Assessment of Evolutionary Relationships for Prioritization of Myxobacteria for Natural Product Discovery

Abstract

Discoveries of novel myxobacteria have started to unveil the potentially vast phylogenetic diversity within the family Myxococcaceae and have brought about an updated approach to myxobacterial classification. While traditional approaches focused on morphology, 16S gene sequences, and biochemistry, modern methods including comparative genomics have provided a more thorough assessment of myxobacterial taxonomy. Herein, we utilize long-read genome sequencing for two myxobacteria previously classified as Archangium primigenium and Chondrococcus macrosporus, as well as four environmental myxobacteria newly isolated for this study. Average nucleotide identity and digital DNA–DNA hybridization scores from comparative genomics suggest previously classified as A. primigenium to instead be a novel member of the genus Melittangium, C. macrosporus to be a potentially novel member of the genus Corallococcus with high similarity to Corallococcus exercitus, and the four isolated myxobacteria to include another novel Corallococcus species, a novel Pyxidicoccus species, a strain of Corallococcus exiguus, and a potentially novel Myxococcus species with high similarity to Myxococcus stipitatus. We assess the biosynthetic potential of each sequenced myxobacterium and suggest that genus-level conservation of biosynthetic pathways support our preliminary taxonomic assignment. Altogether, we suggest that long-read genome sequencing benefits the classification of myxobacteria and improves determination of biosynthetic potential for prioritization of natural product discovery.

Corallococcus soli sp. Nov., a Soil Myxobacterium Isolated from Subtropical Climate, Chalus County, Iran, and Its Potential to Produce Secondary Metabolites

“…High similarity scores (≥60%) were found in all strains for the BGC of VEPE/AEPE/TG-1, and nine strains for a carotenoid and myxochelin A/myxochelin B. Our results are in accordance with a previous study by Ahearne et al [ 64 ], which suggested that all of the myxobacterial strains from the Myxococcaceae family contained the BGC of geosmin, VEPE/AEPE/TG-1, and a carotenoid. Strain ZKHCc1 1396 T appears to be closely similar in the BGC pattern of Corallococcus terminator CA054A T , but lacks the BGC for icosalide A/icosalide B.…”

Chromosomal organization of biosynthetic gene clusters suggests plasticity of myxobacterial specialized metabolism including descriptions for nine novel species:Archangium lansiniumsp. nov.,Myxococcus landrumussp. nov.,Nannocystis bainbridgeasp. nov.,Nannocystis poenicansasp. nov.,Nannocystis radixulmasp. nov.,Polyangium mundeleiniumsp. nov.,Pyxidicoccus parkwaysissp. nov.,Sorangium ateriumsp. nov.,Stigmatella ashevillenasp. nov

“…Environmental isolates NCSPR01 and NCRR are both highly similar subspecies of Corallococcus coralloides DSM 2259 T (Supplemental Table 1 and Supplemental Figure 3A). As previously suggested by Ahearne et al, isolate NCCRE02 is a subspecies of Corallococcus exiguus DSM 14696 T (Supplemental Table 1 and Supplemental Figure 3A) (22). Isolate BB12-1 is likely a subspecies of Corallococcus terminator CA054A T , and isolate BB11-1 is potentially a novel species of Corallococcus (Supplemental Table 1 and Supplemental Figure 3B).…”

“…Lesser-studied myxobacteria include genera with agarolytic phenotypes such as Nannocystis, Polyangium , and Sorangium thus numerous agarolytic isolates with similar morphologies were advanced for genome sequencing (18). We have previously discussed four of the 20 environmental isolates (SCHIC03, SCPEA02, NCCRE02, NCSPR01) (22). Genome sequencing of all isolates provided five complete genomes, seven draft genomes with ≤3 contigs, three draft genomes with 5-8 contigs, and five lower quality genome assemblies with ≤44 contigs (Table 1).…”

Concepts and conjectures concerning predatory performance of myxobacteria

“…Technological and methodological advances over decades have introduced challenges to traditionally accepted theories and premises related to predatory myxobacteria. The transition from morphology-based classification of myxobacteria to a combination of traditional methods and comparative genomics has resulted in various taxonomic reassignments and proposed updates ( Awal et al, 2017 ; Waite et al, 2020 ; Ahearne et al, 2021 ), and descriptions from newly discovered myxobacteria often include predation data ( Figure 2 ; Fudou et al, 2002 ; Sanford et al, 2002 ; Iizuka et al, 2003a , b , 2013 ; Reichenbach et al, 2006 ; Garcia et al, 2009 , 2014 , 2016 ; Mohr et al, 2012 , 2018a , b ; Yamamoto et al, 2014 ; Sood et al, 2015 ; Awal et al, 2016 , 2017 ; Moradi et al, 2017 ; Garcia and Muller, 2018 ; Chambers et al, 2020 ; Livingstone et al, 2020 ; Wang et al, 2021a ; Zhou et al, 2021 ). Myxobacteria are often split into two groups based on presumed nutritional preferences or needs, predatory myxobacteria that acquire nutrients from prey lysate and cellulolytic myxobacteria ( Shimkets et al, 2006 ; Mohr, 2018 ).…”