Chromosomal organization of biosynthetic gene clusters, including those of nine novel species, suggests plasticity of myxobacterial specialized metabolism

Abstract

IntroductionNatural products discovered from bacteria provide critically needed therapeutic leads for drug discovery, and myxobacteria are an established source for metabolites with unique chemical scaffolds and biological activities. Myxobacterial genomes accommodate an exceptional number and variety of biosynthetic gene clusters (BGCs) which encode for features involved in specialized metabolism.MethodsIn this study, we describe the collection, sequencing, and genome mining of 20 myxobacteria isolated from rhizospheric soil samples collected in North America.ResultsNine isolates were determined to be novel species of myxobacteria including representatives from the genera Archangium, Myxococcus, Nannocystis, Polyangium, Pyxidicoccus, Sorangium, and Stigmatella. Growth profiles, biochemical assays, and descriptions were provided for all proposed novel species. We assess the BGC content of all isolates and observe differences between Myxococcia and Polyangiia clusters.DiscussionContinued discovery and sequencing of novel myxobacteria from the environment provide BGCs for the genome mining pipeline. Utilizing complete or near-complete genome sequences, we compare the chromosomal organization of BGCs of related myxobacteria from various genera and suggest that the spatial proximity of hybrid, modular clusters contributes to the metabolic adaptability of myxobacteria.

Natural product biosynthetic potential reflects macroevolutionary diversification within a widely distributed bacterial taxon

“…When placed into a broader context, the most promising Flavobacteriaceae genera possess a rather moderate biosynthetic potential when compared to well-established, highly prolific bacterial taxa such as the genus Streptomyces (phylum Actinomycetota ) and the order Myxococcales (phylum Myxococcota ). Strains in these groups may present up to 83 ( 37 ) and 52 ( 38 ) BGCs per genome, respectively, according to recent genome mining estimates. Larger genomes also tend to possess higher BGC counts within these taxa, whose genome sizes can reach up to 13–14 Mb for some strains ( 38 ), roughly two times larger than the largest Flavobacteriaceae genomes identified in our data set.…”

“…Strains in these groups may present up to 83 ( 37 ) and 52 ( 38 ) BGCs per genome, respectively, according to recent genome mining estimates. Larger genomes also tend to possess higher BGC counts within these taxa, whose genome sizes can reach up to 13–14 Mb for some strains ( 38 ), roughly two times larger than the largest Flavobacteriaceae genomes identified in our data set.…”

Characteristics of a lipase ArEstA with lytic activity against drug-resistant pathogen from a novel myxobacterium, Archangium lipolyticum sp. nov.

“…The baiting method for myxobacteria isolation and the repeated transfers for purification are time-consuming and difficult ( Shimkets et al, 2006 ). Furthermore, the most recently identified new species of myxobacteria belong to the genera Myxococcus and Corallococcus , which are frequently isolated but not dominant in soil indicated by culture-independent methods ( Chambers et al, 2020 ; Livingstone et al, 2020 ; Zhou et al, 2020 ; Petters et al, 2021 ), and relatively fewer members of less-studied myxobacteria species have been reported over the last decade ( Ahearne et al, 2023 ). Therefore, more efforts are encouraged to explore and obtain the less-studied myxobacteria with an extended taxonomic range.…”

Mass lysis of bacterial predators drives the enrichment of antibiotic resistance in soil microbial communities

“…A number of microbial species are proficient antibiotic producers [15][16][17][18] . Such microbes generally harbor multiple biosynthetic clusters and show ability to produce distinct antibiotics [19][20][21][22][23] . However, influence of antibiotic producing microbes on the emergence or maintenance of resistance mechanisms in nature as well as in lab environment remains little explored.…”