Genomic Analysis of Endophytic Bacillus-Related Strains Isolated from the Medicinal Plant Origanum vulgare L. Revealed the Presence of Metabolic Pathways Involved in the Biosynthesis of Bioactive Compounds

Abstract

Multidrug-resistant pathogens represent a serious threat to human health. The inefficacy of traditional antibiotic drugs could be surmounted through the exploitation of natural bioactive compounds of which medicinal plants are a great reservoir. The finding that bacteria living inside plant tissues, (i.e., the endophytic bacterial microbiome) can influence the synthesis of the aforementioned compounds leads to the necessity of unraveling the mechanisms involved in the determination of this symbiotic relationship. Here, we report the genome sequence of four endophytic bacterial strains isolated from the medicinal plant Origanum vulgare L. and able to antagonize the growth of opportunistic pathogens of cystic fibrosis patients. The in silico analysis revealed the presence of gene clusters involved in the production of antimicrobial compounds, such as paeninodin, paenilarvins, polymyxin, and paenicidin A. Endophytes' adaptation to the plant microenvironment was evaluated through the analysis of the presence of antibiotic resistance genes in the four genomes. The diesel fuel degrading potential was also tested. Strains grew in minimum media supplemented with diesel fuel, but no n-alkanes degradation genes were found in their genomes, suggesting that diesel fuel degradation might occur through other steps involving enzymes catalyzing the oxidation of aromatic compounds.

Adaptation of Commensal Escherichia coli in Tomato Fruits: Motility, Stress, Virulence

“…DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany) and following the protocol provided by the manufacturer. DNA extracted from E. coli TOM and E. coli LB was sequenced using MinION (Oxford Nanopore Technology, Oxford, UK) and a PCR-free approach following the native barcoding genomic DNA protocol (version NBE_9065_v109_revY_14Aug2019), as previously described [ 21 ]. In brief, 1 μg of each sample DNA was repaired and end-prepped using the NEBNext Companion Module for Oxford Nanopore Technologies Ligation Sequencing (New England Biolabs, Ipswich, MA, USA).…”

Application of Cloning-Free Genome Engineering to Escherichia coli

“…Nanopore sequencing was performed with a PCR-free approach following the native barcoding genomic DNA protocol provided by Oxford Nanopore Technologies (ONT) (v. NBE_9065_v109_revY_14Aug2019), as reported in Semenzato et al [ 28 ]. An amount of 1 μg of each input gDNA was repaired and end-prepped using the NEBNext Companion Module for Oxford Nanopore Technologies Ligation Sequencing (New England Biolabs, Ipswich, MA, USA).…”

Endophytic Bacteria Associated with Origanum heracleoticum L. (Lamiaceae) Seeds

“…Nanopore sequencing was performed with a PCR-free approach, following the native barcoding genomic DNA protocol provided by Oxford Nanopore Technologies (ONT) (version NBE_9065_v109_revY_14Aug2019), as described in the work of Semenzato et al (2022) [ 37 ]. The gDNA of the selected endophyte was sequenced with 11 other non-related gDNA samples.…”