Comparative Pan- and Phylo-Genomic Analysis of Ideonella and Thermobifida Strains: Dissemination of Biodegradation Potential and Genomic Divergence

Abstract

Ideonella and Thermobifida were the most promising bacterial candidates for degrading plastic polymers. A comparative pan- and phylogenomic analysis of 33 Ideonella and Thermobifida strains was done to determine their plastic degradation potential, niche adaptation and speciation. The BPGA results revealed that the greater number of accessory genes in the strains indicated phenotypic plasticity. Phylogenetic diversity among the strains was inferred using core and pan genomes. The functional roles of the core and adaptive-associated genomes were scrutinized by pathway enrichment analyses. KEGG annotation revealed that the majority of the genes were associated with the metabolism of amino acids and carbohydrates. The detailed COG analysis revealed that approximately 40% of the pan genes performed metabolic functions. The unique gene pool consisted of genes chiefly involved in "general function prediction" and "amino acid transport and metabolism". The results of the present study revealed that these strains could assist in agronomic applications in the future since they devour N- compounds. The rational selection of strains of Ideonella is far more effective at depolymerizing plastics than that of Thermobifida. A greater number of unique genes, 1701 and 692, were identified for Ideonella sakaiensis 201-F6 and Thermobifida alba DSM-43795, respectively. Furthermore, we examined the singletons involved in xenobiotic catabolism. The unique singleton data were used to construct a supertree. To characterize the conserved patterns, we used SMART and MEME to identify domain and transmembrane regions in the unique protein sequences. Therefore, our study unravelled the genomic insights into the ecology-driven speciation of Ideonella and Thermobifida.