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Comparative analysis of human saliva microbiome diversity by barcoded pyrosequencing and cloning approaches

Comparative analysis of human saliva microbiome diversity by barcoded pyrosequencing and cloning approaches,10.1016/j.ab.2009.04.034,Analytical Bioche

Comparative analysis of human saliva microbiome diversity by barcoded pyrosequencing and cloning approaches   (Citations: 7)
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Metagenomic studies traditionally rely on cloning polymerase chain reaction (PCR) products and sequencing multiple clones. However, this approach is tedious and expensive, thereby limiting the range and scale of questions that can be addressed. Recent developments in DNA sequencing technologies enable a dramatic increase in throughput via parallel in-depth analysis of many samples with limited sample processing and lower costs. We directly compared the traditional cloning approach with a barcoded pyrosequencing method to see whether the latter accurately describes microbiome diversity in human saliva. Our results indicate that despite the shorter read lengths, the pyrosequencing approach provides a description of the human salivary microbiome that is in good agreement with results based on the traditional cloning and sequencing approach.
Journal: Analytical Biochemistry - ANAL BIOCHEM , vol. 391, no. 1, pp. 64-68, 2009
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    • ...These 7 phyla were also abundant in other oral samples assessed by means of phyloarrays, sequencing of the 16S rDNA clones and 16S rDNA amplicon pyrosequencing [6,9-11,17,18]...
    • ...A total of 81 genera were identified by the MG-RAST server (Additional File 1). Among them 19 were neither reported in previous studies of oral microbiotas assessed by high-throughput sequencing [6,9,10,17] nor listed in the Human Oral Microbiome Database (HOMD; http:// www.homd.org)...

    Vladimir Lazarevicet al. Study of inter- and intra-individual variations in the salivary microb...

    • ...To evaluate this new technology, several studies have compared microbial community structures determined by pyrosequencing with those developed using well-established clone library technology (Jones et al. 2009; Krober et al. 2009; Nasidze et al. 2009)...
    • ...The V3 region has been used for investigating the microbial communities of fermented seafood (Roh et al.2010 ), the gut flora (Huse et al. 2008; Turnbaugh et al. 2008; Zhang et al. 2010), and the thermal gradients of two alkaline hot springs (Miller et al. 2009; Nasidze et al. 2009)...
    • ...The V1–V2 regions have also been used for this purpose (Nasidze et al. 2009; Bibby et al. 2010)...

    Xiaojun Zhanget al. A diverse bacterial community in an anoxic quinoline-degrading bioreac...

    • ...Distinct microbial communities inhabit different host environments on what can be seen topologically as the body’s surface: the skin, the oral cavity, the upper respiratory tract, the genital tract and the stomach (Cogen et al., 2008; Srinivasan and Fredricks, 2008; Avila et al., 2009; Nasidze et al., 2009b; Parahitiyawa et al., 2009)...
    • ...Such surveys have targeted the microbial inhabitants of the mouth, the skin, the stomach and the vagina (Grice et al., 2009; Nasidze et al., 2009b; Schellenberg et al., 2009)...

    Mark J. Pallen. The Human Microbiome and Host–Pathogen Interactions

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