[Objective]Rummeliibacillus,a genus encompassing three known species,R.stabekisii,R.pycnus,and R.suwonensis,has a wide range of potential applications in biodegradation,probiotics,animal feed,and production of arginin...[Objective]Rummeliibacillus,a genus encompassing three known species,R.stabekisii,R.pycnus,and R.suwonensis,has a wide range of potential applications in biodegradation,probiotics,animal feed,and production of arginine,caproic acid,and other compounds.This study aims to explore the genetic diversity of this genus at the genomic level.[Methods]A comparative pangenome analysis of 12 strains isolated from different sources was conducted.In addition,the phylogenetic analysis,functional annotation,genomic metabolic pathway analysis,and prediction of mobile genetic elements were carried out.[Results]A total of 8024 gene clusters were identified.The core genome,accessory genome,and strain-specific genes comprised 1550,3941,and 2533 gene clusters,respectively.In the core genome,the arginine cycle of six strains was complete.Seven strains had the ability to completely biosynthesize acetoin.However,only R.pycnus and R.suwonensis 3B-1 were able to completely biosynthesize caproic acid.The phylogenetic tree,DNA-DNA hybridization,and average nucleotide identity showed that Rummeliibacillus sp.G93 and Rummeliibacillus sp.TYF-LIM-RU47 were strains of R.stabekisii.Rummeliibacillus sp.POC4 and Rummeliibacillus sp.TYF005 may belong to a new species of this genus.In addition,genomic islands were identified in all the 12 strains,with the number ranging from four(R.stabekisii DSM 25578 and R.stabekisii NBRC 104870)to 14(Rummeliibacillus sp.SL167 and Rummeliibacillus sp.TYF005),and prophage sequences were found in five of the 12strains.[Conclusion]This study provides a genomic framework for Rummeliibacillus that could assist the further exploration of this genus.展开更多
Whether prokaryotes,and other microorganisms,form distinct clusters that can be recognized as species remains an issue of paramount theoretical as well as practical consequence in identifying,regulating,and communicat...Whether prokaryotes,and other microorganisms,form distinct clusters that can be recognized as species remains an issue of paramount theoretical as well as practical consequence in identifying,regulating,and communicating about these organisms.In the past decade,comparisons of thousands of genomes of isolates and hundreds of metagenomes have shown that prokaryotic diversity may be predominantly organized in such sequence-discrete clusters,albeit organisms of intermediate relatedness between the identified clusters are also frequently found.Accumulating evidence suggests,however,that the latter“intermediate”organisms show enough ecological and/or functional distinctiveness to be considered different species.Notably,the area of discontinuity between clusters often—but not always—appears to be around 85%–95%genome-average nucleotide identity,consistently among different taxa.More recent studies have revealed remarkably similar diversity patterns for viruses and microbial eukaryotes as well.This high consistency across taxa implies a specific mechanistic process that underlies the maintenance of the clusters.The underlying mechanism may be a substantial reduction in the efficiency of homologous recombination,which mediates(successful)horizontal gene transfer,around 95%nucleotide identity.Deviations from the 95%threshold(e.g.,species showing lower intraspecies diversity)may be caused by ecological differentiation that imposes barriers to otherwise frequent gene transfer.While this hypothesis that clusters are driven by ecological differentiation coupled to recombination frequency(i.e.,higher recombination within vs.between groups)is appealing,the supporting evidence remains anecdotal.The data needed to rigorously test the hypothesis toward advancing the species concept are also outlined.展开更多
文摘[Objective]Rummeliibacillus,a genus encompassing three known species,R.stabekisii,R.pycnus,and R.suwonensis,has a wide range of potential applications in biodegradation,probiotics,animal feed,and production of arginine,caproic acid,and other compounds.This study aims to explore the genetic diversity of this genus at the genomic level.[Methods]A comparative pangenome analysis of 12 strains isolated from different sources was conducted.In addition,the phylogenetic analysis,functional annotation,genomic metabolic pathway analysis,and prediction of mobile genetic elements were carried out.[Results]A total of 8024 gene clusters were identified.The core genome,accessory genome,and strain-specific genes comprised 1550,3941,and 2533 gene clusters,respectively.In the core genome,the arginine cycle of six strains was complete.Seven strains had the ability to completely biosynthesize acetoin.However,only R.pycnus and R.suwonensis 3B-1 were able to completely biosynthesize caproic acid.The phylogenetic tree,DNA-DNA hybridization,and average nucleotide identity showed that Rummeliibacillus sp.G93 and Rummeliibacillus sp.TYF-LIM-RU47 were strains of R.stabekisii.Rummeliibacillus sp.POC4 and Rummeliibacillus sp.TYF005 may belong to a new species of this genus.In addition,genomic islands were identified in all the 12 strains,with the number ranging from four(R.stabekisii DSM 25578 and R.stabekisii NBRC 104870)to 14(Rummeliibacillus sp.SL167 and Rummeliibacillus sp.TYF005),and prophage sequences were found in five of the 12strains.[Conclusion]This study provides a genomic framework for Rummeliibacillus that could assist the further exploration of this genus.
基金supported by the Us National Science Foundation (Awards Nos.1759831 and 2129823).
文摘Whether prokaryotes,and other microorganisms,form distinct clusters that can be recognized as species remains an issue of paramount theoretical as well as practical consequence in identifying,regulating,and communicating about these organisms.In the past decade,comparisons of thousands of genomes of isolates and hundreds of metagenomes have shown that prokaryotic diversity may be predominantly organized in such sequence-discrete clusters,albeit organisms of intermediate relatedness between the identified clusters are also frequently found.Accumulating evidence suggests,however,that the latter“intermediate”organisms show enough ecological and/or functional distinctiveness to be considered different species.Notably,the area of discontinuity between clusters often—but not always—appears to be around 85%–95%genome-average nucleotide identity,consistently among different taxa.More recent studies have revealed remarkably similar diversity patterns for viruses and microbial eukaryotes as well.This high consistency across taxa implies a specific mechanistic process that underlies the maintenance of the clusters.The underlying mechanism may be a substantial reduction in the efficiency of homologous recombination,which mediates(successful)horizontal gene transfer,around 95%nucleotide identity.Deviations from the 95%threshold(e.g.,species showing lower intraspecies diversity)may be caused by ecological differentiation that imposes barriers to otherwise frequent gene transfer.While this hypothesis that clusters are driven by ecological differentiation coupled to recombination frequency(i.e.,higher recombination within vs.between groups)is appealing,the supporting evidence remains anecdotal.The data needed to rigorously test the hypothesis toward advancing the species concept are also outlined.
