Characterization of the complex bacterial communities colonizing biliary stents reveals a host-dependent diversity.
ABSTRACT This study provides a comprehensive survey of the spatial and temporal bacterial composition of biliary stent biofilms. The bacterial diversity, distribution and dynamics of 59 biliary and 4 pancreatic stent communities from 40 patients being treated at two different hospitals, which implant stents either simultaneously or consecutively, were characterized by single-strand conformation polymorphism (SSCP) analysis. Fifty-one phylotypes belonging to 5 bacterial phyla and 24 bacterial families were detected across 63 stents. This is a much broader diversity than previously detected through culture-dependent methods, particularly in regard to the diversity of obligate anaerobes. Stent bacterial diversity was patient-dependent and more similar when stents were implanted simultaneously rather than consecutively. Stent bacterial community composition differed between hospitals specifically because of the difference in abundance of Bifidobacteria. Co-colonization of Veillonella sp., Streptococcus anginosus and organisms closely related to Fusobacterium nucleatum revealed a potentially important attachment and survival strategy that has yet to be reported in biliary stents. This work reveals a more complete survey of the identities of bacterial species that form biofilms in biliary stents, their co-colonization patterns and the natural variation in species composition between different patients, hospitals and locations along the stent. Consideration of the community composition from individual patients will allow tailoring of prophylactic antibiotic treatments and thus will make the management of stent biofilms more effective.
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ABSTRACT: The Ribosomal Database Project (RDP) Classifier, a naïve Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. The majority of classifications (98%) were of high estimated confidence (> or = 95%) and high accuracy (98%). In addition to being tested with the corpus of 5,014 type strain sequences from Bergey's outline, the RDP Classifier was tested with a corpus of 23,095 rRNA sequences as assigned by the NCBI into their alternative higher-order taxonomy. The results from leave-one-out testing on both corpora show that the overall accuracies at all levels of confidence for near-full-length and 400-base segments were 89% or above down to the genus level, and the majority of the classification errors appear to be due to anomalies in the current taxonomies. For shorter rRNA segments, such as those that might be generated by pyrosequencing, the error rate varied greatly over the length of the 16S rRNA gene, with segments around the V2 and V4 variable regions giving the lowest error rates. The RDP Classifier is suitable both for the analysis of single rRNA sequences and for the analysis of libraries of thousands of sequences. Another related tool, RDP Library Compare, was developed to facilitate microbial-community comparison based on 16S rRNA gene sequence libraries. It combines the RDP Classifier with a statistical test to flag taxa differentially represented between samples. The RDP Classifier and RDP Library Compare are available online at http://rdp.cme.msu.edu/.Applied and Environmental Microbiology 09/2007; 73(16):5261-7. · 3.68 Impact Factor
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ABSTRACT: This study compared the initial (4 h) microflora on enamel in 7 caries-active and in 7 caries-inactive adolescents. In both groups the microflora was dominated by streptococci which comprised 61 and 78% (median values) of the total viable counts in caries-active and caries-inactive individuals, respectively (p less than 0.01). Identification of a total of 700 streptococcal isolates according to a recently revised classification showed that the predominant streptococci belonged to the species Streptococcus oralis, Streptococcus mitis biovar 1, and Streptococcus sanguis. Early plaque from caries-inactive individuals differed from that of caries-active individuals by significantly higher proportions of S. sanguis (p less than 0.05) and IgA1 protease producing streptococci (p less than 0.05). In caries-active individuals, there was a tendency to elevated levels of S. mitis biovar 1 (p less than 0.10). In addition, caries-active individuals were colonized by significantly higher numbers of mutans streptococci on the enamel surfaces (p less than 0.01). However, in both groups Streptococcus mutans (serotype c) comprised less than or equal to 2% of the early streptococcal flora. Streptococcus gordonii, S. mitis biovar 2, and Streptococcus salivarius were present in low proportions and did not show differences in distribution that could be related to caries activity. The observed differences in the composition of the early streptococcal microflora may be a factor that governs the eventual cariogenic potential of dental plaque.Caries Research 02/1990; 24(4):267-72. · 2.51 Impact Factor
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ABSTRACT: Single-strand-conformation polymorphism (SSCP) of DNA, a method widely used in mutation analysis, was adapted to the analysis and differentiation of cultivated pure-culture soil microorganisms and noncultivated rhizosphere microbial communities. A fragment (approximately 400 bp) of the bacterial 16S rRNA gene (V-4 and V-5 regions) was amplified by PCR with universal primers, with one primer phosphorylated at the 5' end. The phosphorylated strands of the PCR products were selectively digested with lambda exonuclease, and the remaining strands were separated by electrophoresis with an MDE polyacrylamide gel, a matrix specifically optimized for SSCP purposes. By this means, reannealing and heteroduplex formation of DNA strands during electrophoresis could be excluded, and the number of bands per organism was reduced. PCR products from 10 of 11 different bacterial type strains tested could be differentiated from each other. With template mixtures consisting of pure-culture DNAs from 5 and 10 bacterial strains, most of the single strains could be detected from such model communities after PCR and SSCP analyses. Purified bands amplified from pure cultures and model communities extracted from gels could be reamplified by PCR, but by this process, additional products were also generated, as detected by further SSCP analysis. Profiles generated with DNAs of rhizosphere bacterial communities, directly extracted from two different plant species grown in the same field site, could be clearly distinguished. This study demonstrates the potential of the selected PCR-single-stranded DNA approach for microbial community analysis.Applied and Environmental Microbiology 01/1999; 64(12):4870-6. · 3.68 Impact Factor