Experimental Design and Bioinformatics Analysis for the Application of Metagenomics in Environmental Sciences and Biotechnology

Recent advances in DNA sequencing technologies have prompted the widespread application of metagenomics for the investigation of novel bioresources (e.g., industrial enzymes and bioactive molecules) and unknown biohazards (e.g., pathogens and antibiotic resistance genes) in natural and engineered mi...

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Bibliographic Details
Published in:Environmental science & technology 2015-11, Vol.49 (21), p.12628-12640
Main Authors: Ju, Feng, Zhang, Tong
Format: Article
Language:English
Subjects:
Biodegradation, Environmental
Biofuels
Biohazards
Bioinformatics
Bioremediation
Biotechnology
Biotechnology - methods
Computational Biology - methods
Design of experiments
Ecology - methods
Environmental science
Enzymes
Genetic engineering
Genome
Genomics
Metagenomics - methods
Microbial Consortia - genetics
Microbial Interactions
Research Design
Sequence Analysis, DNA
Waste Disposal, Fluid - methods
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Summary:Recent advances in DNA sequencing technologies have prompted the widespread application of metagenomics for the investigation of novel bioresources (e.g., industrial enzymes and bioactive molecules) and unknown biohazards (e.g., pathogens and antibiotic resistance genes) in natural and engineered microbial systems across multiple disciplines. This review discusses the rigorous experimental design and sample preparation in the context of applying metagenomics in environmental sciences and biotechnology. Moreover, this review summarizes the principles, methodologies, and state-of-the-art bioinformatics procedures, tools and database resources for metagenomics applications and discusses two popular strategies (analysis of unassembled reads versus assembled contigs/draft genomes) for quantitative or qualitative insights of microbial community structure and functions. Overall, this review aims to facilitate more extensive application of metagenomics in the investigation of uncultured microorganisms, novel enzymes, microbe-environment interactions, and biohazards in biotechnological applications where microbial communities are engineered for bioenergy production, wastewater treatment, and bioremediation.
ISSN:0013-936X
1520-5851
DOI:10.1021/acs.est.5b03719