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Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes

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ABSTRACT

Microbial populations living in environments with temperatures above 50°C (thermophiles) have been widely studied, increasing our knowledge in the composition and function of these ecological communities. Since these populations express a broad number of heat-resistant enzymes (thermozymes), they also represent an important source for novel biocatalysts that can be potentially used in industrial processes. The integrated study of the whole-community DNA from an environment, known as metagenomics, coupled with the development of next generation sequencing (NGS) technologies, has allowed the generation of large amounts of data from thermophiles. In this review, we summarize the main approaches commonly utilized for assessing the taxonomic and functional diversity of thermophiles through metagenomics, including several bioinformatics tools and some metagenome-derived methods to isolate their thermozymes.

No MeSH data available.


Schematic representation of the main approaches used for metagenomic analysis of thermophiles.
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Figure 1: Schematic representation of the main approaches used for metagenomic analysis of thermophiles.

Mentions: Initially, these studies required the amplification of the 16S rRNA genes followed by either denaturing gradient gel electrophoresis (DGGE, Muyzer et al., 1993) and sequencing or by cloning of the amplicons. In this case, the libraries obtained were screened using direct Sanger sequencing or restriction fragment length polymorphism (RFLP) analysis (Liu et al., 1997; Baker et al., 2001), to select and sequence those clones with unique patterns (Figure 1). As an example, the effect of pH, temperature, and sulfide in the hyperthermophilic microbial communities living in hot springs of northern Thailand was determined with the amplification of complete 16S rRNA genes followed by DGGE separation and sequencing (Purcell et al., 2007). In a different study, RFLP analysis and sequencing of clones with unique RFLP patterns was used to reveal the presence of abundant novel Bacteria and Archaea sequences in a 16S rRNA gene clone library prepared from the 55°C water and sediments of Boiling Spring Lake in California, USA (Wilson et al., 2008).


Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes
Schematic representation of the main approaches used for metagenomic analysis of thermophiles.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5037290&req=5

Figure 1: Schematic representation of the main approaches used for metagenomic analysis of thermophiles.
Mentions: Initially, these studies required the amplification of the 16S rRNA genes followed by either denaturing gradient gel electrophoresis (DGGE, Muyzer et al., 1993) and sequencing or by cloning of the amplicons. In this case, the libraries obtained were screened using direct Sanger sequencing or restriction fragment length polymorphism (RFLP) analysis (Liu et al., 1997; Baker et al., 2001), to select and sequence those clones with unique patterns (Figure 1). As an example, the effect of pH, temperature, and sulfide in the hyperthermophilic microbial communities living in hot springs of northern Thailand was determined with the amplification of complete 16S rRNA genes followed by DGGE separation and sequencing (Purcell et al., 2007). In a different study, RFLP analysis and sequencing of clones with unique RFLP patterns was used to reveal the presence of abundant novel Bacteria and Archaea sequences in a 16S rRNA gene clone library prepared from the 55°C water and sediments of Boiling Spring Lake in California, USA (Wilson et al., 2008).

View Article: PubMed Central - PubMed

ABSTRACT

Microbial populations living in environments with temperatures above 50°C (thermophiles) have been widely studied, increasing our knowledge in the composition and function of these ecological communities. Since these populations express a broad number of heat-resistant enzymes (thermozymes), they also represent an important source for novel biocatalysts that can be potentially used in industrial processes. The integrated study of the whole-community DNA from an environment, known as metagenomics, coupled with the development of next generation sequencing (NGS) technologies, has allowed the generation of large amounts of data from thermophiles. In this review, we summarize the main approaches commonly utilized for assessing the taxonomic and functional diversity of thermophiles through metagenomics, including several bioinformatics tools and some metagenome-derived methods to isolate their thermozymes.

No MeSH data available.