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Items: 1 to 20 of 33


Microbiome profiling by illumina sequencing of combinatorial sequence-tagged PCR products.

Gloor GB, Hummelen R, Macklaim JM, Dickson RJ, Fernandes AD, MacPhee R, Reid G.

PLoS One. 2010 Oct 26;5(10):e15406. doi: 10.1371/journal.pone.0015406.


BIPES, a cost-effective high-throughput method for assessing microbial diversity.

Zhou HW, Li DF, Tam NF, Jiang XT, Zhang H, Sheng HF, Qin J, Liu X, Zou F.

ISME J. 2011 Apr;5(4):741-9. doi: 10.1038/ismej.2010.160. Epub 2010 Oct 21.


Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions.

Claesson MJ, Wang Q, O'Sullivan O, Greene-Diniz R, Cole JR, Ross RP, O'Toole PW.

Nucleic Acids Res. 2010 Dec;38(22):e200. doi: 10.1093/nar/gkq873. Epub 2010 Sep 29.


Significant association between sulfate-reducing bacteria and uranium-reducing microbial communities as revealed by a combined massively parallel sequencing-indicator species approach.

Cardenas E, Wu WM, Leigh MB, Carley J, Carroll S, Gentry T, Luo J, Watson D, Gu B, Ginder-Vogel M, Kitanidis PK, Jardine PM, Zhou J, Criddle CS, Marsh TL, Tiedje JM.

Appl Environ Microbiol. 2010 Oct;76(20):6778-86. doi: 10.1128/AEM.01097-10. Epub 2010 Aug 20.


Unlocking short read sequencing for metagenomics.

Rodrigue S, Materna AC, Timberlake SC, Blackburn MC, Malmstrom RR, Alm EJ, Chisholm SW.

PLoS One. 2010 Jul 28;5(7):e11840. doi: 10.1371/journal.pone.0011840.


Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R.

Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4516-22. doi: 10.1073/pnas.1000080107. Epub 2010 Jun 3.


Experimental factors affecting PCR-based estimates of microbial species richness and evenness.

Engelbrektson A, Kunin V, Wrighton KC, Zvenigorodsky N, Chen F, Ochman H, Hugenholtz P.

ISME J. 2010 May;4(5):642-7. doi: 10.1038/ismej.2009.153. Epub 2010 Jan 21.


Ecology of the rare microbial biosphere of the Arctic Ocean.

Galand PE, Casamayor EO, Kirchman DL, Lovejoy C.

Proc Natl Acad Sci U S A. 2009 Dec 29;106(52):22427-32. doi: 10.1073/pnas.0908284106. Epub 2009 Dec 17.


Bacterial community variation in human body habitats across space and time.

Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R.

Science. 2009 Dec 18;326(5960):1694-7. doi: 10.1126/science.1177486. Epub 2009 Nov 5.


Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent.

McLellan SL, Huse SM, Mueller-Spitz SR, Andreishcheva EN, Sogin ML.

Environ Microbiol. 2010 Feb;12(2):378-92. doi: 10.1111/j.1462-2920.2009.02075.x. Epub 2009 Oct 16. Erratum in: Environ Microbiol. 2010 May;12(5):1376.


Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.

Lazarevic V, Whiteson K, Huse S, Hernandez D, Farinelli L, Osterås M, Schrenzel J, François P.

J Microbiol Methods. 2009 Dec;79(3):266-71. doi: 10.1016/j.mimet.2009.09.012. Epub 2009 Sep 29.


Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates.

Kunin V, Engelbrektson A, Ochman H, Hugenholtz P.

Environ Microbiol. 2010 Jan;12(1):118-23. doi: 10.1111/j.1462-2920.2009.02051.x. Epub 2009 Aug 27.


Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys.

Youssef N, Sheik CS, Krumholz LR, Najar FZ, Roe BA, Elshahed MS.

Appl Environ Microbiol. 2009 Aug;75(16):5227-36. doi: 10.1128/AEM.00592-09. Epub 2009 Jun 26.


Characterization of airborne microbial communities at a high-elevation site and their potential to act as atmospheric ice nuclei.

Bowers RM, Lauber CL, Wiedinmyer C, Hamady M, Hallar AG, Fall R, Knight R, Fierer N.

Appl Environ Microbiol. 2009 Aug;75(15):5121-30. doi: 10.1128/AEM.00447-09. Epub 2009 Jun 5.


Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation.

Antonopoulos DA, Huse SM, Morrison HG, Schmidt TM, Sogin ML, Young VB.

Infect Immun. 2009 Jun;77(6):2367-75. doi: 10.1128/IAI.01520-08. Epub 2009 Mar 23.


Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes.

Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ.

Nat Methods. 2009 Apr;6(4):291-5. doi: 10.1038/nmeth.1311. Epub 2009 Mar 15.


Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing.

Huse SM, Dethlefsen L, Huber JA, Mark Welch D, Relman DA, Sogin ML.

PLoS Genet. 2008 Nov;4(11):e1000255. doi: 10.1371/journal.pgen.1000255. Epub 2008 Nov 21. Erratum in: PLoS Genet. 2008 Dec;4(12). doi: 10.1371/annotation/3d8a6578-ce56-45aa-bc71-05078355b851. Welch, David Mark [corrected to Mark Welch, David].


The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing.

Dethlefsen L, Huse S, Sogin ML, Relman DA.

PLoS Biol. 2008 Nov 18;6(11):e280. doi: 10.1371/journal.pbio.0060280.


The Ribosomal Database Project: improved alignments and new tools for rRNA analysis.

Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM.

Nucleic Acids Res. 2009 Jan;37(Database issue):D141-5. doi: 10.1093/nar/gkn879. Epub 2008 Nov 12.


Pyrosequencing analysis of the oral microflora of healthy adults.

Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W.

J Dent Res. 2008 Nov;87(11):1016-20.


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