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Direct sequencing of the human microbiome readily reveals community differences.

Kuczynski J, Costello EK, Nemergut DR, Zaneveld J, Lauber CL, Knights D, Koren O, Fierer N, Kelley ST, Ley RE, Gordon JI, Knight R.

Genome Biol. 2010;11(5):210. doi: 10.1186/gb-2010-11-5-210. Epub 2010 May 5. Review.


Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome.

Jones BV, Sun F, Marchesi JR.

BMC Genomics. 2010 Jan 19;11:46. doi: 10.1186/1471-2164-11-46.


Effect of k-tuple length on sample-comparison with high-throughput sequencing data.

Wang Y, Lei X, Wang S, Wang Z, Song N, Zeng F, Chen T.

Biochem Biophys Res Commun. 2016 Jan 22;469(4):1021-7. doi: 10.1016/j.bbrc.2015.11.094. Epub 2015 Dec 22.


Analysis of the cystic fibrosis lung microbiota via serial Illumina sequencing of bacterial 16S rRNA hypervariable regions.

Maughan H, Wang PW, Diaz Caballero J, Fung P, Gong Y, Donaldson SL, Yuan L, Keshavjee S, Zhang Y, Yau YC, Waters VJ, Tullis DE, Hwang DM, Guttman DS.

PLoS One. 2012;7(10):e45791. doi: 10.1371/journal.pone.0045791. Epub 2012 Oct 2.


Culture enriched molecular profiling of the cystic fibrosis airway microbiome.

Sibley CD, Grinwis ME, Field TR, Eshaghurshan CS, Faria MM, Dowd SE, Parkins MD, Rabin HR, Surette MG.

PLoS One. 2011;6(7):e22702. doi: 10.1371/journal.pone.0022702. Epub 2011 Jul 28.


Study of inter- and intra-individual variations in the salivary microbiota.

Lazarevic V, Whiteson K, Hernandez D, François P, Schrenzel J.

BMC Genomics. 2010 Sep 28;11:523. doi: 10.1186/1471-2164-11-523.


Phylogenetic analysis of a spontaneous cocoa bean fermentation metagenome reveals new insights into its bacterial and fungal community diversity.

Illeghems K, De Vuyst L, Papalexandratou Z, Weckx S.

PLoS One. 2012;7(5):e38040. doi: 10.1371/journal.pone.0038040. Epub 2012 May 29.


Beyond bacteria: a study of the enteric microbial consortium in extremely low birth weight infants.

LaTuga MS, Ellis JC, Cotton CM, Goldberg RN, Wynn JL, Jackson RB, Seed PC.

PLoS One. 2011;6(12):e27858. doi: 10.1371/journal.pone.0027858. Epub 2011 Dec 8.


Preliminary characterization of the oral microbiota of Chinese adults with and without gingivitis.

Huang S, Yang F, Zeng X, Chen J, Li R, Wen T, Li C, Wei W, Liu J, Chen L, Davis C, Xu J.

BMC Oral Health. 2011 Dec 12;11:33. doi: 10.1186/1472-6831-11-33.


Pyrosequencing analysis of the human microbiota of healthy Chinese undergraduates.

Ling Z, Liu X, Luo Y, Yuan L, Nelson KE, Wang Y, Xiang C, Li L.

BMC Genomics. 2013 Jun 10;14:390. doi: 10.1186/1471-2164-14-390.


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.


Genomic approaches to studying the human microbiota.

Weinstock GM.

Nature. 2012 Sep 13;489(7415):250-6. doi: 10.1038/nature11553. Review.


Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.

Schloss PD, Gevers D, Westcott SL.

PLoS One. 2011;6(12):e27310. doi: 10.1371/journal.pone.0027310. Epub 2011 Dec 14.


Estimation of metagenome size and structure in an experimental soil microbiota from low coverage next-generation sequence data.

Frisli T, Haverkamp TH, Jakobsen KS, Stenseth NC, Rudi K.

J Appl Microbiol. 2013 Jan;114(1):141-51. doi: 10.1111/jam.12035. Epub 2012 Nov 1.


Strategy for microbiome analysis using 16S rRNA gene sequence analysis on the Illumina sequencing platform.

Ram JL, Karim AS, Sendler ED, Kato I.

Syst Biol Reprod Med. 2011 Jun;57(3):162-70. doi: 10.3109/19396368.2011.555598. Epub 2011 Mar 1.


Cilantro microbiome before and after nonselective pre-enrichment for Salmonella using 16S rRNA and metagenomic sequencing.

Jarvis KG, White JR, Grim CJ, Ewing L, Ottesen AR, Beaubrun JJ, Pettengill JB, Brown E, Hanes DE.

BMC Microbiol. 2015 Aug 12;15:160. doi: 10.1186/s12866-015-0497-2.


Pyrosequence analysis of unamplified and whole genome amplified DNA from hydrocarbon-contaminated groundwater.

Abbai NS, Govender A, Shaik R, Pillay B.

Mol Biotechnol. 2012 Jan;50(1):39-48. doi: 10.1007/s12033-011-9412-8.


Tracking human sewage microbiome in a municipal wastewater treatment plant.

Cai L, Ju F, Zhang T.

Appl Microbiol Biotechnol. 2014 Apr;98(7):3317-26. doi: 10.1007/s00253-013-5402-z. Epub 2013 Dec 5.


Identification of household bacterial community and analysis of species shared with human microbiome.

Jeon YS, Chun J, Kim BS.

Curr Microbiol. 2013 Nov;67(5):557-63. doi: 10.1007/s00284-013-0401-y. Epub 2013 Jun 7.


Comparative metagenome analysis of an Alaskan glacier.

Choudhari S, Lohia R, Grigoriev A.

J Bioinform Comput Biol. 2014 Apr;12(2):1441003. doi: 10.1142/S0219720014410030. Epub 2014 Mar 6.


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