Publications

using high throughput sequencing to explore the biodiversity in oral bacterial communities.	high throughput sequencing of 16s ribosomal rna gene amplicons is a cost-effective method for characterization of oral bacterial communities. however, before undertaking large-scale studies, it is necessary to understand the technique-associated limitations and intrinsic variability of the oral ecosystem. in this work we evaluated bias in species representation using an in vitro-assembled mock community of oral bacteria. we then characterized the bacterial communities in saliva and buccal mucosa ...	2012	22520388
bacterial phylogenetic tree construction based on genomic translation stop signals.	the efficiencies of the stop codons taa, tag, and tga in protein synthesis termination are not the same. these variations could allow many genes to be regulated. there are many similar nucleotide trimers found on the second and third reading-frames of a gene. they are called premature stop codons (psc). like stop codons, the psc in bacterial genomes are also highly bias in terms of their quantities and qualities on the genes. phylogenetically related species often share a similar psc profile. we ...	2012	22651236
diverse crisprs evolving in human microbiomes.	crispr (clustered regularly interspaced short palindromic repeats) loci, together with cas (crispr-associated) genes, form the crispr/cas adaptive immune system, a primary defense strategy that eubacteria and archaea mobilize against foreign nucleic acids, including phages and conjugative plasmids. short spacer sequences separated by the repeats are derived from foreign dna and direct interference to future infections. the availability of hundreds of shotgun metagenomic datasets from the human m ...	2012	22719260
comparison of oral microbiota in tumor and non-tumor tissues of patients with oral squamous cell carcinoma.	bacterial infections have been linked to malignancies due to their ability to induce chronic inflammation. we investigated the association of oral bacteria in oral squamous cell carcinoma (oscc/tumor) tissues and compared with adjacent non-tumor mucosa sampled 5 cm distant from the same patient (n = 10). by using culture-independent 16s rrna approaches, denaturing gradient gel electrophoresis (dgge) and cloning and sequencing, we assessed the total bacterial diversity in these clinical samples.	2012	22817758
evolutionary and genomic insights into meningococcal biology.	epidemic disease caused by neisseria meningitidis, the meningococcus, has been recognized for two centuries, but remains incompletely controlled and understood. there have been dramatic reductions in serogroup a and c meningococcal disease following the introduction of protein-polysaccharide conjugate vaccines, but there is currently no comprehensive vaccine against serogroup b meningococci. genetic analyses of meningococcal populations have provided many insights into the biology, evolution and ...	2012	22827308
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
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
genome-wide approaches (gwa) in oral and craniofacial diseases research.	oral diseases (2012) underlying molecular genetic mechanisms of diseases can be deciphered with unbiased strategies using recently developed technologies enabling genome-wide scale investigations. these technologies have been applied in scanning for genetic variations, gene expression profiles, and epigenetic changes for oral and craniofacial diseases. however, these approaches as applied to oral and craniofacial conditions are in the initial stages, and challenges remain to be overcome, includi ...	2012	22913301
genome-wide approaches (gwa) in oral and craniofacial diseases research.	oral diseases (2012) underlying molecular genetic mechanisms of diseases can be deciphered with unbiased strategies using recently developed technologies enabling genome-wide scale investigations. these technologies have been applied in scanning for genetic variations, gene expression profiles, and epigenetic changes for oral and craniofacial diseases. however, these approaches as applied to oral and craniofacial conditions are in the initial stages, and challenges remain to be overcome, includi ...	2012	22913301
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
xata, an at-1 autotransporter important for the virulence of xylella fastidiosa temecula1.	xylella fastidiosa temecula1 is the causative agent of pierce's disease of grapevine, which is spread by xylem-feeding insects. an important feature of the infection cycle is the ability of x. fastidiosa to colonize and interact with two distinct environments, the xylem of susceptible plants and the insect foregut. here, we describe our characterization of xata, the x. fastidiosa autotransporter protein encoded by pd0528. xata, which is classified as an at-1 (classical) autotransporter, has a c- ...	2012	22950010
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
beyond streptococcus mutans: dental caries onset linked to multiple species by 16s rrna community analysis.	dental caries in very young children may be severe, result in serious infection, and require general anesthesia for treatment. dental caries results from a shift within the biofilm community specific to the tooth surface, and acidogenic species are responsible for caries. streptococcus mutans, the most common acid producer in caries, is not always present and occurs as part of a complex microbial community. understanding the degree to which multiple acidogenic species provide functional redundan ...	2012	23091642
identification and cluster analysis of streptococcus pyogenes by maldi-tof mass spectrometry.	whole-cell matrix-assisted laser desorption ionization time-of-flight (maldi-tof) mass spectrometry (ms) has been successfully applied for bacterial identification and typing of many pathogens. the fast and reliable qualities of maldi-tof ms make it suitable for clinical diagnostics. maldi-tof ms for the identification and cluster analysis of streptococcus pyogenes, however, has not been reported. the goal of our study was to evaluate this approach for the rapid identification and typing of s. p ...	2012	23144803
microbial modulation of host immunity with the small molecule phosphorylcholine.	all microorganisms dependent on persistence in a host for survival rely on either hiding from or modulating host responses to infection. the small molecule phosphorylcholine, or choline phosphate (chop), is used for both of these purposes by a wide array of bacterial and parasitic microbes. while the mechanisms underlying chop acquisition and expression are diverse, a unifying theme is the use of chop to reduce the immune response to infection, creating an advantage for chop-expressing microorga ...	2013	23230294
emergence of multidrug-resistant, extensively drug-resistant and untreatable gonorrhea.	the new superbug neisseria gonorrhoeae has retained resistance to antimicrobials previously recommended for first-line treatment and has now demonstrated its capacity to develop resistance to the extended-spectrum cephalosporin, ceftriaxone, the last remaining option for first-line empiric treatment of gonorrhea. an era of untreatable gonorrhea may be approaching, which represents an exceedingly serious public health problem. herein, we review the evolution, origin and spread of antimicrobial re ...	2012	23231489
sputum microbiota in tuberculosis as revealed by 16s rrna pyrosequencing.	tuberculosis (tb) remains a global threat in the 21st century. traditional studies of the disease are focused on the single pathogen mycobacterium tuberculosis. recent studies have revealed associations of some diseases with an imbalance in the microbial community. characterization of the tb microbiota could allow a better understanding of the disease.	2013	23365674
various pathways leading to the acquisition of antibiotic resistance by natural transformation.	natural transformation can lead to exchange of dna between taxonomically diverse bacteria. in the case of chromosomal dna, homology-based recombination with the recipient genome is usually necessary for heritable stability. in our recent study, we have shown that natural transformation can promote the transfer of transposons, is elements, and integrons and gene cassettes, largely independent of the genetic relationship between the donor and recipient bacteria. additional results from our study s ...	2012	23482877
neisseria gonorrhoeae false-positive result obtained from a pharyngeal swab by using the roche cobas 4800 ct/ng assay in new zealand in 2012.	the roche cobas 4800 ct/ng assay is a commonly used commercial system for screening for neisseria gonorrhoeae infection, and previous studies have shown the method to be highly sensitive and specific for urogenital samples. we present the first confirmed clinical n. gonorrhoeae false-positive result using the cobas 4800 ng assay, obtained from testing a pharyngeal swab sample and caused by cross-reaction with a commensal neisseria strain.	2013	23486711
investigation of the effect of type 2 diabetes mellitus on subgingival plaque microbiota by high-throughput 16s rdna pyrosequencing.	diabetes mellitus is a major risk factor for chronic periodontitis. we investigated the effects of type 2 diabetes on the subgingival plaque bacterial composition by applying culture-independent 16s rdna sequencing to periodontal bacteria isolated from four groups of volunteers: non-diabetic subjects without periodontitis, non-diabetic subjects with periodontitis, type 2 diabetic patients without periodontitis, and type 2 diabetic patients with periodontitis. a total of 71,373 high-quality seque ...	2013	23613868
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
accurate identification of fastidious gram-negative rods: integration of both conventional phenotypic methods and 16s rrna gene analysis.	accurate identification of fastidious gram-negative rods (gnr) by conventional phenotypic characteristics is a challenge for diagnostic microbiology. the aim of this study was to evaluate the use of molecular methods, e.g., 16s rrna gene sequence analysis for identification of fastidious gnr in the clinical microbiology laboratory.	2013	23855986
genetic characteristics of neisseria meningitidis serogroup b strains carried by adolescents living in milan, italy: implications for vaccine efficacy.	before a protein vaccine is introduced into a country, it is essential to evaluate its potential impact and estimate its benefits and costs. the aim of this study was to determine the genetic characteristics of neisseria meningitidis b (nmb) in the pharyngeal secretions of 1375 healthy adolescents aged 13-19 y living in milan, italy, in september 2012, and the possible protection offered by the two currently available nmb protein vaccines. ninety-one subjects were nm carriers (6.6%), 29 (31.9%) ...	2013	23880917
bacterial community development in experimental gingivitis.	current knowledge of the microbial composition of dental plaque in early gingivitis is based largely on microscopy and cultural methods, which do not provide a comprehensive description of oral microbial communities. this study used 454-pyrosequencing of the v1-v3 region of 16s rrna genes (approximately 500 bp), and bacterial culture, to characterize the composition of plaque during the transition from periodontal health to gingivitis. a total of 20 healthy volunteers abstained from oral hygiene ...	2013	23967169
intraspecific 16s rrna gene diversity among clinical isolates of neisseria species.	in the present work, nearly the entire 16s rrna gene sequences of 46 clinical samples of neisseria spp. were determined, and the aligned sequences were analyzed to investigate the diversity of 16s rrna genes in each commensal neisseria species. two 16s rrna types were identified in two neisseria sicca strains, three 16s rrna types in five neisseria macacae strains, fourteen 16s rrna types in twenty neisseria flavescens isolates, and fourteen 16s rrna types in nineteen neisseria mucosa isolates. ...	2014	24020769
functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter.	targeting sequencing to genes involved in key environmental processes, i.e., ecofunctional genes, provides an opportunity to sample nature's gene guilds to greater depth and help link community structure to process-level outcomes. vastly different approaches have been implemented for sequence processing and, ultimately, for taxonomic placement of these gene reads. the overall quality of next generation sequence analysis of functional genes is dependent on multiple steps and assumptions of unknow ...	2013	24062736
genome sequence analyses show that neisseria oralis is the same species as 'neisseria mucosa var. heidelbergensis'.	phylogenies generated from whole genome sequence (wgs) data provide definitive means of bacterial isolate characterization for typing and taxonomy. the species status of strains recently defined with conventional taxonomic approaches as representing neisseria oralis was examined by the analysis of sequences derived from wgs data, specifically: (i) 53 neisseria ribosomal protein subunit (rps) genes (ribosomal multi-locus sequence typing, rmlst); and (ii) 246 neisseria core genes (core genome mlst ...	2013	24097834
oral bacterial communities in individuals with type 2 diabetes who live in southern thailand.	type 2 diabetes mellitus is increasingly common in thailand and elsewhere. in the present investigation, the bacteriological composition of saliva and supragingival plaque in thai diabetics with and without active dental caries and in nondiabetics was determined by differential culture and eubacterial dna profiling. potential associations between fasting blood sugar and glycosylated hemoglobin (biomarkers of current and historical glucose control, respectively) with decayed, missing, and filled ...	2014	24242241
identifying neisseria species by use of the 50s ribosomal protein l6 (rplf) gene.	the comparison of 16s rrna gene sequences is widely used to differentiate bacteria; however, this gene can lack resolution among closely related but distinct members of the same genus. this is a problem in clinical situations in those genera, such as neisseria, where some species are associated with disease while others are not. here, we identified and validated an alternative genetic target common to all neisseria species which can be readily sequenced to provide an assay that rapidly and accur ...	2014	24523465
three clinically distinct chronic pediatric airway infections share a common core microbiota.	dna-based microbiological studies are moving beyond studying healthy human microbiota to investigate diverse infectious diseases, including chronic respiratory infections, such as those in the airways of people with cystic fibrosis (cf) and non-cf bronchiectasis. the species identified in the respiratory secretion microbiota from such patients can be classified into those that are common and abundant among similar subjects (core) versus those that are infrequent and rare (satellite). this catego ...	2014	24597615
metagenomic analysis of nitrate-reducing bacteria in the oral cavity: implications for nitric oxide homeostasis.	the microbiota of the human lower intestinal tract helps maintain healthy host physiology, for example through nutrient acquisition and bile acid recycling, but specific positive contributions of the oral microbiota to host health are not well established. nitric oxide (no) homeostasis is crucial to mammalian physiology. the recently described entero-salivary nitrate-nitrite-nitric oxide pathway has been shown to provide bioactive no from dietary nitrate sources. interestingly, this pathway is d ...	2014	24670812
exome capture from saliva produces high quality genomic and metagenomic data.	targeted capture of genomic regions reduces sequencing cost while generating higher coverage by allowing biomedical researchers to focus on specific loci of interest, such as exons. targeted capture also has the potential to facilitate the generation of genomic data from dna collected via saliva or buccal cells. dna samples derived from these cell types tend to have a lower human dna yield, may be degraded from age and/or have contamination from bacteria or other ambient oral microbiota. however ...	2014	24708091
maldi-tof identification of the human gut microbiome in people with and without diarrhea in senegal.	in africa, there are several problems with the specific identification of bacteria. recently, maldi-tof mass spectrometry has become a powerful tool for the routine microbial identification in many clinical laboratories.	2014	24784934
necrotizing pneumonia and empyema caused by neisseria flavescens infection.	neisseria flavescens is an uncommon pathogen of human infection, pneumonia and empyema caused by n. flavescens is rarely reported. herein, we report a 56-year-old diabetic patient presenting necrotising pneumonia and empyema due to n. flavescens infection. the main clinical manifestation of this patient was high fever, sticky pus and gradually aggravating dyspnea. the chest computed tomography (ct) scan showed there are mass of high density areas around hilus of the left lung, hollow sign with i ...	2014	24822118
cultivable bacterial microbiota of northern bobwhite (colinus virginianus): a new reservoir of antimicrobial resistance?	the northern bobwhite (colinus virginianus) is an ecologically and economically important avian species. at the present time, little is known about the microbial communities associated with these birds. as the first step to create a quail microbiology knowledge base, the current study conducted an inventory of cultivable quail tracheal, crop, cecal, and cloacal microbiota and associated antimicrobial resistance using a combined bacteriology and dna sequencing approach. a total of 414 morphologic ...	2014	24937705
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
antimicrobial resistance in neisseria gonorrhoeae in the 21st century: past, evolution, and future.	neisseria gonorrhoeae is evolving into a superbug with resistance to previously and currently recommended antimicrobials for treatment of gonorrhea, which is a major public health concern globally. given the global nature of gonorrhea, the high rate of usage of antimicrobials, suboptimal control and monitoring of antimicrobial resistance (amr) and treatment failures, slow update of treatment guidelines in most geographical settings, and the extraordinary capacity of the gonococci to develop and ...	2014	24982323
evaluation of a real-time pcr assay for simultaneous detection of kingella kingae and staphylococcus aureus from synovial fluid in suspected septic arthritis.	direct plating of synovial fluid (sf) on agar-based media often fails to identify pathogens in septic arthritis (sa). we developed a pcr assay for the simultaneous detection of kingella kingae and staphylococcus aureus from sf to evaluate molecular detection in sf and to estimate the incidence of k. kingae in sa in north america. the assay was based on detection of the cpn60 gene of k. kingae and the spa gene of s. aureus in multiplex real-time pcr. k. kingae was identified in 50% of patients be ...	2014	24982837
detection of the amoeba entamoeba gingivalis in periodontal pockets.	periodontitis is a public health issue, being one of the most prevalent diseases worldwide. however, the aetiology of the disease is still unclear: genetics of patients cannot explain the dispersed or isolated localisation of gingival pockets, while bacteria-based models are insufficient to distinguish gingivitis and periodontitis. the possible role of parasites in the establishment of periodontitis has been poorly studied until now. the aim of this project was to study a potential link between ...	2014	24983705
culturable bacterial microbiota of the stomach of helicobacter pylori positive and negative gastric disease patients.	human stomach is the only known natural habitat of helicobacter pylori (hp), a major bacterial pathogen that causes different gastroduodenal diseases. despite this, the impact of hp on the diversity and the composition of the gastric microbiota has been poorly studied. in this study, we have analyzed the culturable gastric microbiota of 215 malaysian patients, including 131 hp positive and 84 hp negative individuals that were affected by different gastric diseases. non-hp bacteria isolated from ...	2014	25105162
filamentous phages prevalent in pseudoalteromonas spp. confer properties advantageous to host survival in arctic sea ice.	sea ice is one of the most frigid environments for marine microbes. in contrast to other ocean ecosystems, microbes in permanent sea ice are space confined and subject to many extreme conditions, which change on a seasonal basis. how these microbial communities are regulated to survive the extreme sea ice environment is largely unknown. here, we show that filamentous phages regulate the host bacterial community to improve survival of the host in permanent arctic sea ice. we isolated a filamentou ...	2014	25303713
filamentous phages prevalent in pseudoalteromonas spp. confer properties advantageous to host survival in arctic sea ice.	sea ice is one of the most frigid environments for marine microbes. in contrast to other ocean ecosystems, microbes in permanent sea ice are space confined and subject to many extreme conditions, which change on a seasonal basis. how these microbial communities are regulated to survive the extreme sea ice environment is largely unknown. here, we show that filamentous phages regulate the host bacterial community to improve survival of the host in permanent arctic sea ice. we isolated a filamentou ...	2014	25303713
sterilizing immunity elicited by neisseria meningitidis carriage shows broader protection than predicted by serum antibody cross-reactivity in ceacam1-humanized mice.	neisseria meningitidis asymptomatically colonizes the human upper respiratory tract but is also the cause of meningitis and severe septicemia. carriage or disease evokes an immune response against the infecting strain. hitherto, we have known little about the breadth of immunity induced by natural carriage of a single strain or its implications for subsequent infectious challenge. in this study, we establish that transgenic mice expressing human ceacam1 support nasal colonization by a variety of ...	2014	25368118
sterilizing immunity elicited by neisseria meningitidis carriage shows broader protection than predicted by serum antibody cross-reactivity in ceacam1-humanized mice.	neisseria meningitidis asymptomatically colonizes the human upper respiratory tract but is also the cause of meningitis and severe septicemia. carriage or disease evokes an immune response against the infecting strain. hitherto, we have known little about the breadth of immunity induced by natural carriage of a single strain or its implications for subsequent infectious challenge. in this study, we establish that transgenic mice expressing human ceacam1 support nasal colonization by a variety of ...	2014	25368118
distinct composition of the oral indigenous microbiota in south korean and japanese adults.	a comparison of national surveys on oral health suggested that the population of south korea has a better periodontal health status than that of japan, despite their similar inherent backgrounds. here, we investigated differences in oral bacterial assemblages between individuals from those two countries. to exclude potential effects of oral health condition on the microbiota, we selected 52 korean and 88 japanese orally healthy adults (aged 40-79 years) from the participants of two cohort studie ...	2014	25384884
gorilla gorilla gorilla gut: a potential reservoir of pathogenic bacteria as revealed using culturomics and molecular tools.	wild apes are considered to be the most serious reservoir and source of zoonoses. however, little data are available about the gut microbiota and pathogenic bacteria in gorillas. for this propose, a total of 48 fecal samples obtained from 21 gorilla gorilla gorilla individuals (as revealed via microsatellite analysis) were screened for human bacterial pathogens using culturomics and molecular techniques. by applying culturomics to one index gorilla and using specific media supplemented by plants ...	2014	25417711
effect of stoned olive pomace on rumen microbial communities and polyunsaturated fatty acid biohydrogenation: an in vitro study.	stoned olive pomace (sop), which represents approximately 50% of the conversion process of olives to olive oil, is largely not utilised and creates costs for its disposal and has negative environmental impacts. in vitro trial experiments were employed to study the effect of feeds integrated with this bio-waste, which is rich in polyphenols, on rumen biohydrogenation, using sheep rumen liquor as inoculum.	2014	25424901
dynamics of tongue microbial communities with single-nucleotide resolution using oligotyping.	the human mouth is an excellent system to study the dynamics of microbial communities and their interactions with their host. we employed oligotyping to analyze, with single-nucleotide resolution, oral microbial 16s ribosomal rna (rrna) gene sequence data from a time course sampled from the tongue of two individuals, and we interpret our results in the context of oligotypes that we previously identified in the oral data from the human microbiome project. our previous work established that many o ...	2014	25426106
subgingival microbiota in health compared to periodontitis and the influence of smoking.	the etiology of periodontitis has traditionally been associated to a consortium of three bacterial species-the so-called "red-complex" of periodontal disease-which has been the target for most diagnostic and therapeutic strategies. however, other species have also been found to correlate with disease severity. in addition, the influence of smoking on periodontal microbiota is poorly understood. in the current manuscript, the composition of the subgingival microbiota in healthy individuals vs. pa ...	2015	25814980
molecular assay for detection of genetic markers associated with decreased susceptibility to cephalosporins in neisseria gonorrhoeae.	the incidence of antimicrobial-resistant neisseria gonorrhoeae continues to rise in canada; however, antimicrobial resistance data are lacking for approximately 70% of gonorrhea infections that are diagnosed directly from clinical specimens by nucleic acid amplification tests (naats). we developed a molecular assay for surveillance use to detect mutations in genes associated with decreased susceptibility to cephalosporins that can be applied to both culture isolates and clinical samples. real-ti ...	2015	25878350
development and pyrosequencing analysis of an in-vitro oral biofilm model.	dental caries and periodontal disease are the commonest bacterial diseases of man and can result in tooth loss. the principal method of prevention is the mechanical removal of dental plaque augmented by active agents incorporated into toothpastes and mouthrinses. in-vitro assays that include complex oral bacterial biofilms are required to accurately predict the efficacy of novel active agents in vivo. the aim of this study was to develop an oral biofilm model using the calgary biofilm device (cb ...	2015	25880819
bacterial composition of the human upper gastrointestinal tract microbiome is dynamic and associated with genomic instability in a barrett's esophagus cohort.	the incidence of esophageal adenocarcinoma (eac) has increased nearly five-fold over the last four decades in the united states. barrett's esophagus, the replacement of the normal squamous epithelial lining with a mucus-secreting columnar epithelium, is the only known precursor to eac. like other parts of the gastrointestinal (gi) tract, the esophagus hosts a variety of bacteria and comparisons among published studies suggest bacterial communities in the stomach and esophagus differ. chronic inf ...	2015	26076489
a multidimensional approach to the management of severe asthma: inflammometry, molecular microbiology and bronchial thermoplasty.	the authors illustrate the merits of identifying the components of diseases (eg, bronchitis and airway hyper-responsiveness) that contribute to exacerbations in the management of a patient with severe asthma. quantitative cell counts in sputum identified a neutrophilic – as opposed to eosinophilic – bronchitis that enabled a stepwise weaning of prednisone. molecular microbiology and extended culture methods identified anaerobes and other airway microbiome that helped to guide the use of antibiot ...	2015	26083543
the influence of smoking on the peri-implant microbiome.	smokers are at high risk for 2 bacterially driven oral diseases: peri-implant mucositis and peri-implantitis. therefore, the purpose of this investigation was to use a deep-sequencing approach to identify the effect of smoking on the peri-implant microbiome in states of health and disease. peri-implant biofilm samples were collected from 80 partially edentulous subjects with peri-implant health, peri-implant mucositis, and peri-implantitis. bacterial dna was isolated and 16s ribsomal rna gene li ...	2015	26124222
comparison of the oral microbiomes of canines and their owners using next-generation sequencing.	the oral microbiome, which is closely associated with many diseases, and the resident pathogenic oral bacteria, which can be transferred by close physical contact, are important public health considerations. although the dog is the most common companion animal, the composition of the canine oral microbiome, which may include human pathogenic bacteria, and its relationship with that of their owners are unclear. in this study, 16s rdna pyrosequencing was used to compare the oral microbiomes of 10 ...	2015	26134411
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
exploring salivary microbiota in aids patients with different periodontal statuses using 454 gs-flx titanium pyrosequencing.	patients with acquired immunodeficiency syndrome (aids) are at high risk of opportunistic infections. oral manifestations have been associated with the level of immunosuppression, these include periodontal diseases, and understanding the microbial populations in the oral cavity is crucial for clinical management. the aim of this study was to examine the salivary bacterial diversity in patients newly admitted to the aids ward of the public health clinical center (china). saliva samples were colle ...	2015	26191508
in vivo imaging and tracking of host-microbiota interactions via metabolic labeling of gut anaerobic bacteria.	the intestine is densely populated by anaerobic commensal bacteria. these microorganisms shape immune system development, but understanding of host-commensal interactions is hampered by a lack of tools for studying the anaerobic intestinal environment. we applied metabolic oligosaccharide engineering and bioorthogonal click chemistry to label various commensal anaerobes, including bacteroides fragilis, a common and immunologically important commensal. we studied the dissemination of b. fragilis ...	2015	26280120
composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls.	the role of the human microbiome in schizophrenia remains largely unexplored. the microbiome has been shown to alter brain development and modulate behavior and cognition in animals through gut-brain connections, and research in humans suggests that it may be a modulating factor in many disorders. this study reports findings from a shotgun metagenomic analysis of the oropharyngeal microbiome in 16 individuals with schizophrenia and 16 controls. high-level differences were evident at both the phy ...	2015	26336637
robust species taxonomy assignment algorithm for 16s rrna ngs reads: application to oral carcinoma samples.	usefulness of next-generation sequencing (ngs) in assessing bacteria associated with oral squamous cell carcinoma (oscc) has been undermined by inability to classify reads to the species level.	2015	26426306
the microbiome in populations with a low and high prevalence of caries.	the oral microbiota was compared between romanian adolescents with a high prevalence of caries and no dental care and swedish caries-active and caries-free adolescents in caries prevention programs and with a low prevalence of caries. biofilm samples were analyzed by flx+ pyrosequencing of the v1 to v4 hypervariable regions of the 16s rrna gene and polymerase chain reaction (pcr)/quantitative pcr (qpcr) for streptococcus mutans and streptococcus sobrinus. sequences obtained blasted to 9 phyla, 6 ...	2016	26442950
the development and application of a molecular community profiling strategy to identify polymicrobial bacterial dna in the whole blood of septic patients.	the application of molecular based diagnostics in sepsis has had limited success to date. molecular community profiling methods have indicated that polymicrobial infections are more common than suggested by standard clinical culture. a molecular profiling approach was developed to investigate the propensity for polymicrobial infections in patients predicted to have bacterial sepsis.	2015	26474751
bacteria that travel: the quality of aircraft water.	the travelling population is increasing globally year on year. international tourist arrival figures reached 1087 million in 2013 and 1133 million in 2014; of which 53% and 54% respectively accounted for air transport. the water on board aircraft is sourced from surface or ground water; piped to a central filling point and distributed to each aircraft by water service vehicles at the home base or at the destination airport. the purpose of this study was to ascertain the microbial, chemical (ph; ...	2015	26529000
dietary nitrate improves vascular function in patients with hypercholesterolemia: a randomized, double-blind, placebo-controlled study.	the beneficial cardiovascular effects of vegetables may be underpinned by their high inorganic nitrate content.	2015	26607938
dietary nitrate improves vascular function in patients with hypercholesterolemia: a randomized, double-blind, placebo-controlled study.	the beneficial cardiovascular effects of vegetables may be underpinned by their high inorganic nitrate content.	2015	26607938
hexr controls glucose-responsive genes and central carbon metabolism in neisseria meningitidis.	neisseria meningitidis, an exclusively human pathogen and the leading cause of bacterial meningitis, must adapt to different host niches during human infection. n. meningitidis can utilize a restricted range of carbon sources, including lactate, glucose, and pyruvate, whose concentrations vary in host niches. microarray analysis of n. meningitidis grown in a chemically defined medium in the presence or absence of glucose allowed us to identify genes regulated by carbon source availability. most ...	2016	26644430
a side by side comparison of bruker biotyper and vitek ms: utility of maldi-tof ms technology for microorganism identification in a public health reference laboratory.	matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms) has emerged as a rapid, highly accurate, and cost-effective method for routine identification of a wide range of microorganisms. we carried out a side by side comparative evaluation of the performance of bruker biotyper versus vitek ms for identification of a large and diverse collection of microorganisms. most difficult and/or unusual microorganisms, as well as commonly encountered microorganisms were se ...	2015	26658918
evaluation of the bruker maldi biotyper for identification of fastidious gram-negative rods.	matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms) has entered clinical laboratories, facilitating identification of bacteria. here, we evaluated the maldi biotyper (bruker daltonics) for the identification of fastidious gram-negative rods (gnr). three sample preparation methods, direct colony transfer, direct transfer plus on-target formic acid preparation, and ethanol-formic acid extraction, were analyzed for 151 clinical isolates. direct colony transfe ...	2016	26659214
different gastric microbiota compositions in two human populations with high and low gastric cancer risk in colombia.	inhabitants of túquerres in the colombian andes have a 25-fold higher risk of gastric cancer than inhabitants of the coastal town tumaco, despite similar h. pylori prevalences. the gastric microbiota was recently shown in animal models to accelerate the development of h. pylori-induced precancerous lesions. 20 individuals from each town, matched for age and sex, were selected, and gastric microbiota analyses were performed by deep sequencing of amplified 16s rdna. in parallel, analyses of h. pyl ...	2016	26729566
temporal stability of the salivary microbiota in oral health.	saliva is a biological fluid suitable for biomarker analysis, and differences in the salivary microbiota in oral health and disease have been reported. for such comparative analyses, time of sampling is critical since the bacterial composition may vary throughout the day, i.e., diurnal variation. the purpose of this study is to compare the salivary microbiome over time to determine the optimal time for sampling.	2016	26799067
multiplex strand invasion based amplification (msiba) assay for detection of chlamydia trachomatis and neisseria gonorrhoeae.	nucleic acid amplification tests have become a common method for diagnosis of stis due to their improved sensitivity over immunoassays and traditional culture-based methods. isothermal nucleic acid amplification methods offer significant advantages over polymerase chain reaction (pcr) because they do not require sophisticated instruments needed for thermal cycling of pcr. we recently reported a novel isothermal nucleic acid amplification method, strand invasion-based amplification (siba), which ...	2016	26837460
bacterial diversity in saliva and oral health-related conditions: the hisayama study.	this population-based study determined the salivary microbiota composition of 2,343 adult residents of hisayama town, japan, using 16s rrna gene next-generation high-throughput sequencing. of 550 identified species-level operational taxonomic units (otus), 72 were common, in ≥75% of all individuals, as well as in ≥75% of the individuals in the lowest quintile of phylogenetic diversity (pd). these "core" otus constituted 90.9 ± 6.1% of each microbiome. the relative abundance profiles of 22 of the ...	2016	26907866
metagenomics reveals dysbiosis and a potentially pathogenic n. flavescens strain in duodenum of adult celiac patients.	celiac disease (cd)-associated duodenal dysbiosis has not yet been clearly defined, and the mechanisms by which cd-associated dysbiosis could concur to cd development or exacerbation are unknown. in this study, we analyzed the duodenal microbiome of cd patients.	2016	27045926
population and functional genomics of neisseria revealed with gene-by-gene approaches.	rapid low-cost whole-genome sequencing (wgs) is revolutionizing microbiology; however, complementary advances in accessible, reproducible, and rapid analysis techniques are required to realize the potential of these data. here, investigations of the genus neisseria illustrated the gene-by-gene conceptual approach to the organization and analysis of wgs data. using the gene and its link to phenotype as a starting point, the bigsdb database, which powers the pubmlst databases, enables the assembly ...	2016	27098959
evaluation of various culture media for detection of rapidly growing mycobacteria from patients with cystic fibrosis.	isolation of nontuberculous mycobacteria (ntm) from the sputum of patients with cystic fibrosis (cf) is challenging due to overgrowth by rapidly growing species that colonize the lungs of patients with cf. extended incubation on burkholderia cepacia selective agar (bcsa) has been recommended as an expedient culture method for the isolation of rapidly growing ntm in this setting. the aim of this study was to assess five selective media designed for the isolation of burkholderia cepacia complex, a ...	2016	27098962
microbiology of peritonsillar abscess in the south estonian population.	the first aim of this study was to compare the microbiota of different locations (pus, tonsillar fossa, blood) in peritonsillar abscess (pta) patients in order to optimize the sampling scheme. the second aim was to estimate the occurrence of tonsillitis episodes and macroscopic oropharyngeal signs characteristic of recurrent tonsillitis in pta patients.	2016	27113570
protist-bacteria associations: gammaproteobacteria and alphaproteobacteria are prevalent as digestion-resistant bacteria in ciliated protozoa.	protistan bacterivory, a microbial process involving ingestion and digestion, is ecologically important in the microbial loop in aquatic and terrestrial ecosystems. while bacterial resistance to protistan ingestion has been relatively well understood, little is known about protistan digestion in which some ingested bacteria could not be digested in cells of major protistan grazers in the natural environment. here we report the phylogenetic identities of digestion-resistant bacteria (drb) that co ...	2016	27148188
species-level core oral bacteriome identified by 16s rrna pyrosequencing in a healthy young arab population.	reports on the composition of oral bacteriome in arabs are lacking. in addition, the majority of previous studies on other ethnic groups have been limited by low-resolution taxonomic assignment of next-generation sequencing reads. furthermore, there has been a conflict about the existence of a 'core' bacteriome.	2016	27193835
a wide spectrum of fastidious and ampicillin-susceptible bacteria dominate in animal-caused wounds.	the main purpose of this study was to assess the actual occurrence of gram-negative oxidase-positive bacteria (gnop) in human wounds caused by animals, mostly cat and dog bites and scratches, and with signs of infection. we report a prospective series of 92 wound samples. routine culturing was combined with a procedure optimised for fastidious gnop. all gnop isolates were identified by 16s rdna sequencing to the species level. we observed a more prominent role of gnop, including at least 30 spec ...	2016	27197725
the use of pcr/electrospray ionization-time-of-flight-mass spectrometry (pcr/esi-tof-ms) to detect bacterial and fungal colonization in healthy military service members.	the role of microbial colonization in disease is complex. novel molecular tools to detect colonization offer theoretical improvements over traditional methods. we evaluated pcr/electrospray ionization-time-of-flight-mass spectrometry (pcr/esi-tof-ms) as a screening tool to study colonization of healthy military service members.	2016	27448413
opportunistic infections in hiv-infected patients differ strongly in frequencies and spectra between patients with low cd4+ cell counts examined postmortem and compensated patients examined antemortem irrespective of the haart era.	aids-related mortality has changed dramatically with the onset of highly active antiretroviral therapy (haart), which has even allowed compensated hiv-infected patients to withdraw from secondary therapy directed against opportunistic pathogens. however, in recently autopsied hiv-infected patients, we observed that associations with a broad spectrum of pathogens remain, although detailed analyses are lacking. therefore, we focused on the possible frequency and spectrum shifts in pathogens associ ...	2016	27611681
resistance to β-lactams in neisseria ssp due to chromosomally encoded penicillin-binding proteins.	neisseria meningitidis and neisseria gonorrhoeae are human pathogens that cause a variety of life-threatening systemic and local infections, such as meningitis or gonorrhoea. the treatment of such infection is becoming more difficult due to antibiotic resistance. the focus of this review is on the mechanism of reduced susceptibility to penicillin and other β-lactams due to the modification of chromosomally encoded penicillin-binding proteins (pbp), in particular pbp2 encoded by the pena gene. th ...	2016	27690121
neisserial heparin binding antigen (nhba) contributes to the adhesion of neisseria meningitidis to human epithelial cells.	neisserial heparin binding antigen (nhba) is a surface-exposed lipoprotein ubiquitously expressed by neisseria meningitidis strains and an antigen of the bexsero® vaccine. nhba binds heparin through a conserved arg-rich region that is the target of two proteases, the meningococcal nalp and human lactoferrin (hlf). in this work, in vitro studies showed that recombinant nhba protein was able to bind epithelial cells and mutations of the arg-rich tract abrogated this binding. all n-terminal and c-t ...	2016	27780200
[systemic lupus erythematosus : unusual cutaneous manifestations].	various different mucocutaneous symptoms may affect up to 80 % of systemic lupus erythematosus (sle) patients.	2016	27878308
a case of bartholin cyst due to neisseria flavescens.		2017	28366430
genotyping of commensal neisseria spp strains by pulsed-field gel electrophoresis and 16s rrna gene sequencing.	we investigated the diversity of the primary sequences of the 16s rrna genes among 46 commensal neisseria strains and evaluated the use of this approach as a molecular typing tool in comparison with pfge analysis.	2017	28374932
high level bacterial contamination of secondary school students' mobile phones.	while contamination of mobile phones in the hospital has been found to be common in several studies, little information about bacterial abundance on phones used in the community is available. our aim was to quantitatively determine the bacterial contamination of secondary school students' mobile phones.	2017	28626737