Genome insight and description of antibiotic producing Massilia antibiotica sp. nov., isolated from oil-contaminated soil

Abstract

An ivory-coloured, motile, Gram-stain-negative bacterium, designated TW-1T was isolated from oil-contaminated experimental soil in Kyonggi University. The phylogenetic analysis based on 16S rRNA gene sequence revealed, strain TW-1T formed a lineage within the family Oxalobacteraceae and clustered as members of the genus Massilia. The closest members were M. pinisoli T33T (98.8% sequence similarity), M. putida 6NM-7T (98.6%), M. arvi THG-RS2OT (98.5%), M. phosphatilytica 12-OD1T (98.3%) and M. niastensis 5516S-1T (98.2%). The sole respiratory quinone is ubiquinone-8. The major cellular fatty acids are hexadeconic acid, cis-9, methylenehexadeconic acid, summed feature 3 and summed feature 8. The major polar lipids are phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The DNA G + C content of the type strain is 66.3%. The average nucleotide identity (ANI) and in silico DNA–DNA hybridization (dDDH) relatedness values between strain TW-1T and closest members were below the threshold value for species demarcation. The genome size is 7,051,197 bp along with 46 contigs and 5,977 protein-coding genes. The genome showed 5 putative biosynthetic gene clusters (BGCs) that are responsible for different secondary metabolites. Cluster 2 showed thiopeptide BGC with no known cluster blast, indicating TW-1T might produce novel antimicrobial agent. The antimicrobial assessment also showed that strain TW-1T possessed inhibitory activity against Gram-negative pathogens (Escherichia coli and Pseudomonas aeruginosa). This is the first report of the species in the genus Massilia which produces antimicrobial compounds. Based on the polyphasic study, strain TW-1T represents novel species in the genus Massilia, for which the name Massilia antibiotica sp. nov. is proposed. The type strain is TW-1T (= KACC 21627T = NBRC 114363T).

Genomic analysis uncovers laccase-coding genes and biosynthetic gene clusters encoding antimicrobial compounds in laccase-producing Acinetobacter baumannii

“…In addition, TP-1161, a thiopeptide antibiotic produced by marine Nocardiopsis species which exhibits antibiotic activity against a broad spectrum of multidrug-resistant Gram-positive bacteria and multidrug-resistant Candida albicans, has been identified in the genome of the NI-65 strain 20 . The last gene cluster identified in the NI-65 strain was N-tetradecanoyl tyrosine, which is a long-chain N-acyl amino acid isolated from soil bacteria with antibacterial activity 21 .…”

Genome-wide and constrained ordination-based analyses of EC code data support reclassification of the species of Massilia La Scola et al. 2000 into Telluria Bowman et al. 1993, Mokoshia gen. nov. and Zemynaea gen. nov.

“…The species 'Massilia cellulosiltytica' , the name of which is misspelled in the original description [28], 'Massilia aromaticivorans' [29] and 'Massilia antibiotica' [30] are all distinct and well-described species despite not having achieved validation. Since the type Fig.…”

Duganella dendranthematis sp. nov. and Massilia forsythiae sp. nov., isolated from flowers

“…In addition, they were found in a high abundance in the rhizosphere of diseased plants [26], from which they were thought to be associated with plant diseases. On the other hand, some species in the genus Massilia are considered as pathogens since they were isolated from human clinical samples [27]. This study, based on a polyphasic approach, describes the taxonomic position of two bacterial strains, each representing a novel species within the genus Duganella and Massilia , isolated from flowers.…”