Bacterial Diversity in Human Subgingival Plaque
Bruce J. Paster,Bruce J. Paster,Susan K. Boches,Jamie L. Galvin,Rebecca E. Ericson,C. N. Lau,Valerie A. Levanos,Ashish Sahasrabudhe,Floyd E. Dewhirst,Floyd E. Dewhirst +9 more
Reads0
Chats0
TLDR
The purpose of this study was to determine the bacterial diversity in the human subgingival plaque by using culture-independent molecular methods as part of an ongoing effort to obtain full 16S rRNA sequences for all cultivable and not-yet-cultivated species of human oral bacteria.Abstract:
The purpose of this study was to determine the bacterial diversity in the human subgingival plaque by using culture-independent molecular methods as part of an ongoing effort to obtain full 16S rRNA sequences for all cultivable and not-yet-cultivated species of human oral bacteria. Subgingival plaque was analyzed from healthy subjects and subjects with refractory periodontitis, adult periodontitis, human immunodeficiency virus periodontitis, and acute necrotizing ulcerative gingivitis. 16S ribosomal DNA (rDNA) bacterial genes from DNA isolated from subgingival plaque samples were PCR amplified with all-bacterial or selective primers and cloned into Escherichia coli. The sequences of cloned 16S rDNA inserts were used to determine species identity or closest relatives by comparison with sequences of known species. A total of 2,522 clones were analyzed. Nearly complete sequences of approximately 1,500 bases were obtained for putative new species. About 60% of the clones fell into 132 known species, 70 of which were identified from multiple subjects. About 40% of the clones were novel phylotypes. Of the 215 novel phylotypes, 75 were identified from multiple subjects. Known putative periodontal pathogens such as Porphyromonas gingivalis, Bacteroides forsythus, and Treponema denticola were identified from multiple subjects, but typically as a minor component of the plaque as seen in cultivable studies. Several phylotypes fell into two recently described phyla previously associated with extreme natural environments, for which there are no cultivable species. A number of species or phylotypes were found only in subjects with disease, and a few were found only in healthy subjects. The organisms identified only from diseased sites deserve further study as potential pathogens. Based on the sequence data in this study, the predominant subgingival microbial community consisted of 347 species or phylotypes that fall into 9 bacterial phyla. Based on the 347 species seen in our sample of 2,522 clones, we estimate that there are 68 additional unseen species, for a total estimate of 415 species in the subgingival plaque. When organisms found on other oral surfaces such as the cheek, tongue, and teeth are added to this number, the best estimate of the total species diversity in the oral cavity is approximately 500 species, as previously proposed.read more
Citations
More filters
Journal ArticleDOI
Bacterial profiles of saliva in relation to diet, lifestyle factors, and socioeconomic status.
Daniel Belstrøm,Palle Holmstrup,Claus Henrik Nielsen,Nikolai Kirkby,Svante Twetman,Berit L. Heitmann,Vanja Klepac-Ceraj,Bruce J. Paster,Nils-Erik Fiehn +8 more
TL;DR: The bacterial profile of saliva seems independent of diet intake, but influenced by smoking and maybe socioeconomic status, as well as two bacterial taxa that were more associated with smokers than non-smokers.
Journal ArticleDOI
Optimal prediction of the number of unseen species
TL;DR: A class of simple algorithms are obtained that provably predict U all of the way up to t∝logn samples, and it is shown that this range is the best possible and that the estimator’s mean-square error is near optimal for any t.
Journal ArticleDOI
Filifactor alocis--involvement in periodontal biofilms.
Sebastian Schlafer,Birgit Riep,Ann L. Griffen,Annett Petrich,Julia Hübner,Moritz Berning,Anton Friedmann,Ulf B. Göbel,Annette Moter +8 more
TL;DR: F. alocis is likely to make a relevant contribution to the pathogenetic structure of biofilms accounting for periodontal inflammation and can be considered an excellent marker organism forperiodontal disease.
Journal ArticleDOI
Quantitative Analysis of Multi-Species Oral Biofilms by TaqMan Real-Time PCR
TL;DR: The development and use of TaqMan real-time PCR for quantifying oral bacteria, its role in the diagnosis of oral infectious diseases and their microbial etiology are reviewed.
Journal ArticleDOI
Intra-individual diversity and similarity of salivary and faecal microbiota
TL;DR: In this article, polyphasic analysis combined with fingerprinting of individual isolates and denaturing gradient gel electrophoresis (DGGE) was applied to study whether similar features concerning the diversity and temporal stability of selected bacterial groups could be detected intra-individually in two different niches (the oral cavity and the colon) from ten adult volunteers consuming probiotics.
References
More filters
Journal ArticleDOI
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Naruya Saitou,Masatoshi Nei +1 more
TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Journal ArticleDOI
Phylogenetic identification and in situ detection of individual microbial cells without cultivation.
TL;DR: Phylogenetic analysis of the retrieved rRNA sequence of an uncultured microorganism reveals its closest culturable relatives and may, together with information on the physicochemical conditions of its natural habitat, facilitate more directed cultivation attempts.
Journal ArticleDOI
Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology
Erko Stackebrandt,B. M. Goebel +1 more
TL;DR: Amorphous metal alloys are employed in acoustic devices dependent upon the properties of low acoustic velocity and low attenuation, such as wire, strip and bulk delay lines.
Journal ArticleDOI
Microbial complexes in subgingival plaque
TL;DR: The purpose of the present investigation was to attempt to define communities using data from large numbers of plaque samples and different clustering and ordination techniques, which related strikingly to clinical measures of periodontal disease particularly pocket depth and bleeding on probing.