Mastering methodological pitfalls for surviving the metagenomic jungle

BioEssays

Volumn 35, Issue 8, 2013, Pages 744-754

  Delmont, Tom O ^a   Simonet, Pascal ^a   Vogel, Timothy M ^a  

^a CNRS   (France)

Author keywords

Biases; Distribution fluctuation; Metagenomic

Indexed keywords

DNA; NUCLEOTIDE;

ANALYTICAL ERROR; ARTICLE; DNA EXTRACTION; ECOSYSTEM; FECES; GRASSLAND; HUMAN; METAGENOME; METAGENOMICS; METHODOLOGY; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROORGANISM; NONHUMAN; PRINCIPAL COMPONENT ANALYSIS; PROTEIN FAMILY; PROTEIN METABOLISM; PYROSEQUENCING; QUANTITATIVE ANALYSIS; REPRODUCIBILITY; SIGNAL TRANSDUCTION; SOIL;

BIASES; DISTRIBUTION FLUCTUATION; METAGENOMIC;

BIODIVERSITY; BIOTECHNOLOGY; COMPUTATIONAL BIOLOGY; DNA; ECOLOGY; ECOSYSTEM; GENES, BACTERIAL; GENETIC VARIATION; HUMANS; METAGENOME; MICROBIOTA; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY;

EID: 84880341510     PISSN: 02659247     EISSN: 15211878     Source Type: Journal    
DOI: 10.1002/bies.201200155     Document Type: Article

References (26)

1. Altermann W, Kazmierczak J. 2003. Archean microfossils: a reappraisal of early life on Earth. Res Microbiol 154: 611-7.
2. Allwood AC, Walter MR, Kamber BS, Marshall CP, et al. 2006. Stromatolite reef from the Early Archaean era of Australia. Nature 441: 714-8.
3. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, et al. 2006. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027-31.
4. Ortiz-Castro R, Contreras-Cornejo HA, Macias-Rodriguez L, Lopez-Bucio J. 2009. The role of microbial signals in plant growth and development. Plant Signal Behav 4: 701-12.
5. Falkowski PG, Godfrey LV. 2008. Electrons, life and the evolution of Earth's oxygen cycle. Philos Trans R Soc Lond B Biol Sci 363: 2705-16.
6. Amann RI, Ludwig W, Schleifer KH. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59: 143-69.
7. Handelsman J, Rondon MR, Brady SF, Clardy J, et al. 1998. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5: R245-9.
8. Gillespie DE, Brady SF, Bettermann AD, Cianciotto NP, et al. 2002. Isolation of antibiotics turbomycin a and B from a metagenomic library of soil microbial DNA. Appl Environ Microbiol 68: 4301-6.
9. Demaneche S, Sanguin H, Pote J, Navarro E, et al. 2008. Antibiotic-resistant soil bacteria in transgenic plant fields. Proc Natl Acad Sci USA 105: 3957-62.
10. Venter JC, Remington K, Heidelberg JF, Halpern AL, et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
11. Tyson GW, Chapman J, Hugenholtz P, Allen EE, et al. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37-43.
12. Tringe SG, von Mering C, Kobayashi A, Salamov AA, et al. 2005. Comparative metagenomics of microbial communities. Science 308: 554-7.
13. Dinsdale EA, Edwards RA, Hall D, Angly F, et al. 2008. Functional metagenomic profiling of nine biomes. Nature 452: 629-32.
14. Delmont TO, Malandain C, Prestat E, Larose C, et al. 2011. Metagenomic mining for microbiologists. ISME J 5: 1837-43.
15. Qin J, Li R, Raes J, Arumugam M, et al. 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65.
16. Hess M, Sczyrba A, Egan R, Kim TW, et al. 2011. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331: 463-7.
17. Delmont TO, Robe P, Cecillon S, Clark IM, et al. 2011. Accessing the soil metagenome for studies of microbial diversity. Appl Environ Microbiol 77: 1315-24.
18. Yilmaz S, Allgaier M, Hugenholtz P. 2010. Multiple displacement amplification compromises quantitative analysis of metagenomes. Nat Methods 7: 943-4.
19. Delmont TO, Prestat E, Keegan KP, Faubladier M, et al. 2012. Structure, fluctuation and magnitude of a natural grassland soil metagenome. ISME J 6: 1677-87.
20. Meyer F, Paarmann D, D'Souza M, Olson R, et al. 2008. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386.
21. Parks DH, Beiko RG. 2010. Identifying biologically relevant differences between metagenomic communities. Bioinformatics 26: 715-21.
22. Niu B, Fu L, Sun S, Li W. 2010. Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics 11: 187.
23. Delmont TO, Simonet P, Vogel TM. 2012. Describing microbial communities and performing global comparisons in the 'omic era. ISME J 6: 1625-8.
24. Frostegard A, Courtois S, Ramisse V, Clerc S, et al. 1999. Quantification of bias related to the extraction of DNA directly from soils. Appl Environ Microbiol 65: 5409-20.
25. Carrigg C, Rice O, Kavanagh S, Collins G, et al. 2007. DNA extraction method affects microbial community profiles from soils and sediment. Appl Microbiol Biotechnol 77: 955-64.
26. Benjamini Y, Speed TP. 2012. Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res 40: e72.