Curr Opin Microbiol. 2007 Oct;10(5):499-503. Epub 2007 Oct 22.

What's in the mix: phylogenetic classification of metagenome sequence samples.

Source

Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, NY 10598, USA. mchardy@mpi-inf.mpg.de

Abstract

Metagenomics is a novel field which deals with the sequencing and study of microbial organisms or viruses isolated directly from a particular environment. This has already provided a wealth of information and new insights for the inhabitants of various environmental niches. For a given sample, one would like to determine the phylogenetic provenance of the obtained fragments, the relative abundance of its different members, their metabolic capabilities, and the functional properties of the community as a whole. To this end, computational analyses are becoming increasingly indispensable tools. In this review, we focus on the problem of determining the phylogenetic identity of the sample fragments, a procedure known as 'binning'. This step is essential for the reconstruction of the metabolic capabilities of individual organisms or phylogenetic clades of a community, and the study of their interactions.

PMID:: 17933580; [PubMed - indexed for MEDLINE]

Publication Types, MeSH Terms, Substances

Publication Types

Review

MeSH Terms

Substances

LinkOut - more resources

Full Text Sources

Other Literature Sources

Supplemental Content

Save items

Related citations in PubMed

Comparative metagenomics of microbial communities. [Science. 2005]
Comparative metagenomics of microbial communities.
Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, et al. Science. 2005 Apr 22; 308(5721):554-7.
Review Get the most out of your metagenome: computational analysis of environmental sequence data. [Curr Opin Microbiol. 2007]
Review Get the most out of your metagenome: computational analysis of environmental sequence data.
Raes J, Foerstner KU, Bork P. Curr Opin Microbiol. 2007 Oct; 10(5):490-8. Epub 2007 Oct 23.
Accurate phylogenetic classification of variable-length DNA fragments. [Nat Methods. 2007]
Accurate phylogenetic classification of variable-length DNA fragments.
McHardy AC, Martín HG, Tsirigos A, Hugenholtz P, Rigoutsos I. Nat Methods. 2007 Jan; 4(1):63-72. Epub 2006 Dec 10.
Environmental genome shotgun sequencing of the Sargasso Sea. [Science. 2004]
Environmental genome shotgun sequencing of the Sargasso Sea.
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, et al. Science. 2004 Apr 2; 304(5667):66-74. Epub 2004 Mar 4.
Review Comparative analysis of environmental sequences: potential and challenges. [Philos Trans R Soc Lond B Biol...]
Review Comparative analysis of environmental sequences: potential and challenges.
Foerstner KU, von Mering C, Bork P. Philos Trans R Soc Lond B Biol Sci. 2006 Mar 29; 361(1467):519-23.

See reviews... See all...

Cited by 17 PubMed Central articles

Metabolic classification of microbial genomes using functional probes. [BMC Genomics. 2012]
Metabolic classification of microbial genomes using functional probes.
Lee CC, Lo WC, Lai SM, Chen YP, Tang CY, Lyu PC. BMC Genomics. 2012 Apr 27; 13(1):157. Epub 2012 Apr 27.
Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition. [Nucleic Acids Res. 2012]
Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition.
Saeed I, Tang SL, Halgamuge SK. Nucleic Acids Res. 2012 Mar; 40(5):e34. Epub 2011 Dec 17.
Taxonomic metagenome sequence assignment with structured output models. [Nat Methods. 2011]
Taxonomic metagenome sequence assignment with structured output models.
Patil KR, Haider P, Pope PB, Turnbaugh PJ, Morrison M, Scheffer T, McHardy AC. Nat Methods. 2011 Mar; 8(3):191-2.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Compound (MeSH Keyword)
PubChem chemical compound records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

What's in the mix: phylogenetic classification of metagenome sequence samples.
What's in the mix: phylogenetic classification of metagenome sequence samples.
Curr Opin Microbiol. 2007 Oct ;10(5):499-503. Epub 2007 Oct 22 .

PubMed
Contrasting features of urea cycle disorders in human patients and knockout mous...
Contrasting features of urea cycle disorders in human patients and knockout mouse models.
Mol Genet Metab. 2008 Jan ;93(1):7-14. Epub 2007 Oct 22 .

PubMed
Phytoestrogens and xenoestrogens: the contribution of diet and environment to en...
Phytoestrogens and xenoestrogens: the contribution of diet and environment to endocrine disruption.
J Steroid Biochem Mol Biol. 2008 Feb ;108(3-5):213-20. Epub 2007 Sep 7 .

PubMed
Effects of symbiotic preparations on constipated irritable bowel syndrome sympto...
Effects of symbiotic preparations on constipated irritable bowel syndrome symptoms.
Acta Biomed. 2007 Aug ;78(2):111-6.

PubMed
[Influenza type A (H5N1) virus infection].
[Influenza type A (H5N1) virus infection].
Mikrobiyol Bul. 2007 Jul ;41(3):485-94.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: