Applications of Advanced Omics Technologies: From Genes to Metabolites

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• Publisher: Elsevier
• Year: 2014
• Print ISBN: 9780444626509
• eBook ISBN: 9780444626691
• Topic: Biological Sciences
• Subtopic: Genetics & Genomics
• Index: Biological Sciences

The book contains contributions concerning the application of the new instrumental and methodological developments in omics technologies, including those related to Genomics, Transcriptomics, Proteomics, Peptidomics and Metabolomics, Lipidomics and Foodomics.The16 chapters discuss in detail: innovative applications of functional gene microarrays for profiling microbial communities, microRNA profiling, novel genotyping applications using microarray technology in cancer research, next-generation sequencing applied to the study of human microbiome, emerging RNA-SEQ applications in food science, recent progress in plant proteomics, applications of gel-free proteomic approaches, the challenges and applications of proteomics tools for food authenticity, the role of salivary peptidomics in clinical applications, metabolomic approaches to the study of degenerative, cardiovascular and renal diseases, and neonatal medicine. Also covered are other omics applications such as profiling of genetically modified organisms, the fundamentals, applications and challenges of foodomics, and MS-based lipidomics. Moreover, this volume includes relevant and updated aspects on bioinformatics, data treatment, data integration and systems biology. This book complements the previous volume "Fundamentals of Advanced Omics Technologies: New Advances from Genes to Metabolites" that covered the fundamental aspects of these new omics technologies. - Describes the latest applications of omics technologies - Provides an excellent reference for applications of advanced omics techniques - Includes advanced tools and methodologies for dealing with the data generated

Part I:

Genomics and Transcriptomics

Chapter 1

Applications of Functional Gene Microarrays for Profiling Microbial Communities

Joy D. Van Nostrand; Jizhong Zhou Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA

Abstract

Microarrays have revolutionized the study of microbiology by providing a means to examine communities for the presence of thousands of genes with a single test and overcoming the limitations of other culture-dependent and culture-independent approaches. Since arrays were first described, many new types of arrays and novel uses have been developed to examine microbial communities. This chapter focuses on functional gene arrays, which probe for structural genes involved in particular functions of interest. Functional gene arrays have been used to examine samples from numerous environments including the deep sea, Antarctic locations, metals-contaminated sites, climate change experimental sites, human environments, and other clinical applications. Novel techniques and applications using microarrays highlight the advantages of this technology.

Keywords

Functional gene arrays

Microarrays

GeoChip

Microbial communities

Pathogen detection

1 Introduction

Microorganisms play important roles in global biogeochemical cycling of carbon, nitrogen, sulfur, phosphorous, and metals as well as being involved in the stabilization or degradation of anthropogenic contaminants. With an estimated 2000–50,000 microbial species per gram of soil (1–4), microorganisms are also the most phylogenetically and functionally diverse group of organisms on the planet. However, our understanding of many of these functions is not well understood due to the difficulty in examining and monitoring microbial activity in the environment. This is due, in part, to the uncultured status of many (> 99%) microorganisms (5–7). As most microorganisms cannot be examined directly, culture-independent approaches are needed to determine what microorganisms are present and what functions they are performing. There are many culture-independent methods available, such as 16S rRNA gene-based cloning, quantitative PCR, denaturing (or temperature) gradient gel electrophoresis, terminal-restriction fragment length polymorphism (T-RFLP), quantitative PCR, and in situ hybridization. However, the resolution and coverage these methods provide are limited. Clone libraries, for example, are often too small by a factor of 10 or more to capture the true diversity of microbial communities (8,9). In addition, many of these methods require a PCR amplification step, which introduces well-known biases (10–12). The use of PCR also limits the number of genes that can be examined since there is so much variance in gene sequences or too few sequences are available, making the use of conserved PCR primers impractical or impossible. Lastly, often phylogenetic markers are used, such as 16S rRNA or DNA gyrase (GyrB) genes (5,13–16), which provide information on the identity of microorganisms within the community but provide limited information on the community's functional abilities and activity. Because of their design, microarrays can overcome many of these limitations and have been shown to be valuable for the study of microbial communities (17).

Microarrays are comprised of probes for specific genes, sequences, or genomes on a solid surface. They are similar to traditional Northern or Southern blots, except that instead of a labeled probe hybridizing to target nucleic acid attached to a membrane, labeled nucleic acids are hybridized to the probes that are attached to the array surface. Microarrays can be produced on glass slides (18–20) or nylon membranes (21); although most arrays use glass slides because they produce less background fluorescence (22,23) and allow higher probe density (24). Microarrays allow for the examination of thousands of genes at one time without the need for PCR amplification of individual genes and can provide detection for a wide range of target microorganisms. With the use of oligonucleotide probes, any gene can be added to the array as long as sequences are available without the need for primers. Since microarrays have a defined probe set that all samples are tested against, they are ideal for comparison of samples across different conditions, sites, or times.

Since they were first reported, several new types of microarrays have been developed for use on microbial communities. These include phylogenetic oligonucleotide arrays (POA), which are designed to examine phylogenetic relatedness or community composition using 16S rRNA or other conserved genes (16,25–27). The most comprehensive POA to date is the PhyloChip (16,28–30). The current version of PhyloChip, G3, has 1.1 million 25-mer probes covering 59,959 taxa (30). Other POAs, designed to study specific environments such as compost (31) or specific groups such as the “Rhodocyclales” order (26), have also been developed. Community genome arrays (CGA) use whole genomic DNA as probes (32,33) and can be used to determine the relatedness of microbial species or strains or to identify community members. CGAs have been used to compare microbial communities from different environments (32), to examine communities from acid mine drainage and bioleaching communities (34), and to determine the relatedness of different Escherichia coli strains (33) and 55 different Azoarcus, Pseudomonas, and Shewanella strains (35). Metagenomic arrays (MGAs) use environmental clone library inserts as probes and can be used as a high-throughput screening method (36–38). MGAs have been used to examine communities from marine environments (39). Whole-genome ORF arrays (WGAs) have probes for all ORFs in one or more genomes and are used for gene expression analysis (40). However, WGAs have also been used for comparative genomics (41). Several Shewanella strains were compared using a WGA containing 192 ORFs from Shewanella oneidensis MR-1 (41), an E. coli K-12 WGA was used to examine similar genes in Klebsiella pneumoniae (42), Pseudomonas syringae strains were compared using a WGA of 353 virulence factors (43), and a Pyrococcus furiosus WGA was used to examine 7 Pyrococcus isolates (44). Functional gene arrays (FGAs) contain probes for specific functional genes involved in various processes of interest, such as carbon cycling or metal resistance, and can provide information on the genes and populations within a community and provide direct linkages between gene functions and ecosystem processes (45). FGAs will be the primary focus of this chapter.

2 Comparison of Microarrays with High-Throughput Sequencing

Although this chapter deals with microarrays, high-throughput sequencing, which has become an increasingly popular choice for studying microbial communities even for metatranscriptome analysis (46), will be discussed here very briefly. High-throughput sequencing has many advantages; however, there are a few distinct disadvantages that bear mention. These disadvantages can be overcome with microarray technology, while high-throughput sequencing can overcome one of the greatest disadvantages of microarrays, making microarrays and high-throughput sequencing ideal as complementary approaches to the study of...

Table of contents

• Cover image
• Title page
• Table of Contents
• Copyright
• Dedication
• Contributors to Volume 64
• Series Editor's Preface
• Preface
• Part I: Genomics and Transcriptomics
• Part II: Proteomics and Peptidomics
• Part III: Metabolomics
• Part IV: Other Omics Strategies, Data Treatment, Integration and Systems Biology
• Index