mibPOPdb: An online database for microbial biodegradation of persistent organic pollutants

Abstract

Microbial biodegradation of persistent organic pollutants (POPs) is an attractive, ecofriendly, and cost‐efficient clean‐up technique for reclaiming POP‐contaminated environments. In the last few decades, the number of publications documenting POP‐degrading microbes, enzymes, and experimental data sets has continuously increased, necessitating the development of a dedicated web resource that catalogs consolidated information on POP‐degrading microbes and tools to facilitate integrative analysis of POP degradation data sets. To address this knowledge gap, we developed the Microbial Biodegradation of Persistent Organic Pollutants Database (mibPOPdb) by accumulating microbial POP degradation information from the public domain and manually curating published scientific literature. Currently, in mibPOPdb, there are 9215 microbial strain entries, including 184 gene (sub)families, 100 enzymes, 48 biodegradation pathways, and 593 intermediate compounds identified in POP‐biodegradation processes, and information on 32 toxic compounds listed under the Stockholm Convention environmental treaty. Besides the standard database functionalities, which include data searching, browsing, and retrieval of database entries, we provide a suite of bioinformatics services to facilitate comparative analysis of users' own data sets against mibPOPdb entries. Additionally, we built a Graph Neural Network‐based prediction model for the biodegradability classification of chemicals. The predictive model exhibited a good biodegradability classification performance and high prediction accuracy. mibPOPdb is a free data‐sharing platform designated to promote research in microbial‐based biodegradation of POPs and fills a long‐standing gap in environmental protection research. Database URL: http://mibpop.genome-mining.cn/

Ecology and risks of the global plastisphere as a newly expanding microbial habitat

“…Functions related to the degradation or decomposition of organic compounds, including ligninolysis, oil bioremediation, hydrocarbon degradation, and aromatic hydrocarbon degradation, showed generally higher potentials in the plastisphere ( Figure 3 ; Table S21 ). Based on databases PlasticDB 32 and Microbial Biodegradation of Persistent Organic Pollutants (POPs) Database (mibPOPdb), 33 we showed that the potential for plastic and POP degradation was remarkably higher in the plastisphere of all of the studied ecosystems ( Figure 3 ; Table S21 ).

Figure 3 Differences in ecologically relevant functions between the plastisphere and the natural environment Plastic degradation potential is revealed based on the PlasticDB database, POP degradation potential is estimated with the mibPOPdb, and other functional potentials are predicted based on the FAPROTAX platform.

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Meta‐omics assisted microbial gene and strain resources mining in contaminant environment

“…BLAST (Basic local alignment search tool), which is based on sequence similarity, and HMM (Hidden Markov model), which is based on functional domains are important tools for gene or protein annotation in meta‐omics datasets [ 23 , 24 ]. With the increasingly updated of many large comprehensive databases (e.g., KEGG, eggNOG, and Uniprot), as well as the release of small specific functional gene databases (e.g., VFDB, BacMet, and NCcyDB), and the development of pollutant biodegradation resources databases (e.g., mibPOPdb, OxDBase, and EAWAG‐BBD) [ 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 ]. Function prediction of metagenomic genes has been accelerated and can be used to evaluate the metabolic potential of microbial communities.…”