regularly updated since its inception. It has a collection of databases related to
organic compounds, enzymes, reactions, biotransformation rules, and different
microorganisms. Further, it contains a biochemical periodic table (UM-BPT) and a
pathway prediction system (UM-PPS) that predicts hypothetical pathways for microbial degradation. Other scientists are accessing UM-BBD data for their research
purposes. Also, UM-BBD compound data are now contributed to PubChem and
ChemSpider, which are other public chemical databases. Another database is being
developed at ETH Zürich to improve the speed and reliability of online access from
anywhere in the world (Gao et al. 2010). Urbance et al. (2003) have developed a
database to provide detailed information on degradative bacteria and the hazardous
substances they degrade (Biodegradative Strain Database, BSD) within the phylogenetic framework of the Ribosomal Database Project II (RDPII: http://rdp.cme.
msu.edu/html). Pazos et al. (2003, 2005) developed a unique system, MetaRouter,
for maintaining the variety of information related to bioremediation in a way that
allows its query and mining. Arora et al. (2009) compiled a database of
biodegradative enzyme oxygenases (OxDBase), taken from primary literature and
converted in the form of a web-accessible database, that consists of two separate
search engines for mono- and dioxygenases, respectively. For each enzyme queried
the database shows its common name and synonym, family and subfamily, reaction
in which enzyme is involved, structure and gene link, and literature citation. It can be
also linked to several other external databases including ENZYME, BRENDA,
KEGG, and UM-BBD, providing more background information. OxDBase, the
first database specially dedicated to oxygenases, consists of more than 200 databases
that provide comprehensive information about them. Moriya et al. (2010) developed
PathPred, a web-based server focused on predicting pathways for microbial biodegradation. The server provides a platform to study the transformation patterns and
reference transformation patterns in each predicted reaction. These patterns are then
displayed in a tree-shaped graph. The transformation of xenobiotic compounds by
microorganisms is essential for the bioremediation, and there is no single resource
available that provides information about environmental contaminants as well as
microorganisms with biodegradative capabilities. Thus, a database that consolidates
the detailed information about xenobiotics, biotransformation methods, and hypothetical pathways would be a handy tool for academic and industrial researchers
(Urbance et al. 2003).
9 Future Challenges
Advances in molecular biology techniques have opened a new era in bioremediation
processes. Further, the development of various OMICs approaches offers efficient
research avenues for analyzing biological systems at different levels. However, the
utility of genome sequence facts and associated numerous OMIC approaches to link
microbial genes and their products with bioremediation potential is an incredible
mission. The goal of this chapter was to review a number of the most current
464
S. K. Shekhar et al.
organic compounds, enzymes, reactions, biotransformation rules, and different
microorganisms. Further, it contains a biochemical periodic table (UM-BPT) and a
pathway prediction system (UM-PPS) that predicts hypothetical pathways for microbial degradation. Other scientists are accessing UM-BBD data for their research
purposes. Also, UM-BBD compound data are now contributed to PubChem and
ChemSpider, which are other public chemical databases. Another database is being
developed at ETH Zürich to improve the speed and reliability of online access from
anywhere in the world (Gao et al. 2010). Urbance et al. (2003) have developed a
database to provide detailed information on degradative bacteria and the hazardous
substances they degrade (Biodegradative Strain Database, BSD) within the phylogenetic framework of the Ribosomal Database Project II (RDPII: http://rdp.cme.
msu.edu/html). Pazos et al. (2003, 2005) developed a unique system, MetaRouter,
for maintaining the variety of information related to bioremediation in a way that
allows its query and mining. Arora et al. (2009) compiled a database of
biodegradative enzyme oxygenases (OxDBase), taken from primary literature and
converted in the form of a web-accessible database, that consists of two separate
search engines for mono- and dioxygenases, respectively. For each enzyme queried
the database shows its common name and synonym, family and subfamily, reaction
in which enzyme is involved, structure and gene link, and literature citation. It can be
also linked to several other external databases including ENZYME, BRENDA,
KEGG, and UM-BBD, providing more background information. OxDBase, the
first database specially dedicated to oxygenases, consists of more than 200 databases
that provide comprehensive information about them. Moriya et al. (2010) developed
PathPred, a web-based server focused on predicting pathways for microbial biodegradation. The server provides a platform to study the transformation patterns and
reference transformation patterns in each predicted reaction. These patterns are then
displayed in a tree-shaped graph. The transformation of xenobiotic compounds by
microorganisms is essential for the bioremediation, and there is no single resource
available that provides information about environmental contaminants as well as
microorganisms with biodegradative capabilities. Thus, a database that consolidates
the detailed information about xenobiotics, biotransformation methods, and hypothetical pathways would be a handy tool for academic and industrial researchers
(Urbance et al. 2003).
9 Future Challenges
Advances in molecular biology techniques have opened a new era in bioremediation
processes. Further, the development of various OMICs approaches offers efficient
research avenues for analyzing biological systems at different levels. However, the
utility of genome sequence facts and associated numerous OMIC approaches to link
microbial genes and their products with bioremediation potential is an incredible
mission. The goal of this chapter was to review a number of the most current
464
S. K. Shekhar et al.