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The environmental fate of organic pollutants through the global microbial metabolism.

Gómez MJ, Pazos F, Guijarro FJ, de Lorenzo V, Valencia A - Mol. Syst. Biol. (2007)

Bottom Line: A machine learning approach has been instrumental to expose a correlation between the frequency of 149 atomic triads (chemotopes) common in organo-chemical compounds and the global capacity of microorganisms to metabolise them.Depending on the type of environmental fate defined, the system can correctly predict the biodegradative outcome for 73-87% of compounds.The application of this predictive tool to chemical species released into the environment provides an early instrument for tentatively classifying the compounds as biodegradable or recalcitrant.

View Article: PubMed Central - PubMed

Affiliation: Centro de Astrobiología (INTA-CSIC), Ctra. Torrejón Ajalvir, Km 4. Torrejón de Ardoz, Madrid, Spain.

ABSTRACT
The production of new chemicals for industrial or therapeutic applications exceeds our ability to generate experimental data on their biological fate once they are released into the environment. Typically, mixtures of organic pollutants are freed into a variety of sites inhabited by diverse microorganisms, which structure complex multispecies metabolic networks. A machine learning approach has been instrumental to expose a correlation between the frequency of 149 atomic triads (chemotopes) common in organo-chemical compounds and the global capacity of microorganisms to metabolise them. Depending on the type of environmental fate defined, the system can correctly predict the biodegradative outcome for 73-87% of compounds. This system is available to the community as a web server (http://www.pdg.cnb.uam.es/BDPSERVER). The application of this predictive tool to chemical species released into the environment provides an early instrument for tentatively classifying the compounds as biodegradable or recalcitrant. Automated surveys of lists of industrial chemicals currently employed in large quantities revealed that herbicides are the group of functional molecules more difficult to recycle into the biosphere through the inclusive microbial metabolism.

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Related in: MedlinePlus

Prediction of environmental fates of selected groups of functional chemical compounds extracted from the PubChem Compound database. The y axis indicate the percentage of compounds within each category (versus the corresponding negated class) of the lists that are predicted to belong to any of the classes: CM, central metabolism path compound; NB, nonbiodegradable path compounds; CD, carbon dioxide path compound; CMCDs, central metabolism and carbon dioxide path compounds. The red coloured is a signal of recalcitrance, whereas the green is an indication of degradability. The category of flame retardants was excluded from this analysis, because only a few (six chemical specimens) were listed in the accessed dabases. Note that, by any criterion, the herbicides form the most-difficult-to-degrade group of chemicals.
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f5: Prediction of environmental fates of selected groups of functional chemical compounds extracted from the PubChem Compound database. The y axis indicate the percentage of compounds within each category (versus the corresponding negated class) of the lists that are predicted to belong to any of the classes: CM, central metabolism path compound; NB, nonbiodegradable path compounds; CD, carbon dioxide path compound; CMCDs, central metabolism and carbon dioxide path compounds. The red coloured is a signal of recalcitrance, whereas the green is an indication of degradability. The category of flame retardants was excluded from this analysis, because only a few (six chemical specimens) were listed in the accessed dabases. Note that, by any criterion, the herbicides form the most-difficult-to-degrade group of chemicals.

Mentions: In a subsequent step, we analysed sets of chemical species of the PubChem database that were explicitly labelled as pesticides (1707 compounds), herbicides (199), fungicides (169), insecticides (279), antibiotics (1365) and flame retardants (6). As indicated in Figure 5, our system exposed that the percentage of CM (∼54%) or CMCD (∼70%) compounds within these lists were roughly similar to those of the species listed by the European Chemical Bureau. However, the percentage of compounds connected to CO2 (CD, ∼34%) and to nonbiodegradable end products (NBs, ∼59%) was significantly higher. The highest percentage of predicted difficult-to-degrade compounds was observed in the collection of herbicides included in PubChem (NB ∼74%). The much feared flame retardants (Darnerud, 2003) incorporated in the study turned out to be in principle amenable to microbial degradation leading to central metabolism or carbon dioxide (CMCD, 100%), although four of them were also classified as precursors of eventually nonbiodegradable compounds (NB, ∼66%). The detailed predictions for all the sets of compounds mentioned in this section are available on-line at http://www.pdg.cnb.uam.es/BDPSERVER.


The environmental fate of organic pollutants through the global microbial metabolism.

Gómez MJ, Pazos F, Guijarro FJ, de Lorenzo V, Valencia A - Mol. Syst. Biol. (2007)

Prediction of environmental fates of selected groups of functional chemical compounds extracted from the PubChem Compound database. The y axis indicate the percentage of compounds within each category (versus the corresponding negated class) of the lists that are predicted to belong to any of the classes: CM, central metabolism path compound; NB, nonbiodegradable path compounds; CD, carbon dioxide path compound; CMCDs, central metabolism and carbon dioxide path compounds. The red coloured is a signal of recalcitrance, whereas the green is an indication of degradability. The category of flame retardants was excluded from this analysis, because only a few (six chemical specimens) were listed in the accessed dabases. Note that, by any criterion, the herbicides form the most-difficult-to-degrade group of chemicals.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1911198&req=5

f5: Prediction of environmental fates of selected groups of functional chemical compounds extracted from the PubChem Compound database. The y axis indicate the percentage of compounds within each category (versus the corresponding negated class) of the lists that are predicted to belong to any of the classes: CM, central metabolism path compound; NB, nonbiodegradable path compounds; CD, carbon dioxide path compound; CMCDs, central metabolism and carbon dioxide path compounds. The red coloured is a signal of recalcitrance, whereas the green is an indication of degradability. The category of flame retardants was excluded from this analysis, because only a few (six chemical specimens) were listed in the accessed dabases. Note that, by any criterion, the herbicides form the most-difficult-to-degrade group of chemicals.
Mentions: In a subsequent step, we analysed sets of chemical species of the PubChem database that were explicitly labelled as pesticides (1707 compounds), herbicides (199), fungicides (169), insecticides (279), antibiotics (1365) and flame retardants (6). As indicated in Figure 5, our system exposed that the percentage of CM (∼54%) or CMCD (∼70%) compounds within these lists were roughly similar to those of the species listed by the European Chemical Bureau. However, the percentage of compounds connected to CO2 (CD, ∼34%) and to nonbiodegradable end products (NBs, ∼59%) was significantly higher. The highest percentage of predicted difficult-to-degrade compounds was observed in the collection of herbicides included in PubChem (NB ∼74%). The much feared flame retardants (Darnerud, 2003) incorporated in the study turned out to be in principle amenable to microbial degradation leading to central metabolism or carbon dioxide (CMCD, 100%), although four of them were also classified as precursors of eventually nonbiodegradable compounds (NB, ∼66%). The detailed predictions for all the sets of compounds mentioned in this section are available on-line at http://www.pdg.cnb.uam.es/BDPSERVER.

Bottom Line: A machine learning approach has been instrumental to expose a correlation between the frequency of 149 atomic triads (chemotopes) common in organo-chemical compounds and the global capacity of microorganisms to metabolise them.Depending on the type of environmental fate defined, the system can correctly predict the biodegradative outcome for 73-87% of compounds.The application of this predictive tool to chemical species released into the environment provides an early instrument for tentatively classifying the compounds as biodegradable or recalcitrant.

View Article: PubMed Central - PubMed

Affiliation: Centro de Astrobiología (INTA-CSIC), Ctra. Torrejón Ajalvir, Km 4. Torrejón de Ardoz, Madrid, Spain.

ABSTRACT
The production of new chemicals for industrial or therapeutic applications exceeds our ability to generate experimental data on their biological fate once they are released into the environment. Typically, mixtures of organic pollutants are freed into a variety of sites inhabited by diverse microorganisms, which structure complex multispecies metabolic networks. A machine learning approach has been instrumental to expose a correlation between the frequency of 149 atomic triads (chemotopes) common in organo-chemical compounds and the global capacity of microorganisms to metabolise them. Depending on the type of environmental fate defined, the system can correctly predict the biodegradative outcome for 73-87% of compounds. This system is available to the community as a web server (http://www.pdg.cnb.uam.es/BDPSERVER). The application of this predictive tool to chemical species released into the environment provides an early instrument for tentatively classifying the compounds as biodegradable or recalcitrant. Automated surveys of lists of industrial chemicals currently employed in large quantities revealed that herbicides are the group of functional molecules more difficult to recycle into the biosphere through the inclusive microbial metabolism.

Show MeSH
Related in: MedlinePlus