Serial analysis of V6 ribosomal sequence tags (SARST-V6): a method for efficient, high-throughput analysis of microbial community composition - PubMed (original) (raw)

Serial analysis of V6 ribosomal sequence tags (SARST-V6): a method for efficient, high-throughput analysis of microbial community composition

David T Kysela et al. Environ Microbiol. 2005 Mar.

Abstract

Serial analysis of ribosomal sequence tags (SARST) is a novel technique for characterizing microbial community composition. The SARST method captures sequence information from concatemers of short 16S rDNA polymerase chain reaction (PCR) amplicons from complex populations of DNA. Here, we describe a similar method, serial analysis of V6 ribosomal sequence tags (SARST-V6), which targets the V6 hypervariable region of bacterial 16S rRNA genes. The SARST-V6 technique exploits internal primer sequences to generate compatible restriction digest overhangs, thereby improving upon the efficiency of SARST. Serial analysis of V6 ribosomal sequence tags of bacterial community composition in hydrothermal marine sediments from Guaymas Basin resembled results of cloning and sequencing of single, full-length PCR products from ribosomal RNA genes of the same microbial community. Both methods identified the same major bacterial groups, but only SARST-V6 recovered thermodesulfobacteria and gamma-proteobacteria sequences, while only full-length PCR product cloning recovered candidate division OP11 se-quences. There were differences in the relative frequencies of some phylotypes. The disparities reflect differences in the amplicon pool obtained during initial amplification that may result from different primer affinities or DNA degradation. These results demonstrate the utility of SARST-V6 in collecting taxonomically informative data for high-throughput analysis of microbial communities.

PubMed Disclaimer

Similar articles

• Assessment of phylogenetic diversity of bacterial microflora in drinking water using serial analysis of ribosomal sequence tags.
  Poitelon JB, Joyeux M, Welté B, Duguet JP, Prestel E, Lespinet O, DuBow MS. Poitelon JB, et al. Water Res. 2009 Sep;43(17):4197-206. doi: 10.1016/j.watres.2009.07.020. Epub 2009 Jul 18. Water Res. 2009. PMID: 19665751
• Serial analysis of ribosomal sequence tags (SARST): a high-throughput method for profiling complex microbial communities.
  Neufeld JD, Yu Z, Lam W, Mohn WW. Neufeld JD, et al. Environ Microbiol. 2004 Feb;6(2):131-44. doi: 10.1046/j.1462-2920.2003.00547.x. Environ Microbiol. 2004. PMID: 14756878
• A survey of the methods for the characterization of microbial consortia and communities.
  Spiegelman D, Whissell G, Greer CW. Spiegelman D, et al. Can J Microbiol. 2005 May;51(5):355-86. doi: 10.1139/w05-003. Can J Microbiol. 2005. PMID: 16088332 Review.
• Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories.
  Woo PC, Lau SK, Teng JL, Tse H, Yuen KY. Woo PC, et al. Clin Microbiol Infect. 2008 Oct;14(10):908-34. doi: 10.1111/j.1469-0691.2008.02070.x. Clin Microbiol Infect. 2008. PMID: 18828852 Review.

Cited by

• Prokaryotic lifestyles in deep sea habitats.
  Lauro FM, Bartlett DH. Lauro FM, et al. Extremophiles. 2008 Jan;12(1):15-25. doi: 10.1007/s00792-006-0059-5. Epub 2007 Jan 17. Extremophiles. 2008. PMID: 17225926 Review.
• 16S rRNA gene sequencing on a benchtop sequencer: accuracy for identification of clinically important bacteria.
  Watts GS, Youens-Clark K, Slepian MJ, Wolk DM, Oshiro MM, Metzger GS, Dhingra D, Cranmer LD, Hurwitz BL. Watts GS, et al. J Appl Microbiol. 2017 Dec;123(6):1584-1596. doi: 10.1111/jam.13590. Epub 2017 Nov 7. J Appl Microbiol. 2017. PMID: 28940494 Free PMC article.
• Contrasting microbial community assembly hypotheses: a reconciling tale from the Río Tinto.
  Palacios C, Zettler E, Amils R, Amaral-Zettler L. Palacios C, et al. PLoS One. 2008;3(12):e3853. doi: 10.1371/journal.pone.0003853. Epub 2008 Dec 4. PLoS One. 2008. PMID: 19052647 Free PMC article.
• Microbial habitat connectivity across spatial scales and hydrothermal temperature gradients at Guaymas Basin.
  Meyer S, Wegener G, Lloyd KG, Teske A, Boetius A, Ramette A. Meyer S, et al. Front Microbiol. 2013 Jul 25;4:207. doi: 10.3389/fmicb.2013.00207. eCollection 2013. Front Microbiol. 2013. PMID: 23898326 Free PMC article.
• Microbial diversity in the deep sea and the underexplored "rare biosphere".
  Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, Arrieta JM, Herndl GJ. Sogin ML, et al. Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):12115-20. doi: 10.1073/pnas.0605127103. Epub 2006 Jul 31. Proc Natl Acad Sci U S A. 2006. PMID: 16880384 Free PMC article.

Publication types

MeSH terms

Substances

LinkOut - more resources

• Full Text Sources

  • Ovid Technologies, Inc.
  • Wiley

• Other Literature Sources

  • The Lens - Patent Citations Database