DNA extraction for streamlined metagenomics of diverse environmental samples

BioTechniques

Volumn 62, Issue 6, 2017, Pages 290-293

  Marotz, Clarisse ^a   Amir, Amnon ^a   Humphrey, Greg ^a   Gaffney, James ^a   Gogul, Grant ^a   Knight, Rob ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

DNA extraction; High throughput; Metagenomics; Microbiome

Indexed keywords

RNA 16S; SEA WATER; BACTERIAL DNA;

ARTICLE; CONTROLLED STUDY; DNA EXTRACTION; DNA ISOLATION; DUST; ENVIRONMENTAL MONITORING; FECES; GENE AMPLIFICATION; GENE SEQUENCE; HUMAN; METAGENOMICS; MOUTH CAVITY; QUALITY CONTROL; RNA GENE; RNA SEQUENCE; SALIVA; SEDIMENT; SEQUENCE ANALYSIS; SKIN; SOIL; TAXONOMIC IDENTIFICATION; BACTERIUM; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; MICROBIOLOGY; MICROFLORA; PROCEDURES;

BACTERIA; DNA, BACTERIAL; FECES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; METAGENOMICS; MICROBIOTA; RNA, RIBOSOMAL, 16S; SALIVA; SEQUENCE ANALYSIS, DNA; SKIN; SOIL MICROBIOLOGY; WATER MICROBIOLOGY;

EID: 85020877465     PISSN: 07366205     EISSN: 19409818     Source Type: Journal    
DOI: 10.2144/000114559     Document Type: Article

References (9)

1. Wu, G.D., J.D. Lewis, C. Hoffmann, Y.Y. Chen, R. Knight, K. Bittinger, J. Hwang, J. Chen, et al. 2010. Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol. 10: 206.
2. Yuan, S., D.B. Cohen, J. Ravel, Z. Abdo, and L.J. Forney. 2012. Evaluation of methods for the extraction and purification of DNA from the human microbiome. PLoS One 7: e33865.
3. Kennedy, N.A., A.W. Walker, S.H. Berry, S.H. Duncan, F.M. Farquarson, P. Louis, and J.M. Thomson. 2014. The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing. PLoS One 9: e88982.
4. Metcalf, J.L., L.W. Parfrey, A. Gonzalez, C.L. Lauber, D. Knights, G. Ackermann, G.C. Humphrey, M.J. Gebert, et al. 2013. A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system. eLife 2: e01104.
5. Gilbert, J.A., D. Field, P. Swift, S. Thomas, D. Cummings, B. Temperton, K. Weynberg, S. Huse, et al. 2010. The taxonomic and functional diversity of microbes at a temperate coastal site: a ‘multi-omic’study of seasonal and diel temporal variation. PLoS One 5: e15545.
6. Bouslimani, A., C. Porto, C.M. Rath, M. Wang, Y. Guo, A. Gonzalez, D. Berg-Lyon, G. Ackermann, et al. 2015. Molecular cartography of the human skin surface in 3D. Proc. Natl. Acad. Sci. USA 112: E2120-E2129.
7. Caporaso, J.G., C.L. Lauber, W.A. Walters, D. Berg-Lyons, J. Huntley, N. Fierer, S.M. Owens, J. Betley, et al. 2012. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6: 1621-1624.
8. Amir, A., D. McDonald, J.A Navas-Molina, E. Kopylova, J.T. Morton, Z.Z. Xu, E.P. Kightley, L.R. Thompson, et al. 2017. Deblur rapidly resolves single-nucleotide community sequence patterns. mSystems. 2: e00191-16.
9. Vázquez-Baeza, Y., M. Pirrung, A. Gonzalez, and R. Knight. 2013. EMPeror: a tool for visualizing high-throughput microbial community data. Gigascience 2: 16.