Metagenomics: Advances in ecology and biotechnology

Steele, H.; Streit, Wolfgang R.

doi:10.1016/j.femsle.2005.05.011

Cited by 107 publications

(56 citation statements)

References 51 publications

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“…Useful molecules for such studies include phospholipids, fatty acids and nucleic acids (Morgan & Winstanley, 1997) where as the microscopic techniques involve either the hybridization of fluorescent-labeled nucleic acid probes with total RNA extracted from water or hybridizations with cells in situ. Metagenomics, also known as environmental genomics, is the culture independent study of a community of microorganisms (Steele & Streit, 2005;Fieseler et. al., 2006).…”

Section: Seasonal Variation Of Bacterial Abundance In Sundarban Estuarymentioning

confidence: 99%

Interplay of Physical, Chemical and Biological Components in Estuarine Ecosystem with Special Reference to Sundarbans, India

Manna¹,

Chaudhuri²,

Sarma³

et al. 2012

Ecological Water Quality - Water Treatment and Reuse

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Section: Seasonal Variation Of Bacterial Abundance In Sundarban Estuarymentioning

confidence: 99%

Interplay of Physical, Chemical and Biological Components in Estuarine Ecosystem with Special Reference to Sundarbans, India

Manna¹,

Chaudhuri²,

Sarma³

et al. 2012

Ecological Water Quality - Water Treatment and Reuse

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“…It is useful to extend Handelsman's definition to also include sequences from higher organisms as well as just microorganisms, thus opening the door to "environmental forensics." By vastly extending the currently available sequences in databases, metagenomics promises to lead to the discovery of new genes that have useful applications in biotechnology and medicine (Steele and Streit 2005).Early metagenomics projects (Béja et al 2000(Béja et al , 2001 were plagued by potential biases that are due to DNA extraction and cloning methods . Clone libraries were constructed from environmental DNA using fosmid and BAC vectors as vehicles for DNA propagation and amplification.…”

mentioning

confidence: 99%

mentioning

confidence: 99%

MEGAN analysis of metagenomic data

Huson¹,

Auch²,

Qi³

et al. 2007

Genome Res.

2,812

2,430

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Metagenomics is the study of the genomic content of a sample of organisms obtained from a common habitat using targeted or random sequencing. Goals include understanding the extent and role of microbial diversity. The taxonomical content of such a sample is usually estimated by comparison against sequence databases of known sequences. Most published studies use the analysis of paired-end reads, complete sequences of environmental fosmid and BAC clones, or environmental assemblies. Emerging sequencing-by-synthesis technologies with very high throughput are paving the way to low-cost random "shotgun" approaches. This paper introduces MEGAN, a new computer program that allows laptop analysis of large metagenomic data sets. In a preprocessing step, the set of DNA sequences is compared against databases of known sequences using BLAST or another comparison tool. MEGAN is then used to compute and explore the taxonomical content of the data set, employing the NCBI taxonomy to summarize and order the results. A simple lowest common ancestor algorithm assigns reads to taxa such that the taxonomical level of the assigned taxon reflects the level of conservation of the sequence. The software allows large data sets to be dissected without the need for assembly or the targeting of specific phylogenetic markers. It provides graphical and statistical output for comparing different data sets. The approach is applied to several data sets, including the Sargasso Sea data set, a recently published metagenomic data set sampled from a mammoth bone, and several complete microbial genomes. Also, simulations that evaluate the performance of the approach for different read lengths are presented.[MEGAN is freely available at http://www-ab.informatik.uni-tuebingen.de/software/megan.]The genomic revolution of the early 1990s targeted the study of individual genomes of microorganisms, plants, and animals. While this type of analysis has almost become routine, the genomic analysis of complex mixtures of organisms remains challenging. Metagenomics has been defined as "the genomic analysis of microorganisms by direct extraction and cloning of DNA from an assemblage of microorganisms" (Handelsman 2004), and its importance stems from the fact that 99% or more of all microbes are deemed to be unculturable. Goals of metagenomic studies include assessing the coding potential of environmental organisms, quantifying the relative abundances of (known) species, and estimating the amount of unknown sequence information (environmental sequences) for which no species, or only distant relatives, have yet been described. It is useful to extend Handelsman's definition to also include sequences from higher organisms as well as just microorganisms, thus opening the door to "environmental forensics." By vastly extending the currently available sequences in databases, metagenomics promises to lead to the discovery of new genes that have useful applications in biotechnology and medicine (Steele and Streit 2005).Early metagenomics projects (Béja et al. 2000(Béja et...

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“…Modern metagenomic developments and cloning strategies have recently been reviewed in detail (8,9,16,46). Once constructed, metagenomic libraries can be screened for a wide range of ecologically and biotechnologically interesting phenotypes (44).…”

mentioning

confidence: 99%

Isolation and Biochemical Characterization of Two Novel Metagenome-Derived Esterases

Elend

Schmeisser

Leggewie

et al. 2006

Appl Environ Microbiol

175

121

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The metagenomes of uncultured microbial communities are rich sources for novel biocatalysts. In this study, esterase EstA3 was derived from a drinking water metagenome, and esterase EstCE1 was derived from a soil metagenome. Both esterases are approximately 380 amino acids in size and show similarity to ␤-lactamases, indicating that they belong to family VIII of the lipases/esterases. EstA3 had a temperature optimum at 50°C and a pH optimum at pH 9.0. It was remarkably active and very stable in the presence of solvents and over a wide temperature and pH range. It is active in a multimeric form and displayed a high level of activity against a wide range of substrates including one secondary ester, 7-[3-octylcarboxy-(3-hydroxy-3-methyl-butyloxy)]-coumarin, which is normally unreactive. EstCE1 was active in the monomeric form and had a temperature optimum at 47°C and a pH optimum at pH 10. It exhibited the same level of stability as EstA3 over wide temperature and pH ranges and in the presence of dimethyl sulfoxide, isopropanol, and methanol. EstCE1 was highly enantioselective for (؉)-menthylacetate. These enzymes display remarkable characteristics that cannot be related to the original environment from which they were derived. The high level of stability of these enzymes together with their unique substrate specificities make them highly useful for biotechnological applications.Modern biotechnology has a steadily increasing demand for novel biocatalysts, thereby prompting the development of novel experimental approaches to find and identify novel biocatalyst-encoding genes. Recently, there has been an increase in the number of studies using a metagenomic approach to investigate the catalytic potential of uncultured microorganisms (8, 28). The term metagenome was introduced to describe the genomes of complex microbial communities found in natural habitats, only a small fraction of which can be cultured (1, 17). Investigation of metagenomes became possible after the development of strategies for the isolation and cloning of environmental DNA (41, 47). Modern metagenomic developments and cloning strategies have recently been reviewed in detail (8,9,16,46). Once constructed, metagenomic libraries can be screened for a wide range of ecologically and biotechnologically interesting phenotypes (44).In the search for novel biocatalysts, there are various metagenomic strategies that are used for targeting specific catalyst characteristics such as substrate range or temperature and pH optima. One approach is to generate the metagenomic library from soils or sediments that are known to harbor a high level of microbial diversity and thus, potentially, a wide diversity of biocatalysts (7). This approach has been used successfully to find a wide variety of novel catalysts and secondary metabolites (9,19,20,27,30,39). A further development of this approach is to create the metagenomic library from an environment that has been subjected to extreme conditions in the likelihood that enzymes from such an environment will be able to f...

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Metagenomics: Advances in ecology and biotechnology

Cited by 107 publications

References 51 publications

Interplay of Physical, Chemical and Biological Components in Estuarine Ecosystem with Special Reference to Sundarbans, India

Interplay of Physical, Chemical and Biological Components in Estuarine Ecosystem with Special Reference to Sundarbans, India

MEGAN analysis of metagenomic data

Isolation and Biochemical Characterization of Two Novel Metagenome-Derived Esterases

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