Article

Metagenomics - The key to the uncultured microbes

Institut für Mikrobiologie und Genetik, Universität Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany.
Current Opinion in Microbiology (Impact Factor: 5.9). 11/2004; 7(5):492-8. DOI: 10.1016/j.mib.2004.08.002
Source: PubMed

ABSTRACT

It is widely accepted that up to 99.8% of the microbes present in many environments are not readily culturable. 'Metagenome technology' tries to overcome this bottleneck by developing and using culture-independent approaches. From the outset, metagenome-based approaches have led to the accumulation of an increasing number of DNA sequences, but until this time the sequences retrieved have been those of uncultured microbes. These genomic sequences are currently exploited for novel biotechnological and pharmaceutical applications and to increase our knowledge on microbial ecology and physiology of these microbes. Using the metagenome sequences to fully understand how complex microbial communities function and how microbes interact within these niches represents a major challenge for microbiologists today.

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    • "As shown in Figure 1, DNA extracted from environmental samples can be cloned into plasmids, fosmids, bacterial artificial chromosomes, or cosmids for proliferation in a suitable heterologous host organism, such as Escherichia coli, and then be screened for catalytic activities. The rapid development of functional screening on metagenomic libraries to find a new enzymatic activity has indicated the importance of microbial diversity in the novel enzyme detection [42] [43] [44] [45]. However, the DNA quality of the environmental samples remains a challenge, because of the low copy number of clones and the different insert sizes of metagenomic libraries [46]. "
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    ABSTRACT: More than 99% of identified prokaryotes, including many from the marine environment, cannot be cultured in the laboratory. This lack of capability restricts our knowledge of microbial genetics and community ecology. Metagenomics, the culture-independent cloning of environmental DNAs that are isolated directly from an environmental sample, has already provided a wealth of information about the uncultured microbial world. It has also facilitated the discovery of novel biocatalysts by allowing researchers to probe directly into a huge diversity of enzymes within natural microbial communities. Recent advances in these studies have led to great interest in recruiting microbial enzymes for the development of environmentally-friendly industry. Although the metagenomics approach has many limitations, it is expected to provide not only scientific insights but also economic benefits, especially in industry. This review highlights the importance of metagenomics in mining microbial lipases, as an example, by using high-throughput techniques. In addition, we discuss challenges in the metagenomics as an important part of bioinformatics analysis in big data.
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    • "Despite such vigorous and constant growth of the use of microorganisms, most of the bacterial species thriving within culture systems and their particular roles in such microcosms remain unknown. For instance, up to 99% of bacterial species thriving in most of the environments are not readily culturable, and therefore, the microbial diversity is not accessible even for basic research purposes (Streit & Schmitz 2004). "
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    ABSTRACT: The use and study of microbes in aquaculture has become a common practice in the last decade. Metagenomics is a relative recent genomics subdiscipline that has emerged as a promising scientific tool to analyse the complex genomes contained within microbial communities. However, despite the potential of metagenomics, its use is not yet common in some agro-industrial disciplines such as aquaculture. In this review, we analyse some of the potential uses of metagenomics in aquaculture to highlight the microbial diversity and dynamics of the culture systems. This review addresses some potential uses of metagenomics in the study of microbial diversity, microbial roles in microcosms, antibiotic resistance genes, novel and potential pathogens, microbial communities forming bioflocs, probiotics and other applications.
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    • "Another obstacle faced in heterologous expression is the possibility of a DNA fragment being too short to contain a functional gene cluster or operon . The availability of a vector able to accommodate large DNA inserts is also fundamental ( Streit and Schmitz , 2004 ) . The use of large insert vectors capable of accommodating biosynthetic gene clusters or operons , and the development of shuttle vectors capable of propagating in more than one heterologous host , are examples of strategies being explored to overcome methodological limitations . "
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    ABSTRACT: Microorganisms are found throughout nature, thriving in a vast range of environmental conditions. The majority of them are unculturable or difficult to culture by traditional methods. Metagenomics enables the study of all microorganisms, regardless of whether they can be cultured or not, through the analysis of genomic data obtained directly from an environmental sample, providing knowledge of the species present, and allowing the extraction of information regarding the functionality of microbial communities in their natural habitat. Function-based screenings, following the cloning and expression of metagenomic DNA in a heterologous host, can be applied to the discovery of novel proteins of industrial interest encoded by the genes of previously inaccessible microorganisms. Functional metagenomics has considerable potential in the food and pharmaceutical industries, where it can, for instance, aid (i) the identification of enzymes with desirable technological properties, capable of catalyzing novel reactions or replacing existing chemically synthesized catalysts which may be difficult or expensive to produce, and able to work under a wide range of environmental conditions encountered in food and pharmaceutical processing cycles including extreme conditions of temperature, pH, osmolarity, etc; (ii) the discovery of novel bioactives including antimicrobials active against microorganisms of concern both in food and medical settings; (iii) the investigation of industrial and societal issues such as antibiotic resistance development. This review article summarizes the state-of-the-art functional metagenomic methods available and discusses the potential of functional metagenomic approaches to mine as yet unexplored environments to discover novel genes with biotechnological application in the food and pharmaceutical industries.
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