Microarrays: Current Technology, Innovations and Applications
"a valuable and useful source ... recommended" (Biotechnol. Agron. Soc. Environ.)
"a valuable and useful one stop source" (Fungal Diversity)
Caister Academic Press
University of Oklahoma, Norman, OK, USA
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Microorganisms are the most diverse group of organisms and play important and distinctive roles in their ecosystems. They interact with their peers and other organisms (e.g., plants, animals) to form a complicated food web, significantly impacting ecosystem functions and services. However, understanding the diversity, composition, structure, function, activity and dynamics of microbial communities remains challenging. Over the past decade, microarray-based technologies have been developed to address such challenges.
Written by expert authors this book is focused on current microarray technologies and their applications in environmental microbiology. In the first chapter microarray technologies and applications are briefly introduced and in following chapters microarray probe design, development and evaluation, and data analysis are described in detail. In later chapters, more attention is paid to phylogenetic arrays (e.g., PhyloChip) and functional gene arrays (e.g., GeoChip). These generic tools for analyzing microbial communities from disparate environments, ecosystems, and habitats including soil, water, sediment, animals and humans, are described in detail with examples of specific applications. Also included are microarrays for analyzing microbial communities from specific environments, such as soil, bioleaching ecosystems, and human microbiomes, and microarrays for detecting specific microorganisms (e.g., pathogens) in the environment. The authors also discuss the advantages and limitations of microarray technologies compared to high throughput sequencing technologies.
This book is a valuable and useful source of information about microarrays for microbial community analysis and is recommended for anyone working on microbial communities, biofilms or environmental microbiology.
"Written by expert authors ... This book is a valuable and useful source of information ... recommended for anyone working on microbial communities, biofilms or environmental microbiology" from Biotechnol. Agron. Soc. Environ. (2014) 18: 589-591.
"This book is a valuable and useful one stop source of information on microarrays for microbial community analysis and is recommended for anyone working on microbial communities, biofilms or environmental microbiology." from Fungal Diversity
Table of contents
1. Microarrays for Microbial Community Analysis at a Glance
Zhili He and Jizhong Zhou
Microorganisms are the most diverse group of organisms, and play important and distinctive roles in their ecosystems, such as biogeochemical cycling of carbon, nitrogen, sulfur, phosphorus and metals, and biodegradation or stabilization of environmental contaminants. They also interact with their peers and/or other organisms (e.g., plants, animals) to form a complicated food web, significantly impacting ecosystem functions and services. However, understanding the diversity, composition, structure, functions, activities and dynamics of microbial communities remains challenging. Over the past decade, microarray-based technologies have been developed to address such a challenge. In this chapter, we provide an introduction of various microarrays for microbial community analysis, describe crucial issues in applications of microarray technologies for addressing fundamental scientific questions, and highlight their recent applications in environmental microbiology. In addition, we discuss the advantages and limitations of microarray technologies compared to high throughput sequencing technologies as well as challenges and future directions.
2. Software Tools for the Selection of Oligonucleotide Probes for Microarrays
Nicolas Parisot, Jérémie Denonfoux, Eric Dugat-Bony, Eric Peyretaillade and Pierre Peyret
Oligonucleotide microarrays have been widely used for gene detection and quantification of gene expression. Recently, they have been adapted for profiling microbial communities in a flexible and easy-to-use manner. In fact, it is possible to analyse both the microbial diversity and the metabolic capacity of complex communities in one experiment. However, the quality of the result is largely dependent on the quality of designed probes. Probe design, which is not a trivial task, should thus take into account multiple parameters such as the oligonucleotide sequence and its binding capacity in order to ensure high specificity, sensitivity, and uniformity as well as potentially quantitative capability for each probe. Furthermore, the exploration of the not-yet-described fraction of complex communities requires consideration of the explorative power of oligonucleotide probes. To design such probes, multiple tools have been developed based on different algorithms. These algorithms and the different probe criteria that they used are described in the present chapter. However, the best algorithm to guarantee a high-quality design must be chosen with the knowledge of biological questions and biological samples.
3. Development and Evaluation of Functional Gene Arrays with GeoChip as an Example
Qichao Tu, Ye Deng, Jizhong Zhou and Zhili He
Functional gene arrays (FGAs) are special microarrays that containing probes targeting functional gene families involved in different microbial functional processes, such as microbially mediated biogeochemical cycling of carbon (C), nitrogen (N), sulfur (S), phosphorous (P), and metals, biodegradation of organic environmental contaminants, stress responses, virulence and antibiotic resistance. FGAs have been demonstrated as a highly specific, sensitive and quantitative high throughput metagenomic tool for microbial ecology studies and have been widely applied to analyze the functional diversity, composition, structure, function and dynamics of microbial communities from various habitats (e.g., water, soil, sediment, bioreactor). In this chapter, using GeoChip as an example, we will focus on the technical details of the development and evaluation of FGAs, including gene selection, sequence retrieval and verification, probe design and verifications, and computational and experimental evaluation of the specificity, sensitivity and quantification. We also introduce the core functional gene families included in GeoChip. Finally, we will discuss the challenges and future directions for future GeoChip development.
4. Microarray Data Analysis
Ye Deng and Zhili He
Microarray technology allows to examine the existence or expression levels of thousands to millions genes simultaneously in a small space but generates massive amounts of signal intensity data after the image scanning. How to extract and organize these signal intensity data to reflect true concentrations and how to dig into these complicate data for mining useful information are of great challenge. This chapter focuses on microarray data analysis, especially for environmental samples, and it includes a brief tutorial for the basic analysis steps, and basic statistical methods. This chapter is organized into three major sections: (1) microarray image processing for data extraction; (2) true spots determination, paired-comparison ratio and data normalization for data preprocessing; and (3) statistical analysis and network analysis for data mining.
5. Microarray of 16S rRNA Gene Probes for Quantifying Population Differences Across Microbiome Samples
Alexander J. Probst, Pek Yee Lum, Bettina John, Eric A. Dubinsky, Yvette M. Piceno, Lauren M. Tom, Gary L. Andersen, Zhili He and Todd Z. DeSantis
Deciphering microbial communities and their role in Earth's biosphere is crucial for addressing challenges in human health, agriculture, bioremediation and other natural processes. While next-generation sequencing platforms are still under development to improve accuracy, read length and sequencing depth, microarray-based methods have become an attractive alternative for 16S rRNA gene microbial community comparisons. The hybridization method is well-established in the laboratory. Thus main areas of improvement lie with the development of improved bioinformatics and statistical procedures for microarray data, rather than with improvements to the platform itself. In this communication we applied recently-developed bioinformatics tools to re-analyze G3 PhyloChip™ DNA microarray data acquired from deep ocean samples collected during the 2010 Deepwater Horizon oil spill in the Gulf of Mexico. We show that data collected with the G3 PhyloChip™ assay can be analyzed at various stages of resolution, from individual probes to pairs of probes to quartets of probes and finally at the commonly used probe-set level where each probe-set is associated with one operational taxonomic unit (OTU). Our analysis methods comprised topological data analysis to facilitate the detection of outlier bio-specimens and the reconstruction of empirical OTUs (eOTUs) in an unsupervised manner, without the need of pre-defined reference OTUs (rOTUs). We observed that the quartet level provided sufficient resolution for identifying a subtle outlier sample with TDA while the eOTU reconstruction was useful for annotation of the taxa associated with significant population changes in the elevated hydrocarbon waters. The presented methods will improve the deduction of important biological processes from G3 PhyloChip experiments.
6. GeoChip Applications in Bioremediation Studies
Joy D. Van Nostrand and Jizhong Zhou
Microarrays provide the ability to examine thousands of genes with a single test and overcome the limitations of other culture-independent approaches. Functional gene arrays (FGA) probe for structural genes involved in particular functions of interest. The most comprehensive FGA to date is the GeoChip array. These arrays targets tens of thousands of genes, from both cultured and uncultured microorganisms, involved in the geochemical cycling of carbon, nitrogen, phosphorus, and sulfur, metal resistance and reduction, energy processing, antibiotic resistance and contaminant degradation. The GeoChip arrays provide a sensitive and specific examination of microbial communities and have been used to examine microbial communities before, during and after in situ bioremediation at a variety of contaminated sites. This technology is well-suited for linking geochemical processes with microbial community function and structure and bioremediation-based studies have provided a greater understanding of the microbial communities involved in the biodegradation and bioremediation processes. This chapter provides a brief overview of GeoChip development and focuses on GeoChip studies examining bioremediation systems and other contaminated sites.
7. GeoChip Applications for Analysing Soil and Water Microbial Communities in Oil-contaminated Sites
Yuting Liang, Liangyin Yi and Chaopeng Song
Oil contamination of soils, waters and sediments has become a global issue. Understanding the functional diversity, composition, dynamics and metabolic potential of microbial communities is critical for successful bioremediation of oil-contaminated sites. As an ideal metagenomic tool, GeoChip, a functional gene array, has been widely used in tracking microbial functional genes in oil contaminated soil, aquifer, sea water, and sediment environments. Those studies indicated that the overall microbial functional composition and structure changed in response to oil contamination. Although a decreased microbial diversity by oil-contamination is always observed, GeoChip detected that the hydrocarbon degrading genes were stimulated in both oil contaminated soils and deep sea oil plume if contamination occurred, indicating the potential of indigenous microbes in oil removal. GeoChip also provided useful information about the dynamics of functional genes involved in important geochemical processes in oil contaminated sites, such as carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycling. The relationship between the abundance of microbial functional genes and oil contamination and other environmental variables was also examined by GeoChip. In addition, the dynamics of microbial functional genes during remediation of oil contaminated sites was studied with GeoChip. However, several challenges remain in applications of GeoChip for microbial community analysis in oil-contaminated sites.
8. GeoChip Analysis of Soil Microbial Community Responses to Global Change
Kai Xue, Zhili He, Joy D. Van Nostrand, and Jizhong Zhou
Global climate change resulting from anthropogenic activities has become a great concern for human society, which would affect ecosystems deeply. Although responses of plant communities to global change factors have been well established, influences on belowground soil microbial communities still remains poorly understood, at least partly due to the challenges of analyzing soil microbial communities by conventional molecular tools. However, the development of metagenomic technologies, including microarray-based GeoChip, have overcome these limitations and revolutionized microbial research. GeoChip technology allows us to investigate the ecological functions of soil microbial communities involved in important biochemistry cycles. It has been utilized to investigate responses of soil microbial communities to several climate change factors, including elevated atmospheric CO2 concentrations, rising temperature, and increased O3 concentrations. Here, we summarize the application of GeoChip in these studies and discuss how information obtained from GeoChip enhances our understanding of ecological consequences of global changes. Moreover, the challenges of this technique will also be discussed.
9. Soil Functional Gene Microarrays and Applications in Plant-Microbe Interactions
Lilia C. Carvalhais, Vivian Rincon and Peer M. Schenk
Undoubtedly, soil is one of the most complex microbial environments that harbours thousands of species of bacteria, fungi, archaea and protists. This diversity can be functionally characterized by soil microarrays that either contain 16S rDNA sequences (microbial community analyses) or other genomic or cDNA sequences from functional genes (functional gene arrays). Microorganisms play essential roles for nutrient acquisition, nutrient conversion and mineralization in soil. These processes are also critical for plant growth, nutrient uptake, plant health and the recycling of organic matter, but some soil microorganisms also act as plant pathogens. Recent technological advances have led to simultaneous time-course analyses of plant hosts and their interacting microorganism(s). Apart from the use of functional gene arrays, this "interaction transcriptome" profiling can also be achieved by quantitative real-time PCR (qRT-PCR), as well as next generation sequencing, especially if at least one genome sequence of the interacting organisms (host or colonizing microorganism) is known. Furthermore, several laboratories are currently pursuing a metatranscriptomics approach to analyse interactions of plants with soil microbial communities. This chapter compares available techniques for gene expression profiling in soil and plants with a focus on soil functional gene microarrays and their applications to study plant-microbe interactions in the rhizosphere.
10. Bioleaching Microarrays for Profiling Microbial Communities in Acid Mine Drainage and Bioleaching Ecosystems
Huaqun Yin and Xueduan Liu
The dissolution of sulfide minerals yields hot, sulfuric acid-rich solutions generally referred to as ‘acid mine drainage' (AMD) that contains high concentrations of toxic metals. The resulting AMD may contaminate surrounding ecosystems. However, there populate a diverse range of microbes being utilized for "bioleaching" process, in which the use of acidophilic microorganisms to dissolve metals from mineral ores for subsequent recovery. Therefore, to deepen the understanding of ecosystem functioning and bioleaching mechanisms, it is necessary to study the diversity, composition, structure, function, and dynamics of microbial communities from AMD and bioleaching systems as well as the gene function, regulation and network of acidophilic microorganisms. In this chapter, we focus on the development and application of four types of bioleaching microarrays for analyzing microbial communities and isolated microorganisms from AMD and bioleaching systems. Also, we discuss the challenges and future directions of bioleaching microarray technologies.
11. Applications of Phylogenetic Microarrays to Profiling of Human Microbiomes
Oleg Paliy and Vijay Shankar
Human associated microbial communities are known to be highly diverse, comprising between hundreds to a thousand species, depending on the body area. The sheer numbers of species as well as the fastidious nature of most of these organisms make culture-based techniques both inefficient and challenging to study these communities. As a result, analyses of such communities are best accomplished by the use of high-throughput molecular methods such as phylogenetic microarrays and next generation sequencing. Phylogenetic microarrays have recently become a popular tool for the compositional analysis of complex microbial communities, owing to their ability to provide simultaneous quantitative data for many community members. This chapter will focus on currently available phylogenetic microarrays for the interrogation of human-associated microbiota, the technologies used to construct the arrays, as well as several key features that distinguish them from other approaches. We will also discuss optimization strategies for the development and usage of phylogenetic microarrays as well as opportunities to complement microarray analysis with other techniques.
12. Microbial Diagnostic Microarrays for Detection and Typing of Water-borne Pathogens
Even nowadays water quality assessment relies on the detection of so called indicator organisms (e.g. E. coli, coliforms, Enterococci, heterotrophic plate count) and utilizes cultivation-based methods. But it is waterborne pathogens that pose a major threat to human health, and the correlation between indicator organisms and pathogens was shown to be questionable. Therefore, having the possibility to detect pathogens directly would be of great advantage for water quality monitoring. However, detection of pathogens in an environment (i.e., water) requires a diagnostic tool of high specificity and sensitivity, with multiplexing potential and high degree of robustness. Microbial diagnostic microarrays (MDMs) present one possibility of addressing these requirements, and many promising microarray systems for the detection or typing of waterborne pathogens were developed and validated over past years. The current state of the art and needs for further developments will be discussed.
13. Broad Spectrum Viral and Bacterial Pathogen Detection by Microarrays
Kevin McLoughlin, Crystal Jaing, Shea Gardner, Nicholas A. Be, James B. Thissen and Tom Slezak
Broad spectrum viral and bacterial pathogen detection microarrays have proven useful to analyze pathogenic organisms in clinical and environmental samples. The microbial detection arrays are less costly and faster than next generation sequencing, and more comprehensive than single-plex and multiplex PCR assays. Pathogen detection arrays have been used for detection and genotyping of viral and bacterial pathogens for biodefense, public health, and food and drug safety. These arrays have also contributed to the discovery of novel viruses. Pathogen microarrays are cost-effective, rapid genomic assays that are expected to gain a wider use both in research settings and in the regulatory and diagnostic environment.
How to buy this book
(EAN: 9781908230492 9781908230591 Subjects: [microbiology] [molecular microbiology] [environmental microbiology] [molecular biology] )