Integrating multiple 'omics' analysis for microbial biology: application and methodologies.

Authors:
Weiwen Zhang
Weiwen Zhang
Tianjin University
China
Mr Feng Li, MD
Mr Feng Li, MD
Tongji Hospital
China
Lei Nie
Lei Nie
School of Pharmaceutical Sciences
United States

Microbiology 2010 Feb 12;156(Pt 2):287-301. Epub 2009 Nov 12.

Center for Ecogenomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287-6501, USA.

Recent advances in various 'omics' technologies enable quantitative monitoring of the abundance of various biological molecules in a high-throughput manner, and thus allow determination of their variation between different biological states on a genomic scale. Several popular 'omics' platforms that have been used in microbial systems biology include transcriptomics, which measures mRNA transcript levels; proteomics, which quantifies protein abundance; metabolomics, which determines abundance of small cellular metabolites; interactomics, which resolves the whole set of molecular interactions in cells; and fluxomics, which establishes dynamic changes of molecules within a cell over time. However, no single 'omics' analysis can fully unravel the complexities of fundamental microbial biology. Therefore, integration of multiple layers of information, the multi-'omics' approach, is required to acquire a precise picture of living micro-organisms. In spite of this being a challenging task, some attempts have been made recently to integrate heterogeneous 'omics' datasets in various microbial systems and the results have demonstrated that the multi-'omics' approach is a powerful tool for understanding the functional principles and dynamics of total cellular systems. This article reviews some basic concepts of various experimental 'omics' approaches, recent application of the integrated 'omics' for exploring metabolic and regulatory mechanisms in microbes, and advances in computational and statistical methodologies associated with integrated 'omics' analyses. Online databases and bioinformatic infrastructure available for integrated 'omics' analyses are also briefly discussed.

Download full-text PDF

Source
http://dx.doi.org/10.1099/mic.0.034793-0DOI Listing
February 2010
28 Reads

Publication Analysis

Top Keywords

integrated 'omics'
12
'omics'
9
microbial systems
8
'omics' analysis
8
multi-'omics' approach
8
microbial biology
8
'omics' analyses
8
required acquire
4
acquire precise
4
approach required
4
multiple layers
4
biology integration
4
integration multiple
4
layers multi-'omics'
4
living micro-organisms
4
task attempts
4
attempts integrate
4
integrate heterogeneous
4
challenging task
4
spite challenging
4

Altmetric Statistics

Similar Publications

Integrated omics approaches in plant systems biology.

Curr Opin Chem Biol 2009 Dec;13(5-6):532-8

RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan.

Understanding cellular metabolic systems is vital not only for determining the function of enzymatic genes, but also for elucidating the coordination among various metabolic pathways. In this context, high-throughput experiments can provide us with essential, albeit only partial information. Integration of metabolite profiling with other multiple 'omics' data (e. Read More

View Article
December 2009

Toxicology and genetic toxicology in the new era of "toxicogenomics": impact of "-omics" technologies.

Mutat Res 2002 Jan;499(1):13-25

Miami Valley Laboratories, The Procter & Gamble Co., P.O. Box 538707, Cincinnati, OH 45253, USA.

The unprecedented advances in molecular biology during the last two decades have resulted in a dramatic increase in knowledge about gene structure and function, an immense database of genetic sequence information, and an impressive set of efficient new technologies for monitoring genetic sequences, genetic variation, and global functional gene expression. These advances have led to a new sub-discipline of toxicology: "toxicogenomics". We define toxicogenomics as "the study of the relationship between the structure and activity of the genome (the cellular complement of genes) and the adverse biological effects of exogenous agents". Read More

View Article
January 2002

Metabolomics and fluxomics approaches.

Essays Biochem 2008 ;45:67-81

Department of Biochemistry and Molecular Biology and Institute of Biomedicine of University of Barcelona (IBUB), Faculty of Biology, University of Barcelona, Avda, Diagonal, 645, Edifici Nou, pl -2, 08028 Barcelona, Spain.

Systems biology is based on the understanding that the behaviour of the whole is greater than would be expected from the sum of its parts. Thus the ultimate goal of systems biology is to predict the behaviour of the whole system on the basis of the list of components involved. Recent advances in '-omics' technologies and the development of new computational techniques and algorithms have greatly contributed to progress in this field of biology. Read More

View Article
December 2008

Integrative analysis of transcriptomic and proteomic data: challenges, solutions and applications.

Crit Rev Biotechnol 2007 Apr-Jun;27(2):63-75

Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University. Washington, DC, USA.

Recent advances in high-throughput technologies enable quantitative monitoring of the abundance of various biological molecules and allow determination of their variation between biological states on a genomic scale. Two popular platforms are DNA microarrays that measure messenger RNA transcript levels, and gel-free proteomic analyses that quantify protein abundance. Obviously, no single approach can fully unravel the complexities of fundamental biology and it is equally clear that integrative analysis of multiple levels of gene expression would be valuable in this endeavor. Read More

View Article
September 2007