Phylogenomic Analysis Substantiates the gyrB Gene as a Powerful Molecular Marker to Efficiently Differentiate the Most Closely Related Genera Myxococcus, Corallococcus, and Pyxidicoccus

Abstract

Rapid and accurate strain identification of the most closely related genera Myxococcus, Corallococcus, and Pyxidicoccus can enhance the efficiency of the mining of novel secondary metabolites through dereplication. However, the commonly used 16S rRNA gene sequencing cannot accurately differentiate members of the three genera above, and the whole-genome sequencing is unable to rapidly and inexpensively provide species assignation toward a large number of isolates. To overcome the limitations, the gyrB gene was investigated as a candidate genetic marker for exploring the phylogenetic relationships of bacteria within the three genera and for developing the gyrB-based typing method. Here, the bacterial phylogeny and species affiliations of the three genera were determined based on the phylogenomic reconstruction and the analysis of digital DNA–DNA hybridization values among 90 genomes, further confirming nine novel taxa and assigning over one-third of genomes to defined species. The phylogenetic relationships of these strains based on the gyrB gene sequences were congruent with those based on their genome sequences, allowing the use of the gyrB gene as a molecular marker. The gyrB gene-specific primers for the PCR-amplification and sequencing of bacteria within the three genera were designed and validated for 31 isolates from our group collection. The gyrB-based taxonomic tool proved to be able to differentiate closely related isolates at the species level. Based on the newly proposed 98.6% identity threshold for the 966-bp gyrB gene and the phylogenetic inference, these isolates were assigned into two known species and eight additional putative new species. In summary, this report demonstrated that the gyrB gene is a powerful phylogenetic marker for taxonomy and phylogeny of bacteria within the closely related genera Myxococcus, Corallococcus, and Pyxidicoccus, particularly in the case of hundreds or thousands of isolates in environmental studies.

Comparative genomics of Myxococcus and Pyxidicoccus, including the description of four novel species: Myxococcus guangdongensis sp. nov., Myxococcus qinghaiensis sp. nov., Myxococcus dinghuensis sp. nov., and Pyxidicoccus xibeiensis sp. nov.

“…The gyrB gene sequences were extracted from genomic sequences. Strains K38C18041901 T , K15C18031901 T , QH3KD-4-1 T , and QH1ED-7-1 T showed the highest gyrB gene sequence similarities of 94.0, 95.9, 91.4, and 93.7% with M. fulvus DSM 16525 T , M. stipitatus DSM 14675 T , M. eversor AB053B T , and P. trucidator CA060A T , respectively ( Supplementary Table 1 ), all of which were lower than 98.7% threshold for species boundaries of three genera Myxococcus , Pyxidicoccus , and Corallococcus ( Liu et al, 2021 ), indicating the four strains were potential new species.…”

“…The three genera Myxococcus , Pyxidicoccus , and Corallococcus of the family Myxococcaceae have often been isolated from various habitats, and their 16S rRNA genes show highly homologous ( Mohr et al, 2016 , 2017 ; Livingstone et al, 2017 ; Wang et al, 2020 ). Compared with the 98.65% of 16S rRNA gene sequence similarity, the 98.7% of gyrB gene sequence similarity is suitable as the threshold for species boundaries of the three genera above ( Liu et al, 2021 ). With the advance of next-generation sequencing technologies, comparative genomics analysis has been applied to identify and classify myxobacterial species.…”

Novel fast pathogen diagnosis method for severe pneumonia patients in the intensive care unit: randomized clinical trial

“…For example, two typical strains PAO1 and PAO7 of P. aeruginosa (NCBI representative genome database) demonstrate less than 94% nucleotide identity, while E. coli and Shigella sonnei both belong to Enterobateriaceae and their representative genomes share more than 98% nucleotide identity. Therefore, the widely used method to identify bacteria with conserved genes may not be a good choice ( Maslunka et al, 2015 ; Liu et al, 2021 ). We developed an innovative algorithm and designed a workflow to figure out the best DNA tag for each species for diagnostic application based on 1791 microbe genomes from 232 species ( Figure 2A ).…”

Comparing microbiological and molecular diagnostic tools for the surveillance of anthrax

“…Bacillus anthracis is in the phylum Firmicutes, family Bacillaceae, and belongs to the group referred to as the B. cereus group. The B. cereus group consists of 8 Bacillus species ( B. anthracis , B. cereus , B. thuringiensis , B. mycoides , B. pseudomycoides , B. weihenstephanensis , B. cytotoxicus , and B. toyonensis) that have closely related phylogenies (Radnedge et al, 2003, Rasko et al, 2005) as reflected by high similarities in 16S rRNA gene sequences (Ash et al, 1991, Somerville and Jones, 1972) and other genetic markers such as gyrB within the B. cereus group (Liu et al, 2021). These species also differ in their aetiology, pathogenesis, clinical manifestations and host preferences (Drobniewski, 1993, Rasko et al, 2005, Pilo and Frey, 2011, Helgason et al, 2000, Ehling-Schulz et al, 2019).…”

“…The gyrB gene encodes the B subunit of DNA gyrase, an enzyme critical for DNA replication, transcription, and repair in bacteria. The gyrB gene sequence is highly conserved among bacterial species but varies enough to distinguish between them (Yamamoto and Harayama, 1995, Liu et al, 2021). Studies have shown that gyrB sequencing can offer higher resolution than the more commonly used 16S rRNA gene sequencing in differentiating closely related bacterial species (La Duc et al, 2004, Fox et al, 1992).…”