Isolation and Whole Genome Sequence Analysis of Alcaligenes and Chromobacterium Strains with Antimicrobial Activity...

Discovery, development, and production of new antibiotic drugs in a form safe for human consumption have become increasingly difficult, expensive, and time-consuming, especially with an increase in antibiotic-resistant pathogens. The ESKAPE pathogens are a group of six pathogenic bacteria that can be highly virulent and are likely to, or already have, developed antibiotic resistance to many of the currently available antibiotics. New antibiotics or new activities of existing natural products are needed to combat these multi-drug resistant pathogens. Our approach was to search for soil microbes that produce antimicrobial compounds that could potentially inhibit the growth of the ESKAPE pathogens. We report one draft genome of Chromobacterium and one draft genome of Alcaligenes cultured from soil with antimicrobial activity against Staphylococcus epidermidis, a relative of ESKAPE pathogen Staphylococcus aureus. The lengths of the genomes were 5.2 and 4.0 Mbps and GC content was at 64.4% and 56.1% for Chromobacterium sp. HL1 and Alcaligenes parafaecalis HL2, respectively. Chromobacterium sp. HL1 has not been assigned to any previously known species. Phylogenetic analysis revealed that Chromobacterium sp. HL1 may be closely related to Chromobacterium fluminis and Chromobacterium alkanivorans. A. parafaecalis HL2 is likely related to Alcaligenes faecalis subsp. parafaecalis. Functional analysis revealed biosynthetic gene clusters related to betalactone, terpene, isocyanide, and T1PKS in one or both genomes analyzed. Antimicrobial properties were previously reported from the products of these gene clusters that could further aid our search for the active component of the analyzed strains.