Isolation and whole-genome sequencing of Pseudomonas sp. RIT 623, a slow-growing bacterium endowed with antibiotic properties

Abstract

Objective There is an urgent need for the discovery and/or development of novel antibiotics. We report an exploration of “slow”-growing bacteria, which can be difficult to isolate using rich media as they are usually outcompeted by “fast”-growing bacteria, as potential sources of novel antimicrobials. Results Pseudomonas sp. RIT 623 was isolated using pond water agar from a pond located on the campus of the Rochester Institute of Technology (RIT). The genome was sequenced and analyzed for potential secondary metabolite gene clusters. Bioinformatics analysis revealed 14 putative gene clusters predicted to encode pathways for the anabolism of secondary metabolites. Ethyl acetate extracts from spent growth medium of Pseudomonas sp. RIT 623 were tested against two Gram-negative ( E. coli ATCC 25922 and P. aeruginosa ATCC 27853) and two Gram-positive ( B. subtilis BGSC 168 and S. aureus ATCC 25923) type strains to assess antibiotic activity. The antibiotic assays demonstrated that extracts of Pseudomonas sp. RIT 623 were able to inhibit the growth of the four strains. The active compound was separated using diethyl ether in a multi-solvent extraction and reverse phase chromatography. The bioactive compound/s were subsequently eluted in two consecutive fractions corresponding to approximately 16–22% acetonitrile, indicative of polar compound/s.

Exiguobacterium sp. is endowed with antibiotic properties against Gram positive and negative bacteria

“…RIT452 grown in 3 mL of TSB for 24 h at 30 °C. The DNA isolation and subsequent steps were performed as in Steiner et al [ 34 ].…”

“…RIT 452 was cultured in 100 mL LB medium at 30 °C shaken at 130 rpm for 24 h. This was inoculated in 900 mL of LB medium and grown for an additional 48 h at 30 °C shaken at 130 rpm. The extraction of organics from the spent media and storage of concentrated extracts were performed as published earlier [ 34 ].…”

“…A five-step extraction and the subsequent separation of the most active extract by liquid chromatography were conducted using known methods [ 34 ].…”

“…Disc diffusion tests of the organics extracted with different solvents was performed according to Steiner et al [ 34 ].…”

Isolation, Whole-Genome Sequencing, and Annotation of Three Unclassified Antibiotic-Producing Bacteria, Enterobacter sp. Strain RIT 637, Pseudomonas sp. Strain RIT 778, and Deinococcus sp. Strain RIT 780

“… Enterobacter species are generally considered human pathogens, but some strains have been shown to possess antibacterial ( 1 – 3 ) and antifungal ( 4 ) activities. Pseudomonas species also produce antibacterial ( 5 – 9 ) and antifungal compounds ( 10 , 11 ); their genomes have been mined for the ability to synthesize secondary metabolites and drug-like natural products ( 12 ), and P. putida produces a number of natural product families ( 13 ). Deinococcus radiodurans produces an antioxidant exopolysaccharide, while a Deinococcus strain isolated from ants produces cancer-preventing aminoglycolipids ( 14 ).…”