Skip to content
1887

Abstract

The actinobacterial family comprises a diverse group of Gram-positive bacteria with high G+C content and complex taxonomic challenges. Traditional polyphasic approaches, based on 16S rRNA phylogeny and phenotypic traits, have in some instances resulted in polyphyletic taxonomic groupings, necessitating genome-wide methodologies to better resolve evolutionary relationships. This study employs a taxogenomic approach – incorporating 16S rRNA gene sequencing, core protein phylogeny, average amino acid identity and percentage of conserved proteins – to reassess the genera , , , , and . The findings reveal significant polyphyly in , and , indicating ecological convergence rather than shared ancestry. Proposed taxonomic revisions include the reclassification of and into , and into , and and into . should be incorporated into . Additionally, is reassigned to . Two new genera were also proposed to encompass “Leifsonia flava” and , named gen. nov. and another to encompass , named gen. nov. These genome-based insights provide a refined framework for the taxonomy of , enhancing our understanding of their evolutionary and ecological roles.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006809
2025-06-18
2026-03-09

Metrics

Loading full text...

Full text loading...

References

  1. Park YH, Suzuki K, Yim DG, Lee KC, Kim E et al. Suprageneric classification of peptidoglycan group B actinomycetes by nucleotide sequencing of 5S ribosomal RNA. Antonie Van Leeuwenhoek 1993; 64:307–313 [View Article] [PubMed]
    [Google Scholar]
  2. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article]
    [Google Scholar]
  3. Ludwig W, Viver T, Westram R, Francisco Gago J, Bustos-Caparros E et al. Release LTP_12_2020, featuring a new ARB alignment and improved 16S rRNA tree for prokaryotic type strains. Syst Appl Microbiol 2021; 44:126218 [View Article] [PubMed]
    [Google Scholar]
  4. Riesco R, Trujillo ME. Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2024; 74:006300 [View Article] [PubMed]
    [Google Scholar]
  5. Konstantinidis KT, Tiedje JM. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. COMICR 2007; 10:504–509 [View Article] [PubMed]
    [Google Scholar]
  6. Whitman WB. Genome sequences as the type material for taxonomic descriptions of prokaryotes. Syst Appl Microbiol 2015; 38:217–222 [View Article] [PubMed]
    [Google Scholar]
  7. Kitts PA, Church DM, Thibaud-Nissen F, Choi J, Hem V et al. Assembly: a resource for assembled genomes at NCBI. Nucleic Acids Res 2016; 44:D73–80 [View Article] [PubMed]
    [Google Scholar]
  8. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
    [Google Scholar]
  9. Kim J, Na S-I, Kim D, Chun J. UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis. J Microbiol 2021; 59:609–615 [View Article] [PubMed]
    [Google Scholar]
  10. Hölzer M. POCP-nf: an automatic Nextflow pipeline for calculating the percentage of conserved proteins in bacterial taxonomy. Bioinformatics 2024; 40: [View Article]
    [Google Scholar]
  11. Wan Y, Xiong M, Zhu L, Ni H, Chen X et al. Salinibacterium soli sp. nov., isolated from lakeside soil. Int J Syst Evol Microbiol 2024; 74:6479 [View Article] [PubMed]
    [Google Scholar]
  12. Liu ZS, Wang KH, Cai M, Yang ML, Wang XK et al. Agromyces chromiiresistens sp. nov., Novosphingobium album sp. nov., Sphingobium arseniciresistens sp. nov., Sphingomonas pollutisoli sp. nov., and Salinibacterium metalliresistens sp. nov.: five new members of microbacteriaceae and sphingomonadaceae from polluted soil. Front Microbiol 2023; 14:1289110 [View Article]
    [Google Scholar]
  13. Toumi M, Whitman WB, Kyrpides NC, Woyke T, Wolf J et al. Antiquaquibacter oligotrophicus gen. nov., sp. nov., a novel oligotrophic bacterium from groundwater. Int J Syst Evol Microbiol 2023; 73:6205 [View Article] [PubMed]
    [Google Scholar]
  14. Evtushenko LI. Microbacteriaceae. In Bergey’s Manual of Systematics of Archaea and Bacteria 2015 pp 1–14 [View Article]
    [Google Scholar]
  15. Li J, Lu S, Jin D, Yang J, Lai X-H et al. Salinibacterium hongtaonis sp. nov., isolated from faeces of Tibetan antelope (pantholops hodgsonii) on the Qinghai-Tibet Plateau. Int J Syst Evol Microbiol 2019; 69:1093–1098 [View Article]
    [Google Scholar]
  16. Lu C-Y, Dong L, Li S, Lian W-H, Lin Z-L et al. Salinibacterium sedimenticola sp. nov., Isolated from tidal flat sediment. Curr Microbiol 2023; 80: [View Article]
    [Google Scholar]
  17. Kim S-J, Jang Y-H, Hamada M, Tamura T, Ahn J-H et al. Homoserinimonas aerilata gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from an air sample in Korea. J Microbiol 2012; 50:673–679 [View Article]
    [Google Scholar]
  18. Reddy GSN, Prakash JSS, Srinivas R, Matsumoto GI, Shivaji S. Leifsonia rubra sp. nov. and Leifsonia aurea sp. nov., psychrophiles from a pond in Antarctica. Int J Syst Evol Microbiol 2003; 53:977–984 [View Article] [PubMed]
    [Google Scholar]
  19. Han SK, Nedashkovskaya OI, Mikhailov VV, Kim SB, Bae KS. Salinibacterium amurskyense gen. nov., sp. nov., a novel genus of the family Microbacteriaceae from the marine environment. Int J Syst Evol Microbiol 2003; 53:2061–2066 [View Article] [PubMed]
    [Google Scholar]
  20. Evtushenko LI, Dorofeeva LV, Subbotin SA, Cole JR, Tiedje JM. Leifsonia poae gen. nov., sp. nov., isolated from nematode galls on poa annua, and reclassification of “corynebacterium aquaticum” leifson 1962 as leifsonia aquatica (ex leifson 1962) gen. nov., comb. nov.. Int J Syst Evol Microbiol 2000; 50:371–380 [View Article]
    [Google Scholar]
  21. Kim S-J, Ahn J-H, Weon H-Y, Hamada M, Suzuki K et al. Diaminobutyricibacter tongyongensis gen. nov., sp. nov. and Homoserinibacter gongjuensis gen. nov., sp. nov. belong to the family Microbacteriaceae. J Microbiol 2014; 52:527–533 [View Article] [PubMed]
    [Google Scholar]
  22. Ganzert L, Bajerski F, Mangelsdorf K, Lipski A, Wagner D. Leifsonia psychrotolerans sp. nov., a psychrotolerant species of the family Microbacteriaceae from Livingston Island, Antarctica. Int J Syst Evol Microbiol 2011; 61:1938–1943 [View Article] [PubMed]
    [Google Scholar]
  23. Pindi PK, Kishore KH, Reddy GSN, Shivaji S. Description of Leifsonia kafniensis sp. nov. and Leifsonia antarctica sp. nov. Int J Syst Evol Microbiol 2009; 59:1348–1352 [View Article] [PubMed]
    [Google Scholar]
  24. Katayama T, Kato T, Tanaka M, Douglas TA, Brouchkov A et al. Glaciibacter superstes gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from a permafrost ice wedge. Int J Syst Evol Microbiol 2009; 59:482–486 [View Article]
    [Google Scholar]
  25. Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJ. Leifsonia bigeumensis sp. nov., isolated from soil on Bigeum Island, Korea. Int J Syst Evol Microbiol 2008; 58:1935–1938 [View Article] [PubMed]
    [Google Scholar]
  26. Cai Y, Tao WZ, Ma YJ, Cheng J, Zhang MY et al. Leifsonia flava sp. nov., a novel actinobacterium isolated from the rhizosphere of Aquilegia viridiflora. J Microbiol 2018; 56:549–555 [View Article] [PubMed]
    [Google Scholar]
  27. An D-F, Jiang L-Q, Zhang K, Li G-D, Wang X-Y et al. Glaciibacter flavus sp. nov., isolated from a lichen sample. Arch Microbiol 2021; 203:2439–2444 [View Article] [PubMed]
    [Google Scholar]
  28. Yarza P, Richter M, Peplies J, Euzeby J, Amann R et al. The all-species living tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008; 31:241–250 [View Article] [PubMed]
    [Google Scholar]
  29. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article] [PubMed]
    [Google Scholar]
  30. Rosselló-Móra R, Amann R. Past and future species definitions for Bacteria and Archaea. Syst Appl Microbiol 2015; 38:209–216 [View Article] [PubMed]
    [Google Scholar]
  31. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. The ISME Journal 2017; 11:2399–2406 [View Article]
    [Google Scholar]
  32. Konstantinidis KT, Tiedje JM. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol 2007; 10:504–509 [View Article] [PubMed]
    [Google Scholar]
  33. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species: culture-independent genomic approaches identify credibly distinct clusters, avoid cultivation bias, and provide true insights into microbial species. Microbe 2014; 9:111–118
    [Google Scholar]
  34. Qin Q, Xie B, Zhang X, Chen X, Zhou B et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article] [PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006809
Loading
/content/journal/ijsem/10.1099/ijsem.0.006809
Loading

Data & Media loading...

Supplements

Supplementary material 1

EXCEL
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An error occurred
Approval was partially successful, following selected items could not be processed due to error