 63 a. actinomycetemcomitans-positive periodontally healthy subjects were enrolled, sampled, examined, and radiographed ... | 2013 | 23784124 |
| neutrophil activation by campylobacter concisus. | campylobacter concisus is an emerging enteric pathogen associated with prolonged diarrhoea and possibly inflammatory bowel disease in children as well as adults, but the interaction with cells of the innate immune system is unclear. the magnitude of systemic immunoglobulin response in acute infection is unknown. | 2013 | 23819746 |
| functional relationship between campylobacter concisus and the stomach ecosystem in health and disease. | 2013 | 23823497 | |
| duodenal-mucosal bacteria associated with celiac disease in children. | celiac disease (cd) is an immune-mediated enteropathy triggered by the ingestion of cereal gluten proteins. this disorder is associated with imbalances in the gut microbiota composition that could be involved in the pathogenesis of cd. the aim of this study was to characterize the composition and diversity of the cultivable duodenal mucosa-associated bacteria of cd patients and control children. duodenal biopsy specimens from patients with active disease on a gluten-containing diet (n = 32), pat ... | 2013 | 23835180 |
| subglacial lake vostok (antarctica) accretion ice contains a diverse set of sequences from aquatic, marine and sediment-inhabiting bacteria and eukarya. | lake vostok, the 7(th) largest (by volume) and 4(th) deepest lake on earth, is covered by more than 3,700 m of ice, making it the largest subglacial lake known. the combination of cold, heat (from possible hydrothermal activity), pressure (from the overriding glacier), limited nutrients and complete darkness presents extreme challenges to life. here, we report metagenomic/metatranscriptomic sequence analyses from four accretion ice sections from the vostok 5g ice core. two sections accreted in t ... | 2013 | 23843994 |
| nitrate ammonification by nautilia profundicola amh: experimental evidence consistent with a free hydroxylamine intermediate. | the process of nitrate reduction via nitrite controls the fate and bioavailability of mineral nitrogen within ecosystems; i.e., whether it is retained as ammonium (ammonification) or lost as nitrous oxide or dinitrogen (denitrification). here, we present experimental evidence for a novel pathway of microbial nitrate reduction, the reverse hydroxylamine:ubiquinone reductase module (reverse-hurm) pathway. instead of a classical ammonia-forming nitrite reductase that performs a 6 electron-transfer ... | 2013 | 23847604 |