Technology and techniques for microbial ecology via DNA sequencing

Annals of the American Thoracic Society

Volumn 11, Issue SUPPL. 1, 2014, Pages

  Walters, William A ^a   Knight, Rob ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

Metagenomics; Microbial ecology; Microbiome; Phylogenetics; Sequencing

Indexed keywords

DNA, BACTERIAL; DNA, RIBOSOMAL; HUMANS; METAGENOME; MICROBIOTA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84893898594     PISSN: 23256621     EISSN: None     Source Type: Journal    
DOI: 10.1513/AnnalsATS.201306-160MG     Document Type: Conference Paper

References (34)

1. Madigan M, Martinko J, editors. Brock biology of microorganisms, 11th ed. New Jersey: Prentice Hall; 2006.
2. Sleator, RD. The human superorganism - of microbes and men. Med Hypotheses 2010;74:214-215.
3. Savage DC. Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol 1977;31:107-133.
4. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE. Metagenomic analysis of the human distal gut microbiome. Science 2006;312:1355-1359.
5. Woese CR, Fox GE. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 1977;74:5088-5090.
6. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 1977;74:5463-5467.
7. Saiki RK, Scharf S, Faloona F, Mullis KB, Horn GT, Erlich HA, Arnheim N. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 1985;230:1350-1354.
8. Pace NR, Stahl DA, Lane DJ, Olsen GJ. The analysis of natural microbial populations by ribosomal RNA sequences. Am Soc Microbiol News 1985;51:4-12.
9. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005;437:376-380. [Published erratum appears in Nature 2006;441:120. Ho, Chun He (corrected to Ho, Chun Heen).]
10. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci USA 2010;108:4516-4522
11. Kuczynski J, Lauber CL, Walters WA, Parfrey LW, Clemente JC, Gevers D, Knight R. Experimental and analytical tools for studying the human microbiome. Nat Rev Genet 2012;13:47-58.
12. Hongoh Y, Ohkuma M, Kudo T. Molecular analysis of bacterial microbiota in the gut of the termite Reticulitermes speratus (Isoptera; Rhinotermitidae). FEMS Microbiol Ecol 2003;44:231-242.
13. Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knight R, Gordon J. Obesity alters gut microbial ecology. Proc Natl Acad Sci USA 2005;102:11070-11075.
14. Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 2005;71:8228-8235.
15. Lozupone C, Knight R. Global patterns in bacterial diversity. Proc Natl Acad Sci USA 2007;104:11436-11440.
16. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 2009;75:7537-7541.
17. Caporaso J, Kuczynski J, Stombaugh J, Bittinger K, Bushman F, Costello EK, Fierer N, Peña A, Goodrich JK, Gordon J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010;7:335-336.
18. Huson, H, Auch, A, Qi, J, Schuster, SC. MEGAN Analysis of metagenomic data. Genome Res 2007;17:377-386.
19. Glass E, Wilkening J, Wilke A, Antonopoulos D, Meyer F. Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. Cold Spring Harb Protoc 2010;2010(1):pdb.prot5368.
20. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, et al. A core gut microbiome in obese and lean twins. Nature 2009;457:480-484.
21. Fierer N, Hamady M, Lauber CL, Knight R. The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci USA 2008;105:17994-17999.
22. Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, Stombaugh J, Knights D, Gajer P, Ravel J, Fierer N, et al. Moving pictures of the human microbiome. Genome Biol 2011;12:R50.
23. Dominguez-Bello MG, Costella EK, Contreras M, Magris M, Hidalgo G, Fierer N, Knight R. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci USA 2010;107:11971-11975.
24. Gilbert JA. Constructing the microbial biomap for earth. [Internet] Argonne National Laboratory [updated 2013 Dec 12; accessed 2013 Dec 28]. Available from: http://www.earthmicrobiome.org/
25. Knight RD. World's largest open-source science project to understand the microbial diversity of the human gut. [Internet] Biofrontiers Institute at the University of Colorado-Boulder [updated 2013 Oct 2, accessed 2013 Dec 28]. Available from http://humanfoodproject.com/americangut/
26. Tringe, SG, Hugenholtz, P. A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol 2008;11:442-446.
27. Muegge BD, Kuczynski J, Knights D, Clemente JC, González A, Fontana L, Henrissat B, Knight R, Gordon JI. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 2011;332:970-974.
28. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 2012;486:207-214.
29. Smith MI, Yatsunenko T, Manary MJ, Trehan I, Mkakosya R, Cheng J, Kau AL, Rich SS, Concannon P, Mychaleckyj JC, et al. Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science 2013;339:548-554.
30. McNulty NP, Yatsunenko T, Hsiao A, Faith JJ, Muegge BD, Goodman AL, Henrissat B, Oozeer R, Cools-Portier S, Gobert G, et al. The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci Transl Med 2011;3:106ra106.
31. Clayton TA, Baker D, Lindon JC, Everett JR, Nicholson JK. Pharmacometabonomic identi fication of a signi ficant host-microbiome metabolic interaction affecting human drug metabolism. Proc Natl Acad Sci USA 2009;106:14728-14733.
32. Claus SP, Ellero SL, Berger B, Krause L, Bruttin A, Molina J, Paris A, Want EJ, de Waziers I, Cloarec O, et al. Colonization-induced host-gut microbial metabolic interaction. MBio 2011;2:e00271-10.
33. Gonzalez A, Knight R. Advancing analytical algorithms and pipelines for billions of microbial sequences. Curr Opin Biotechnol 2012;23:64-71.
34. Gonzalez A, Clemente JC, Shade A, Metcalf JL, Song S, Prithiviraj B, Palmer BE, Knight R. Our microbial selves: what ecology can teach us. EMBO Rep 2011;12:775-784.