title: Metagenomic mining for microbiologists.
abstract: Microbial ecologists can now start digging into the accumulating mountains of metagenomic data to uncover the occurrence of functional genes and their correlations to microbial community members. Limitations and biases in DNA extraction and sequencing technologies impact sequence distributions, and therefore, have to be considered. However, when comparing metagenomes from widely differing environments, these fluctuations have a relatively minor role in microbial community discrimination. As a consequence, any functional gene or species distribution pattern can be compared among metagenomes originating from various environments and projects. In particular, global comparisons would help to define ecosystem specificities, such as involvement and response to climate change (for example, carbon and nitrogen cycle), human health risks (eg, presence of pathogen species, toxin genes and viruses) and biodegradation capacities. Although not all scientists have easy access to high-throughput sequencing technologies, they do have access to the sequences that have been deposited in databases, and therefore, can begin to intensively mine these metagenomic data to generate hypotheses that can be validated experimentally. Information about metabolic functions and microbial species compositions can already be compared among metagenomes from different ecosystems. These comparisons add to our understanding about microbial adaptation and the role of specific microbes in different ecosystems. Concurrent with the rapid growth of sequencing technologies, we have entered a new age of microbial ecology, which will enable researchers to experimentally confirm putative relationships between microbial functions and community structures.
authors: Environmental Microbial Genomics, Laboratoire Ampère, Ecole Centrale de Lyon, Université de Lyon, Ecully, France.
authors: Tom O
authors: TO
authors: Delmont
authors: Cedric
authors: C
authors: Malandain
authors: Emmanuel
authors: E
authors: Prestat
authors: Catherine
authors: C
authors: Larose
authors: Jean-Michel
authors: JM
authors: Monier
authors: Pascal
authors: P
authors: Simonet
authors: Timothy M
authors: TM
authors: Vogel
references: Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):3160-5
references: 14973198
references: Appl Environ Microbiol. 2011 Feb;77(4):1315-24
references: 21183646
references: Nature. 2004 Mar 4;428(6978):37-43
references: 14961025
references: BMC Bioinformatics. 2008 Sep 19;9:386
references: 18803844
references: Nature. 2002 Jul 18;418(6895):317-20
references: 12124622
references: Science. 2002 May 10;296(5570):1064-6
references: 12004116
references: FEMS Microbiol Rev. 2009 Mar;33(2):430-49
references: 19207745
references: Science. 2005 Apr 22;308(5721):554-7
references: 15845853
references: DNA Res. 2007 Aug 31;14(4):169-81
references: 17916580
references: Indian J Exp Biol. 2009 Jun;47(6):393-400
references: 19634702
references: Drugs. 2004;64(2):159-204
references: 14717618
references: Nature. 2008 Apr 3;452(7187):629-32
references: 18337718
references: Bioinformatics. 2010 Mar 15;26(6):715-21
references: 20130030
references: Environ Microbiol. 2009 Jul;11(7):1752-66
references: 19302541
references: Nat Rev Microbiol. 2008 Oct;6(10):776-88
references: 18794915
references: Science. 2005 Aug 26;309(5739):1387-90
references: 16123304
references: Nature. 2011 Jan 13;469(7329):162
references: 21228857
references: ISME J. 2007 Jul;1(3):185-7
references: 18043628
references: Nat Rev Microbiol. 2009 Oct;7(10):756; author reply 756-7
references: 19756015
references: Nat Rev Genet. 2010 Oct;11(10):733-9
references: 20838408
references: Nat Biotechnol. 2006 Oct;24(10):1263-9
references: 16998472
references: J Antimicrob Chemother. 2007 Dec;60(6):1288-97
references: 17884830
references: J Mol Biol. 1990 Oct 5;215(3):403-10
references: 2231712