a stable variant of simonsiella muelleri with unusual colonial and cellular morphology.the unusual morphology and cellular arrangement of a member of the genus simonsiella is described. the organism is characterized by the formation of very long trichomes, which can be greater than 1,000 microns in length.19902307662
bacterial community dynamics during start-up of a trickle-bed bioreactor degrading aromatic compounds.this study was performed with a laboratory-scale fixed-bed bioreactor degrading a mixture of aromatic compounds (solvesso100). the starter culture for the bioreactor was prepared in a fermentor with a wastewater sample of a care painting facility as the inoculum and solvesso100 as the sole carbon source. the bacterial community dynamics in the fermentor and the bioreactor were examined by a conventional isolation procedure and in situ hybridization with fluorescently labeled rrna-targeted oligon ...19989501433
identification of candidate periodontal pathogens and beneficial species by quantitative 16s clonal analysis.most studies of the bacterial etiology of periodontitis have used either culture-based or targeted dna approaches, and so it is likely that pathogens remain undiscovered. the purpose of this study was to use culture-independent, quantitative analysis of biofilms associated with chronic periodontitis and periodontal health to identify pathogens and beneficial species. samples from subjects with periodontitis and controls were analyzed using ribosomal 16s cloning and sequencing. several genera, ma ...200516081935
relationship between oral malodor and the global composition of indigenous bacterial populations in saliva.oral malodor develops mostly from the metabolic activities of indigenous bacterial populations within the oral cavity, but whether healthy or oral malodor-related patterns of the global bacterial composition exist remains unclear. in this study, the bacterial compositions in the saliva of 240 subjects complaining of oral malodor were divided into groups based on terminal-restriction fragment length polymorphism (t-rflp) profiles using hierarchical cluster analysis, and the patterns of the microb ...201020228112
sequence, structure and functional diversity of pd-(d/e)xk phosphodiesterase superfamily.proteins belonging to pd-(d/e)xk phosphodiesterases constitute a functionally diverse superfamily with representatives involved in replication, restriction, dna repair and trna-intron splicing. their malfunction in humans triggers severe diseases, such as fanconi anemia and xeroderma pigmentosum. to date there have been several attempts to identify and classify new pd-(d/e)kk phosphodiesterases using remote homology detection methods. such efforts are complicated, because the superfamily exhibit ...201222638584
the dental plaque microbiome in health and 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 ...201323520516
natural competence and the evolution of dna uptake specificity.many bacteria are naturally competent, able to actively transport environmental dna fragments across their cell envelope and into their cytoplasm. because incoming dna fragments can recombine with and replace homologous segments of the chromosome, competence provides cells with a potent mechanism of horizontal gene transfer as well as access to the nutrients in extracellular dna. this review starts with an introductory overview of competence and continues with a detailed consideration of the dna ...201424488316
mouthguards: does the indigenous microbiome play a role in maintaining oral health?the existence of symbiotic relationships between bacteria and their hosts in various ecosystems have long been known to science. the human body also hosts vast numbers of bacteria in several habitats. emerging evidence from the gastro-intestinal tract, genito-urinary tract and respiratory indicates that there are several health benefits to hosting a complex and diverse microbial community. bacteria colonize the oral cavity within a few minutes after birth and form stable communities. our knowled ...201526000251
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 ...201526124222
diversity takes shape: understanding the mechanistic and adaptive basis of bacterial morphology.the modern age of metagenomics has delivered unprecedented volumes of data describing the genetic and metabolic diversity of bacterial communities, but it has failed to provide information about coincident cellular morphologies. much like metabolic and biosynthetic capabilities, morphology comprises a critical component of bacterial fitness, molded by natural selection into the many elaborate shapes observed across the bacterial domain. in this essay, we discuss the diversity of bacterial morpho ...201627695035
molecular and virulence characteristics of an outer membrane-associated rtx exoprotein in pasteurella pneumotropica.pasteurella pneumotropica is a ubiquitous bacterium that is frequently isolated from laboratory rodents and causes various clinical symptoms in immunodeficient animals. currently two rtx toxins, pnxia and pnxiia, which are similar to hemolysin-like high-molecular-weight exoproteins are known in this species. in this study, we identified and analyzed a further rtx toxin named pnxiiia and the corresponding type i secretion system.201121410992
defining the normal bacterial flora of the oral cavity.more than 700 bacterial species or phylotypes, of which over 50% have not been cultivated, have been detected in the oral cavity. our purposes were (i) to utilize culture-independent molecular techniques to extend our knowledge on the breadth of bacterial diversity in the healthy human oral cavity, including not-yet-cultivated bacteria species, and (ii) to determine the site and subject specificity of bacterial colonization. nine sites from five clinically healthy subjects were analyzed. sites i ...200516272510
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 ...201324097834
a novel family of integrases associated with prophages and genomic islands integrated within the trna-dihydrouridine synthase a (dusa) gene.genomic islands play a key role in prokaryotic genome plasticity. genomic islands integrate into chromosomal loci such as transfer rna genes and protein coding genes, whilst retaining various cargo genes that potentially bestow novel functions on the host organism. a gene encoding a putative integrase was identified at a single site within the 5' end of the dusa gene in the genomes of over 200 bacteria. this integrase was discovered to be a component of numerous genomic islands, which appear to ...201525883135
common cell shape evolution of two nasopharyngeal pathogens.respiratory infectious diseases are the third cause of worldwide death. the nasopharynx is the portal of entry and the ecological niche of many microorganisms, of which some are pathogenic to humans, such as neisseria meningitidis and moraxella catarrhalis. these microbes possess several surface structures that interact with the actors of the innate immune system. in our attempt to understand the past evolution of these bacteria and their adaption to the nasopharynx, we first studied differences ...201526162030
dialects of the dna uptake sequence in all sexual organisms, adaptations exist that secure the safe reassortment of homologous alleles and prevent the intrusion of potentially hazardous alien dna. some bacteria engage in a simple form of sex known as transformation. in the human pathogen neisseria meningitidis and in related bacterial species, transformation by exogenous dna is regulated by the presence of a specific dna uptake sequence (dus), which is present in thousands of copies in the respective genomes. dus affects transform ...201323637627
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 ...201626811460
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