| the interplay between campylobacter and helicobacter species and other gastrointestinal microbiota of commercial broiler chickens. | poultry represent an important source of foodborne enteropathogens, in particular thermophilic campylobacter species. many of these organisms colonize the intestinal tract of broiler chickens as harmless commensals, and therefore, often remain undetected prior to slaughter. the exact reasons for the lack of clinical disease are unknown, but analysis of the gastrointestinal microbiota of broiler chickens may improve our understanding of the microbial interactions with the host. | 2014 | 24940386 |
| 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 |
| comparative genomics of campylobacter concisus isolates reveals genetic diversity and provides insights into disease association. | in spite of its association with gastroenteritis and inflammatory bowel diseases, the isolation of campylobacter concisus from both diseased and healthy individuals has led to controversy regarding its role as an intestinal pathogen. one proposed reason for this is the presence of high genetic diversity among the genomes of c. concisus strains. | 2013 | 23984967 |
| research advances in the study of campylobacter, helicobacter, and related organisms. | | 2012 | 23267439 |
| 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 |
| comprehensive genomic characterization of campylobacter genus reveals some underlying mechanisms for its genomic diversification. | campylobacter species.are phenotypically diverse in many aspects including host habitats and pathogenicities, which demands comprehensive characterization of the entire campylobacter genus to study their underlying genetic diversification. up to now, 34 campylobacter strains have been sequenced and published in public databases, providing good opportunity to systemically analyze their genomic diversities. in this study, we first conducted genomic characterization, which includes genome-wide alig ... | 2013 | 23940551 |
| 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 |
| 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 |
| global epidemiology of campylobacter infection. | campylobacter jejuni infection is one of the most widespread infectious diseases of the last century. the incidence and prevalence of campylobacteriosis have increased in both developed and developing countries over the last 10 years. the dramatic increase in north america, europe, and australia is alarming, and data from parts of africa, asia, and the middle east indicate that campylobacteriosis is endemic in these areas, especially in children. in addition to c. jejuni, there is increasing rec ... | 2015 | 26062576 |
| microbial profiles and detection techniques in peri-implant diseases: a systematic review. | to describe the microbial profiles of peri-implant diseases and the main detection methods. | 2016 | 27833735 |
| 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 |
| molecular diagnosis of actinomadura madurae infection by 16s rrna deep sequencing. | next-generation dna sequencing can be used to catalog individual organisms within complex, polymicrobial specimens. here, we utilized deep sequencing of 16s rrna to implicate actinomadura madurae as the cause of mycetoma in a diabetic patient when culture and conventional molecular methods were overwhelmed by overgrowth of other organisms. | 2013 | 24108607 |
| intestinal microbiota pathogenesis and fecal microbiota transplantation for inflammatory bowel disease. | the intestinal microbiota plays an important role in inflammatory bowel disease (ibd). the pathogenesis of ibd involves inappropriate ongoing activation of the mucosal immune system driven by abnormal intestinal microbiota in genetically predisposed individuals. however, there are still no definitive microbial pathogens linked to the onset of ibd. the composition and function of the intestinal microbiota and their metabolites are indeed disturbed in ibd patients. the special alterations of gut m ... | 2014 | 25356041 |
| deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes. | proteins of unknown function belonging to cog1816 and cog0402 were characterized. sav2595 from steptomyces avermitilis ma-4680, acel0264 from acidothermus cellulolyticus 11b, nis0429 from nitratiruptor sp. sb155-2 and dr0824 from deinococcus radiodurans r1 were cloned, purified, and their substrate profiles determined. these enzymes were previously incorrectly annotated as adenosine deaminases or chlorohydrolases. it was shown here that these enzymes actually deaminate 6-aminodeoxyfutalosine. th ... | 2013 | 23972005 |
| the cell shape-determining csd6 protein from helicobacter pylori constitutes a new family of l,d-carboxypeptidase. | helicobacter pylori causes gastrointestinal diseases, including gastric cancer. its high motility in the viscous gastric mucosa facilitates colonization of the human stomach and depends on the helical cell shape and the flagella. in h. pylori, csd6 is one of the cell shape-determining proteins that play key roles in alteration of cross-linking or by trimming of peptidoglycan muropeptides. csd6 is also involved in deglycosylation of the flagellar protein flaa. to better understand its function, b ... | 2015 | 26306031 |
| oral campylobacter species: initiators of a subgroup of inflammatory bowel disease? | in recent years, a number of studies detected a significantly higher prevalence of campylobacter species such as campylobacter concisus (c. concisus) in intestinal biopsies and fecal samples collected from patients with inflammatory bowel disease (ibd) compared to controls. most of these campylobacter species are not of zoonotic origin but are human oral campylobacter species. bacterial species usually cause diseases in the location where they colonize. however, c. concisus and other oral campyl ... | 2015 | 26309350 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| novel drug targets for food-borne pathogen campylobacter jejuni: an integrated subtractive genomics and comparative metabolic pathway study. | campylobacters are a major global health burden and a cause of food-borne diarrheal illness and economic loss worldwide. in developing countries, campylobacter infections are frequent in children under age two and may be associated with mortality. in developed countries, they are a common cause of bacterial diarrhea in early adulthood. in the united states, antibiotic resistance against campylobacter is notably increased from 13% in 1997 to nearly 25% in 2011. novel drug targets are urgently nee ... | 2015 | 26061459 |
| 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 |
| 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 |
| 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 |
| campylobacter concisus pseudo-outbreak caused by improved culture conditions. | an unusual increase in the number of campylobacter concisus isolates found in stool cultures provoked an outbreak investigation at bern university hospital. no epidemiological links were found between the cases, and the campylobacter isolates were clonally unrelated. a change in culture conditions to a hydrogen-rich atmosphere enhancing growth of c. concisus was deemed responsible for this pseudo-outbreak. | 2014 | 25411171 |
| campylobacter concisus pseudo-outbreak caused by improved culture conditions. | an unusual increase in the number of campylobacter concisus isolates found in stool cultures provoked an outbreak investigation at bern university hospital. no epidemiological links were found between the cases, and the campylobacter isolates were clonally unrelated. a change in culture conditions to a hydrogen-rich atmosphere enhancing growth of c. concisus was deemed responsible for this pseudo-outbreak. | 2014 | 25411171 |
| biofilm community diversity after exposure to 0·4% stannous fluoride gels. | to test the effect of 0·4% stannous fluoride (snf2 ) glycerine-based gels on specific portions of the bacterial community in both a clinical observational study and in vitro multispecies plaque-derived (mspd) biofilm model. | 2014 | 25263195 |
| a cationic cysteine-hydrazide as an enrichment tool for the mass spectrometric characterization of bacterial free oligosaccharides. | in campylobacterales and related ε-proteobacteria with n-linked glycosylation (nlg) pathways, free oligosaccharides (fos) are released into the periplasmic space from lipid-linked precursors by the bacterial oligosaccharyltransferase (pglb). this hydrolysis results in the same molecular structure as the oligosaccharide that is transferred to a protein to be glycosylated. this allowed for the general elucidation of the fos-branched structures and monosaccharides from a number of species using sta ... | 2015 | 26100547 |
| taxonomic identification of ruminal epithelial bacterial diversity during rumen development in goats. | understanding of the colonization process of epithelial bacteria attached to the rumen tissue during rumen development is very limited. ruminal epithelial bacterial colonization is of great significance for the relationship between the microbiota and the host and can influence the early development and health of the host. miseq sequencing of 16s rrna genes and quantitative real-time pcr (qpcr) were applied to characterize ruminal epithelial bacterial diversity during rumen development in this st ... | 2015 | 25769827 |
| dissecting the interplay between intestinal microbiota and host immunity in health and disease: lessons learned from germfree and gnotobiotic animal models. | this review elaborates the development of germfree and gnotobiotic animal models and their application in the scientific field to unravel mechanisms underlying host-microbe interactions and distinct diseases. strictly germfree animals are raised in isolators and not colonized by any organism at all. the germfree state is continuously maintained by birth, raising, housing and breeding under strict sterile conditions. however, isolator raised germfree mice are exposed to a stressful environment an ... | 2016 | 27980855 |
| examination of the anaerobic growth of campylobacter concisus strains. | campylobacter concisus is an oral bacterium that is associated with intestinal diseases. c. concisus was previously described as a bacterium that requires h2-enriched microaerobic conditions for growth. the level of h2 in the oral cavity is extremely low, suggesting that c. concisus is unlikely to have a microaerobic growth there. in this study, the anaerobic growth of c. concisus was investigated. the growth of fifty-seven oral c. concisus strains and six enteric c. concisus strains under vario ... | 2014 | 25214843 |
| functional expression of dental plaque microbiota. | dental caries remains a significant public health problem and is considered pandemic worldwide. the prediction of dental caries based on profiling of microbial species involved in disease and equally important, the identification of species conferring dental health has proven more difficult than anticipated due to high interpersonal and geographical variability of dental plaque microbiota. we have used rna-seq to perform global gene expression analysis of dental plaque microbiota derived from 19 ... | 2014 | 25177549 |
| azithromycin vs. placebo for the clinical outcome in campylobacter concisus diarrhoea in adults: a randomized, double-blinded, placebo-controlled clinical trial. | campylobacter concisus has been associated with prolonged mild diarrhoea, but investigations regarding the efficacy of antimicrobial treatment have not been reported previously. we initiated a phase 3, single-centre, randomized, double-blinded, placebo-controlled study comparing the efficacy of 500 mg once-daily dose of azithromycin with a 500 mg once-daily dose of placebo for three days, for the treatment of c. concisus diarrhoea in adult patients with a follow-up period of ten days. if symptom ... | 2016 | 27893820 |
| multilocus sequence typing of campylobacter concisus from danish diarrheic patients. | the emerging enteric pathogen campylobacter concisus is associated with prolonged diarrhea and inflammatory bowel disease. previous studies have shown that c. concisus strains are very genetically diverse. nevertheless, c. concisus strains have been divided into two genomospecies, where gs1 strains have been isolated predominantly from healthy individuals, while the gs2 cluster consists of isolates primarily from diarrheic individuals. the aim of the present study was to determine the genetic di ... | 2016 | 27688814 |
| zonula occludens toxins and their prophages in campylobacter species. | we previously showed that zonula occludens toxin (zot) encoded by campylobacter concisus zot (808t) gene has the potential to initiate inflammatory bowel disease. this zot protein caused prolonged intestinal epithelial barrier damage, induced intestinal epithelial and macrophage production of tumor necrosis factor-α and enhanced the responses of macrophages to other microbes. in order to understand the potential virulence of zot proteins in other campylobacter species, in this study we examined ... | 2016 | 27651834 |
| role of clinicogenomics in infectious disease diagnostics and public health microbiology. | clinicogenomics is the exploitation of genome sequence data for diagnostic, therapeutic, and public health purposes. central to this field is the high-throughput dna sequencing of genomes and metagenomes. the role of clinicogenomics in infectious disease diagnostics and public health microbiology was the topic of discussion during a recent symposium (session 161) presented at the 115th general meeting of the american society for microbiology that was held in new orleans, la. what follows is a co ... | 2016 | 26912755 |
| precision-guided antimicrobial peptide as a targeted modulator of human microbial ecology. | one major challenge to studying human microbiome and its associated diseases is the lack of effective tools to achieve targeted modulation of individual species and study its ecological function within multispecies communities. here, we show that c16g2, a specifically targeted antimicrobial peptide, was able to selectively kill cariogenic pathogen streptococcus mutans with high efficacy within a human saliva-derived in vitro oral multispecies community. importantly, a significant shift in the ov ... | 2015 | 26034276 |
| the role of il-23, il-22, and il-18 in campylobacter jejuni infection of conventional infant mice. | we have recently shown that, within 1 week following peroral campylobacter jejuni infection, conventional infant mice develop self-limiting enteritis. we here investigated the role of il-23, il-22, and il-18 during c. jejuni strain 81-176 infection of infant mice. the pathogen efficiently colonized the intestines of il-18(-/-) mice only, but did not translocate to extra-intestinal compartments. at day 13 postinfection (p.i.), il-22(-/-) mice displayed lower colonic epithelial apoptotic cell numb ... | 2016 | 27429795 |
| 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 |
| activities of abt-773 against microaerophilic and fastidious organisms. | abt-773 was tested against 317 fastidious isolates; it inhibited 99% of organisms at a concentration of 4.0 microg/ml. with ampicillin-sulbactam and levofloxacin, only 2 and 6% of these strains, respectively, were resistant at the breakpoint. with clindamycin, penicillin g, and metronidazole, 22, 26, and 58% of the strains, respectively, were resistant. | 2002 | 12121965 |
| the burden of different pathogens in acute diarrhoeal episodes among a cohort of egyptian children less than five years old. | diarrhoea continues to cause significant morbidity in egypt. | 2015 | 26516385 |
| effects of azithromycin, metronidazole, amoxicillin, and metronidazole plus amoxicillin on an in vitro polymicrobial subgingival biofilm model. | chronic periodontitis is one of the most prevalent human diseases and is caused by dysbiosis of the subgingival microbiota. treatment involves primarily mechanical disruption of subgingival biofilms and, in certain cases, adjunctive use of systemic antibiotic therapy. in vitro biofilm models have been developed to study antimicrobial agents targeting subgingival species. however, these models accommodate a limited number of taxa, lack reproducibility, and have low throughput. we aimed to develop ... | 2015 | 25733510 |
| comparison of oral microbial profiles between children with severe early childhood caries and caries-free children using the human oral microbe identification microarray. | early childhood caries (ecc) has become a prevalent public health problem among chinese preschool children. the bacterial microflora is considered to be an important factor in the formation and progress of dental caries. however, high-throughput and large-scale studies of the primary dentition are lacking. the present study aimed to compare oral microbial profiles between children with severe ecc (secc) and caries-free children. | 2015 | 25821962 |
| subantimicrobial dose doxycycline effects on osteopenic bone loss: microbiologic results. | based on microbiologic concerns, the safety of a 24-month regimen of subantimicrobial dose doxycycline (sdd; 20 mg twice a day) was evaluated in postmenopausal osteopenic women with periodontitis in a double-blind, placebo-controlled, randomized clinical trial. | 2007 | 17668979 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| comparative genomics of closely related salmonella enterica serovar typhi strains reveals genome dynamics and the acquisition of novel pathogenic elements. | typhoid fever is an infectious disease of global importance that is caused by salmonella enterica subsp. enterica serovar typhi (s. typhi). this disease causes an estimated 200,000 deaths per year and remains a serious global health threat. s. typhi is strictly a human pathogen, and some recovered individuals become long-term carriers who continue to shed the bacteria in their faeces, thus becoming main reservoirs of infection. | 2014 | 25412680 |
| microbial diversity similarities in periodontal pockets and atheromatous plaques of cardiovascular disease patients. | the immune and infectious alterations occurring in periodontitis have been shown to alter the development and severity of cardiovascular disease. one of these relationships is the translocation of oral bacteria to atheroma plaques, thereby promoting plaque development. thus, the aim of this study was to assess, by 16s cloning and sequencing, the microbial diversity of the subgingival environment and atheroma plaques of patients concomitantly suffering from periodontitis and obstructive coronary ... | 2014 | 25329160 |
| anaerobic culture to detect periodontal and caries pathogens. | anaerobic culture has been critical in our understanding of the oral microbiotas. | 2014 | 25678835 |
| anaerobic culture to detect periodontal and caries pathogens. | anaerobic culture has been critical in our understanding of the oral microbiotas. | 2014 | 25678835 |
| oligotyping analysis of the human oral microbiome. | the human microbiome project provided a census of bacterial populations in healthy individuals, but an understanding of the biomedical significance of this census has been hindered by limited taxonomic resolution. a high-resolution method termed oligotyping overcomes this limitation by evaluating individual nucleotide positions using shannon entropy to identify the most information-rich nucleotide positions, which then define oligotypes. we have applied this method to comprehensively analyze the ... | 2014 | 24965363 |
| 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 |
| tick-borne encephalitis virus replication, intracellular trafficking, and pathogenicity in human intestinal caco-2 cell monolayers. | tick-borne encephalitis virus (tbev) is one of the most important vector-borne viruses in europe and asia. its transmission mainly occurs by the bite of an infected tick. however, consuming milk products from infected livestock animals caused tbev cases. to better understand tbev transmission via the alimentary route, we studied viral infection of human intestinal epithelial cells. caco-2 cells were used to investigate pathological effects of tbev infection. tbev-infected caco-2 monolayers showe ... | 2014 | 24820351 |
| 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 |
| 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 |
| 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 |
| erratum: genome analysis of campylobacter concisus strains from patients with inflammatory bowel disease and gastroenteritis provides new insights into pathogenicity. | | 2017 | 28205571 |
| increased prevalence of methanosphaera stadtmanae in inflammatory bowel diseases. | the gut microbiota is associated with the modulation of mucosal immunity and the etiology of inflammatory bowel diseases (ibd). previous studies focused on the impact of bacterial species on ibd but seldom suspected archaea, which can be a major constituent of intestinal microbiota, to be implicated in the diseases. recent evidence supports that two main archaeal species found in the digestive system of humans, methanobrevibacter smithii (mbs) and methanosphaera stadtmanae (mss) can have differe ... | 2014 | 24498365 |
| antimicrobial photoinactivation using visible light plus water-filtered infrared-a (vis + wira) alters in situ oral biofilms. | recently, growing attention has been paid to antimicrobial photodynamic therapy (apdt) in dentistry. changing the microbial composition of initial and mature oral biofilm by apdt using visible light plus water-filtered infrared-a wavelengths (vis + wira) has not yet been investigated. moreover, most apdt studies have been conducted on planktonic bacterial cultures. therefore, in the present clinical study we cultivated initial and mature oral biofilms in six healthy volunteers for 2 hours or 3 d ... | 2015 | 26162100 |
| campylobacter concisus utilizes blood but not short chain fatty acids despite showing associations with firmicutes taxa. | campylobacter concisus is a member of the oral microbiota that has been associated with the development of inflammatory bowel diseases. however, the role of the bacterium in disease aetiology remains poorly understood. here, we examine optimal conditions for the growth of c. concisus, and the pathogenic potential of this bacterium in human gastrointestinal cells from the upper tract. further, the presence of c. concisus in the lower tract of crohn's disease (cd) patients undergoing therapy is ob ... | 2016 | 27339421 |
| the oral mucosal and salivary microbial community of behçet's syndrome and recurrent aphthous stomatitis. | behçet's syndrome (bs) is a multisystem immune-related disease of unknown etiology. recurrent aphthous stomatitis (ras) is characterized by the presence of idiopathic oral ulceration without extraoral manifestation. the interplay between the oral microbial communities and the immune response could play an important role in the etiology and pathogenesis of both bs and ras. | 2015 | 26037240 |
| maturation of oral microbiota in children with or without dental caries. | the aim of this longitudinal study was to evaluate the oral microbiota in children from age 3 months to 3 years, and to determine the association of the presence of caries at 3 years of age. | 2015 | 26020247 |
| oral microbiota shift after 12-week supplementation with lactobacillus reuteri dsm 17938 and pta 5289; a randomized control trial. | lactobacillus spp. potentially contribute to health by modulating bacterial biofilm formation, but their effects on the overall oral microbiota remain unclear. | 2015 | 25946126 |
| intraluminal containment of commensal outgrowth in the gut during infection-induced dysbiosis. | shifts in commensal microbiota composition are emerging as a hallmark of gastrointestinal inflammation. in particular, outgrowth of γ-proteobacteria has been linked to the etiology of inflammatory bowel disease and the pathologic consequences of infections. here we show that following acute toxoplasma gondii gastrointestinal infection of mice, control of commensal outgrowth is a highly coordinated process involving both the host response and microbial signals. notably, neutrophil emigration to t ... | 2013 | 24034617 |
| 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 |
| functional relationship between campylobacter concisus and the stomach ecosystem in health and disease. | | 2013 | 23823497 |
| campylobacter concisus pathotypes induce distinct global responses in intestinal epithelial cells. | the epithelial response to the opportunistic pathogen campylobacter concisus is poorly characterised. here, we assessed the intestinal epithelial responses to two c. concisus strains with different virulence characteristics in caco-2 cells using rnaseq, and validated a subset of the response using qpcr arrays. c. concisus strains induced distinct response patterns from intestinal epithelial cells, with the toxigenic strain inducing a significantly more amplified response. a range of cellular fun ... | 2016 | 27677841 |
| microrna response of primary human macrophages to arcobacter butzleri infection. | the role of micrornas (mirnas) in infectious diseases is becoming more and more apparent, and the use of mirnas as a diagnostic tool and their therapeutic application has become the major focus of investigation. the aim of this study was to identify mirnas involved in the immune signaling of macrophages in response to arcobacter (a.) butzleri infection, an emerging foodborne pathogen causing gastroenteritis. therefore, primary human macrophages were isolated and infected, and mirna expression wa ... | 2016 | 27429792 |
| microbiome, metabolome and inflammatory bowel disease. | inflammatory bowel disease (ibd) is a multifactorial disorder that conceptually occurs as a result of altered immune responses to commensal and/or pathogenic gut microbes in individuals most susceptible to the disease. during crohn's disease (cd) or ulcerative colitis (uc), two components of the human ibd, distinct stages define the disease onset, severity, progression and remission. epigenetic, environmental (microbiome, metabolome) and nutritional factors are important in ibd pathogenesis. whi ... | 2016 | 27681914 |
| examination of the effects of campylobacter concisus zonula occludens toxin on intestinal epithelial cells and macrophages. | campylobacter concisus is a gram-negative bacterium that is associated with inflammatory bowel disease (ibd). some c. concisus strains carry zonula occludens toxin (zot) gene which has polymorphisms. this study investigated the effects of c. concisus zot on intestinal epithelial cells and macrophages using cell line models. | 2016 | 27195022 |
| bifidobacteria abundance-featured gut microbiota compositional change in patients with behcet's disease. | gut microbiota compositional alteration may have an association with immune dysfunction in patients with behcet's disease (bd). we conducted a fecal metagenomic analysis of bd patients. we analyzed fecal microbiota obtained from 12 patients with bd and 12 normal individuals by sequencing of 16s ribosomal rna gene. we compared the relative abundance of bacterial taxa. direct comparison of the relative abundance of bacterial taxa demonstrated that the genera bifidobacterium and eggerthella increas ... | 2016 | 27105322 |
| biogeography of a human oral microbiome at the micron scale. | the spatial organization of complex natural microbiomes is critical to understanding the interactions of the individual taxa that comprise a community. although the revolution in dna sequencing has provided an abundance of genomic-level information, the biogeography of microbiomes is almost entirely uncharted at the micron scale. using spectral imaging fluorescence in situ hybridization as guided by metagenomic sequence analysis, we have discovered a distinctive, multigenus consortium in the mic ... | 2016 | 26811460 |
| understanding host-adherent-invasive escherichia coli interaction in crohn's disease: opening up new therapeutic strategies. | a trillion of microorganisms colonize the mammalian intestine. most of them have coevolved with the host in a symbiotic relationship and some of them have developed strategies to promote their replication in the presence of competing microbiota. recent evidence suggests that perturbation of the microbial community favors the emergence of opportunistic pathogens, in particular adherent-invasive escherichia coli (aiec) that can increase incidence and severity of gut inflammation in the context of ... | 2014 | 25580435 |
| the effect of campylobacter concisus on expression of il-18, tnf-α and p53 in barrett's cell lines. | barrett's oesophagus is a pre-malignant condition at gastroesophageal junction in which normal squamous epithelium is replaced by columnar shape epithelium, which predisposes oesophageal adenocarcinoma. it is known that barrett's oesophagus evolves as a consequence of chronic gastro-oesophageal reflux disease. although progression of barrett's oesophagus to adenocarcinoma is still unclear, increasing incidence of oesophageal cancer and mortality worldwide make its study necessary. several invest ... | 2015 | 26865939 |
| 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 |
| 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 |
| 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 |
| unsupervised statistical discovery of spaced motifs in prokaryotic genomes. | dna sequences contain repetitive motifs which have various functions in the physiology of the organism. a number of methods have been developed for discovery of such sequence motifs with a primary focus on detection of regulatory motifs and particularly transcription factor binding sites. most motif-finding methods apply probabilistic models to detect motifs characterized by unusually high number of copies of the motif in the analyzed sequences. | 2017 | 28056763 |
| genome analysis of campylobacter concisus strains from patients with inflammatory bowel disease and gastroenteritis provides new insights into pathogenicity. | campylobacter concisus is an oral bacterium that is associated with inflammatory bowel disease. c. concisus has two major genomospecies, which appear to have different enteric pathogenic potential. currently, no studies have compared the genomes of c. concisus strains from different genomospecies. in this study, a comparative genome analysis of 36 c. concisus strains was conducted including 27 c. concisus strains sequenced in this study and nine publically available c. concisus genomes. the c. c ... | 2016 | 27910936 |
| molecular diagnosis of arcobacter and campylobacter in diarrhoeal samples among portuguese patients. | the present study was conducted to investigate the prevalence and diversity of arcobacter and campylobacter spp. in 298 stool samples of patients with diarrhoea, collected from 22 portuguese hospitals, between september and november 2012. detection of arcobacter and campylobacter spp. was performed using molecular-based detection techniques, such as real-time fluorescence resonance energy transfer pcr, species-specific pcr, and sequencing of amplified pcr products. overall, 1.3% of the samples w ... | 2014 | 24361090 |
| incidence of campylobacter concisus and c. ureolyticus in traveler's diarrhea cases and asymptomatic controls in nepal and thailand. | campylobacter concisus and c. ureolyticus have emerged in recent years as being associated with acute and prolonged gastroenteritis and implicated in the development of inflammatory bowel diseases. however, there are limited data on the prevalence of these microorganisms in southeast asia. in this study, 214 pathogen-negative stool samples after laboratory examination for common enteric pathogens to include c. jejuni and c. coli by culture from two case-control traveler's diarrhea (td) studies c ... | 2017 | 28824712 |
| campylobacter concisus genomospecies 2 is better adapted to the human gastrointestinal tract as compared with campylobacter concisus genomospecies 1. | campylobacter concisus was previously shown to be associated with inflammatory bowel disease including crohn's disease (cd) and ulcerative colitis (uc). c. concisus has two genomospecies (gs). this study systematically examined the colonization of gs1 and gs2 c. concisus in the human gastrointestinal tract. gs1 and gs2 specific polymorphisms in 23s rrna gene were identified by comparison of the 23s rrna genes of 49 c. concisus strains. two newly designed pcr methods, based on the polymorphisms o ... | 2017 | 28824443 |
| complete genome sequence of campylobacter concisus atcc 33237(t) and draft genome sequences for an additional eight well-characterized c. concisus strains. | we report the complete genome sequence of the campylobacter concisus type strain atcc 33237 and the draft genome sequences of eight additional well-characterized c. concisus strains. c. concisus has been shown to be a genetically heterogeneous species, and these nine genomes provide valuable information regarding the diversity within this taxon. | 2017 | 28729281 |
| 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 |
| motility of campylobacter concisus isolated from saliva, feces, and gut mucosal biopsies. | campylobacter concisus is an emerging pathogen associated with gastrointestinal disorders such as gastroenteritis and inflammatory bowel diseases (ibd), but the species is also found in healthy subjects. the heterogeneous genome of c. concisus increases the likelihood of varying virulence between strains. flagella motility is a crucial virulence factor for the well-recognized campylobacter jejuni; therefore, this study aimed to analyze the motility of c. concisus isolated from saliva, gut biopsi ... | 2017 | 28116789 |
| the consequences of campylobacter infection. | the purpose of this review is to provide an update on the clinical, public health and economic consequences of campylobacter infection. | 2017 | 27798443 |
| campylobacter concisus pathotypes are present at significant levels in patients with gastroenteritis. | given that campylobacter jejuni is recognized as the most common cause of bacterial gastroenteritis worldwide, recent findings showing comparable levels of campylobacter concisus in patients with gastroenteritis would suggest that this bacterium is clinically important. the prevalence and abundance of campylobacter concisus in stool samples collected from patients with acute gastroenteritis was examined using quantitative real-time pcr. the associated virulence determinants exotoxin 9 and zonula ... | 2016 | 26698172 |
| immunoglobulin g response in patients with campylobacter concisus diarrhea. | limited information is available on the systemic immunoglobulin response in patients infected with the emerging pathogen campylobacter concisus. the aim of the present study was to detect anti-c. concisus antibodies in serum of 88 patients with c. concisus gastroenteritis. specific igg antibodies to c. concisus were measured in serum using an in-house enzyme-linked immunosorbent assay, and pooled donor serum was used as a control. the mean optical density was 0.135 (sem: 0.020) for the 88 adult ... | 2016 | 26643061 |
| tlr4, nod1 and nod2 mediate immune recognition of putative newly identified periodontal pathogens. | periodontitis is a polymicrobial inflammatory disease that results from the interaction between the oral microbiota and the host immunity. although the innate immune response is important for disease initiation and progression, the innate immune receptors that recognize both classical and putative periodontal pathogens that elicit an immune response have not been elucidated. by using the human oral microbe identification microarray (homim), we identified multiple predominant oral bacterial speci ... | 2016 | 26177212 |
| polycarbonate filtration technique is noninferior to mccda for isolation of campylobacter species from stool samples. | a total of 5963 diarrheic stool samples were cultivated for campylobacter spp. with use of modified charcoal cefoperazone deoxycholate agar (mccda) plates as well as a polycarbonate (pc) filter technique on blood agar plates. a total of 376 campylobacter jejuni/coli were isolated from both pc and mccda. six and three were isolated from pc and mccda only, respectively (p = ns). the pc technique is noninferior to mccda for isolation of c. jejuni/coli. | 2015 | 26022656 |
| pulp and plaque microbiotas of children with severe early childhood caries. | bacterial invasion into pulps of primary teeth can lead to infection and premature tooth loss in children. this pilot study aimed to explore whether the microbiota of carious exposures of dental pulps resembles that of carious dentin or that of infected root canals. | 2015 | 25651832 |
| the relationship between the immune system and oral manifestations of inflammatory bowel disease: a review. | inflammatory bowel diseases (ibds) are chronic, relapsing inflammatory diseases characterized by exacerbations and remissions of the gastrointestinal tract, clinically manifested as crohn's disease and ulcerative colitis. the etiology of ibds is considered to be multi factorial, comprising environmental, immune, microbial and genetic factors. clinical signs may include abdominal pain, frequent bloody diarrheas, mucorrhea, vomiting, fever, fatigue or weight loss. changes in the oral cavity often ... | 2016 | 27833449 |