Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 75, Issue 5

Phylogenomic studies and molecular markers clarifying the evolutionary relationships and classification of species: proposal for the family fam. nov. harbouring the genera gen. nov. and gen. nov. Open Access

Abstract

The genus , created by the reclassification of specific deep-branching species, exhibits polyphyletic branching. The Genome Taxonomy Database (GTDB) also assigns species into two families and three genera. To clarify the evolutionary relationships and classification of species, we report detailed investigations using phylogenomic and molecular signature-based approaches. In phylogenomic trees, species are distributed within two family-level lineages. One of these clades, containing the type species (viz. ), represents the genus , groups within the family . Ten novel conserved signature indels (CSIs) identified in this study are specific for this clade, providing a robust means for the differentiation of the emended genus . The remaining species form a separate family-level clade, designated as f_HBI72195 in the GTDB. Within this clade, all species except form a robust clade designated as clade −2 in our work and g__A in the GTDB. We have also identified 15 novel CSIs specific to this clade. As the clade −2 is distinct from , we propose transferring species from this clade into a new genus, gen. nov. The species branches distinctly from other species, and the GTDB considers it a novel genus (g_BR). Six newly identified CSIs are specific to this species, and we are proposing the transfer of this species into a new genus, gen. nov. Two additional identified CSIs are shared by members of the novel family-level taxon (f_HBI72195) comprising the proposed genera and , for which we are proposing the name fam. nov. Lastly, the results presented here also show that ‘’ and ‘’ are later heterotypic synonyms of . These changes, which reliably depict the evolutionary relationships among species, should be helpful in future studies of these organisms.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): AAI analysis , conserved signature indels (CSIs) , phylogenomic and comparative genomic analyses , proposals for the family Guptibacillaceae fam. nov. and thegenera Exobacillus gen. nov. and Guptibacillus gen. nov. and taxon-specific molecular markers
Funding
This study was supported by the:
  • Ontario Ministry of Research Innovation and Science
    • Principle Award Recipient: HerbE Schellhorn
  • Natural Science and Engineering Research Council of Canada
    • Principle Award Recipient: HerbE Schellhorn
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006757
2025-05-07
2025-05-18
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/75/5/ijsem006757.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.006757&mimeType=html&fmt=ahah

References

  1. Bello S, Rudra B, Schellhorn HE. Phylogenomic studies and molecular markers clarifying the evolutionary relationships and classification of Pseudalkalibacillus species: proposal for the family Guptibacillaceae fam. nov. harbouring the genera Guptibacillus gen. nov. and Exobacillus gen. nov Figshare 2025 [View Article]
     [Google Scholar]
  2. Joshi A, Thite S, Karodi P, Joseph N, Lodha T. Alkalihalobacterium elongatum gen. nov. sp. nov.: an antibiotic-producing bacterium isolated from lonar lake and reclassification of the genus Alkalihalobacillus into seven novel genera. Front Microbiol 2021; 12:722369 [View Article]
     [Google Scholar]
  3. Patel S, Gupta RS. A phylogenomics and comparative genomic framework for resolving the polyphyly of the genus Bacillus: proposal for six new genera of Bacillus species, peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. Int J Syst Evol Microbiol 2020; 70:406–438 [View Article]
     [Google Scholar]
  4. Santini JM, Streimann ICA, Hoven RNV. Bacillus macyae sp. nov., an arsenate-respiring bacterium isolated from an Australian gold mine. Int J Syst Evol Microbiol 2004; 54(pt 6):2241–2244 [View Article] [PubMed]
     [Google Scholar]
  5. Mo K, Huang H, Bao S, Hu Y. Bacillus caeni sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2020; 70:1503–1507 [View Article] [PubMed]
     [Google Scholar]
  6. Gupta RS, Kanter-Eivin DA. AppIndels.com server: a web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences. validation of its usefulness by predicting the taxonomic affiliation of >700 unclassified strains of Bacillus species. Int J Syst Evol Microbiol 2023; 73: [View Article] [PubMed]
     [Google Scholar]
  7. Liu G-H, Han S, Li B, Li R-L, Shi H et al. Two novel alkalitolerant species Pseudalkalibacillus spartinae sp. nov. and Pseudalkalibacillus sedimenti sp. nov. Int J Syst Evol Microbiol 2023; 73: [View Article] [PubMed]
     [Google Scholar]
  8. Gao L, Fang B-Z, Liu Y-H, Huang Y, Zhang D-D et al. Pseudalkalibacillus salsuginis sp. nov., a novel salt-tolerant bacterium isolated from a saline lake sediment. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  9. Sayers EW, Agarwala R, Bolton EE, Brister JR, Canese K et al. Database resources of the national center for biotechnology information. Nucleic Acids Res 2019; 47:D23–D28 [View Article] [PubMed]
     [Google Scholar]
  10. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [View Article] [PubMed]
     [Google Scholar]
  11. Chuvochina M, Mussig AJ, Chaumeil P-A, Skarshewski A, Rinke C et al. Proposal of names for 329 higher rank taxa defined in the genome taxonomy database under two prokaryotic codes. FEMS Microbiol Lett 2023; 370:fnad071 [View Article] [PubMed]
     [Google Scholar]
  12. 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] [PubMed]
     [Google Scholar]
  13. Bello S, Rudra B, Schellhorn HE. Supplemental data for phylogenomic and molecular markers studies clarifying the evolutionary relationships and classification of Pseudalkalibacillus species: proposal for the family Guptibacillaceae fam. nov. harboring the genera Guptibacillus gen. nov. and Exobacillus gen. nov. Int J Syst Evol Microbiol 2025
     [Google Scholar]
  14. Wang Z, Wu M. A phylum-level bacterial phylogenetic marker database. Mol Biol Evol 2013; 30:1258–1262 [View Article] [PubMed]
     [Google Scholar]
  15. Adeolu M, Alnajar S, Naushad S, Gupta RS. Genome-based phylogeny and taxonomy of the 'Enterobacteriales': proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Int J Syst Evol Microbiol 2016; 66:5575–5599 [View Article]
     [Google Scholar]
  16. Bello S, Howard-Azzeh M, Schellhorn HE, Gupta RS. Phylogenomic analyses and molecular signatures elucidating the evolutionary relationships amongst the Chlorobia and Ignavibacteria species: robust demarcation of two family-level clades within the order Chlorobiales and proposal for the family Chloroherpetonaceae fam. nov. Microorganisms 2022; 10:1312 [View Article] [PubMed]
     [Google Scholar]
  17. Rudra B, Gupta RS. Phylogenomics studies and molecular markers reliably demarcate genus Pseudomonas sensu stricto and twelve other Pseudomonadaceae species clades representing novel and emended genera. Front Microbiol 2024; 14:1273665 [View Article] [PubMed]
     [Google Scholar]
  18. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K et al. Fast, scalable generation of high-quality protein multiple sequence alignments using clustal omega. Mol Syst Biol 2011; 7:539 [View Article] [PubMed]
     [Google Scholar]
  19. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article] [PubMed]
     [Google Scholar]
  20. Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490 [View Article] [PubMed]
     [Google Scholar]
  21. Whelan S, Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 2001; 18:691–699 [View Article] [PubMed]
     [Google Scholar]
  22. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article] [PubMed]
     [Google Scholar]
  23. Le SQ, Gascuel O. An improved general amino acid replacement matrix. Mol Biol Evol 2008; 25:1307–1320 [View Article] [PubMed]
     [Google Scholar]
  24. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
     [Google Scholar]
  25. Gupta RS, Patel S, Saini N, Chen S. Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species. Int J Syst Evol Microbiol 2020; 70:5753–5798 [View Article] [PubMed]
     [Google Scholar]
  26. Saini N, Gupta RS. A robust phylogenetic framework for members of the order Legionellales and its main genera (Legionella, Aquicella, Coxiella and Rickettsiella) based on phylogenomic analyses and identification of molecular markers demarcating different clades. Antonie Van Leeuwenhoek 2021; 114:957–982 [View Article] [PubMed]
     [Google Scholar]
  27. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E et al. Microbial genomic taxonomy. BMC Genomics 2013; 14:913 [View Article] [PubMed]
     [Google Scholar]
  28. Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E et al. The SILVA and “all-species living tree project (LTP)” taxonomic frameworks. Nucleic Acids Res 2014; 42:D643–8 [View Article] [PubMed]
     [Google Scholar]
  29. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article] [PubMed]
     [Google Scholar]
  30. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389–3402 [View Article] [PubMed]
     [Google Scholar]
  31. Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res 2015; 43:6761–6771 [View Article] [PubMed]
     [Google Scholar]
  32. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
     [Google Scholar]
  33. Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 2012; 28:3150–3152 [View Article] [PubMed]
     [Google Scholar]
  34. Chen S, Rudra B, Gupta RS. Phylogenomics and molecular signatures support division of the order Neisseriales into emended families Neisseriaceae and Chromobacteriaceae and three new families Aquaspirillaceae fam. nov., Chitinibacteraceae fam. nov., and Leeiaceae fam. nov. Syst Appl Microbiol 2021; 44:126251 [View Article] [PubMed]
     [Google Scholar]
  35. Wickham H. Ggplot2: Elegant Graphics for Data Analysis Springer International Publishing; 2016
     [Google Scholar]
  36. Gupta RS. Identification of conserved indels that are useful for classification and evolutionary studies. In Goodfellow M, Sutcliffe IC, Chun J. eds Bacterial Taxonomy, Methods in Microbiology London: Elsevier; 2014 pp 153–182
     [Google Scholar]
  37. Bello S, Mudassir SH, Rudra B, Gupta RS. Phylogenomic and molecular markers based studies on Staphylococcaceae and Gemella species. Proposals for an emended family Staphylococcaceae and three new families (Abyssicoccaceae fam. nov., Salinicoccaceae fam. nov. and Gemellaceae fam. nov.) harboring four new genera, Lacicoccus gen. nov., Macrococcoides gen. nov., Gemelliphila gen. nov., and Phocicoccus gen. nov. Antonie Van Leeuwenhoek 2023; 116:937–973 [View Article] [PubMed]
     [Google Scholar]
  38. Naushad S, Adeolu M, Wong S, Sohail M, Schellhorn HE et al. A phylogenomic and molecular marker based taxonomic framework for the order Xanthomonadales: proposal to transfer the families Algiphilaceae and Solimonadaceae to the order Nevskiales ord. nov. and to create a new family within the order Xanthomonadales, the family Rhodanobacteraceae fam. nov., containing the genus Rhodanobacter and its closest relatives. Antonie Van Leeuwenhoek 2015; 107:467–485 [View Article] [PubMed]
     [Google Scholar]
  39. Heyrman J, Balcaen A, Rodriguez-Diaz M, Logan NA, Swings J et al. Bacillus decolorationis sp. nov., isolated from biodeteriorated parts of the mural paintings at the Servilia tomb (Roman necropolis of Carmona, Spain) and the saint-catherine chapel (Castle Herberstein, Austria). Int J Syst Evol Microbiol 2003; 53:459–463 [View Article] [PubMed]
     [Google Scholar]
  40. Li Y, Zhang D, Bo D, Peng D, Sun M et al. A taxonomic note on the order Caryophanales: description of 12 novel families and emended description of 21 families. Int J Syst Evol Microbiol 2024; 74: [View Article] [PubMed]
     [Google Scholar]
  41. Zavarzina DG, Tourova TP, Kolganova TV, Boulygina ES, Zhilina TN. Description of Anaerobacillus alkalilacustre gen. nov., sp. nov.—strictly anaerobic diazotrophic bacillus isolated from soda lake and transfer of Bacillus arseniciselenatis, Bacillus macyae, and Bacillus alkalidiazotrophicus to Anaerobacillus as the new combinations A. arseniciselenatis comb. nov., A. macyae comb. nov., and A. alkalidiazotrophicus comb. nov. Microbiology 2009; 78:723–731 [View Article]
     [Google Scholar]
  42. Barbour AG, Adeolu M, Gupta RS. Division of the genus Borrelia into two genera (corresponding 667 to Lyme disease and relapsing fever groups) reflects their genetic and phenotypic distinctiveness and will lead to a better understanding of these two groups of microbes (Margos et al. (2016) There is inadequate evidence to support the division of the genus Borrelia. Int J Syst Evol Microbiol 2017; 67:2058–2067 [View Article]
     [Google Scholar]
  43. Gupta RS. Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin’s views on classification. FEMS Microbiol Rev 2016; 40:520–553 [View Article] [PubMed]
     [Google Scholar]
  44. Howard-Azzeh M, Shamseer L, Schellhorn HE, Gupta RS. Phylogenetic analysis and molecular signatures defining a monophyletic clade of heterocystous cyanobacteria and identifying its closest relatives. Photosynth Res 2014; 122:171–185 [View Article]
     [Google Scholar]
  45. Dobritsa AP, Samadpour M. Reclassification of Burkholderia insecticola as Caballeronia insecticola comb. nov. and reliability of conserved signature indels as molecular synapomorphies. Int J Syst Evol Microbiol 2019; 69:2057–2063 [View Article] [PubMed]
     [Google Scholar]
  46. Janda JM, Abbott SL. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J Clin Microbiol 2007; 45:2761–2764 [View Article] [PubMed]
     [Google Scholar]
  47. Caudill MT, Brayton KA. The use and limitations of the 16S rRNA sequence for species classification of Anaplasma samples. Microorganisms 2022; 10:605 [View Article] [PubMed]
     [Google Scholar]
  48. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
     [Google Scholar]
  49. 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]
  50. Parker CT, Tindall BJ, Garrity GM. International code of nomenclature of prokaryotes. Int J Syst Evol Microbiol 2019; 69:1–S [View Article]
     [Google Scholar]
  51. Oren A, Arahal DR, Göker M, Moore ERB, Rossello-Mora R et al. International code of nomenclature of prokaryotes.prokaryotic code (2022 revision). Int J Syst Evol Microbiol 2023; 73: [View Article]
     [Google Scholar]
  52. Bello S, McQuay S, Rudra B, Gupta RS. Robust demarcation of the family Peptostreptococcaceae and its main genera based on phylogenomic studies and taxon-specific molecular markers. Int J Syst Evol Microbiol 2024; 74: [View Article] [PubMed]
     [Google Scholar]
  53. Gupta RS. Editorial: applications of genome sequences for discovering characteristics that are unique to different groups of organisms and provide insights into evolutionary relationships. Front Genet 2016; 7:27 [View Article] [PubMed]
     [Google Scholar]
  54. Malhotra M, Bello S, Gupta RS. Phylogenomic and molecular markers based studies on clarifying the evolutionary relationships among Peptoniphilus species. Identification of several Genus-Level clades of Peptoniphilus species and transfer of some Peptoniphilus species to the genus Aedoeadaptatus. Syst Appl Microbiol 2024; 47:126499 [View Article] [PubMed]
     [Google Scholar]
  55. Ahmod NZ, Gupta RS, Shah HN. Identification of a Bacillus anthracis specific indel in the yeaC gene and development of a rapid pyrosequencing assay for distinguishing B. anthracis from the B. cereus group. J Microbiol Methods 2011; 87:278–285 [View Article] [PubMed]
     [Google Scholar]
  56. Gao B, Gupta RS. Conserved indels in protein sequences that are characteristic of the phylum Actinobacteria. Int J Syst Evol Microbiol 2005; 55:2401–2412 [View Article] [PubMed]
     [Google Scholar]
  57. Khadka B, Gupta RS. Identification of a conserved 8 aa insert in the PIP5K protein in the Saccharomycetaceae family of fungi and the molecular dynamics simulations and structural analysis to investigate its potential functional role. Proteins 2017; 85:1454–1467 [View Article] [PubMed]
     [Google Scholar]
  58. Khadka B, Persaud D, Gupta RS. Novel sequence feature of SecA translocase protein unique to the thermophilic bacteria: bioinformatics analyses to investigate their potential roles. Microorganisms 2019; 8:59 [View Article] [PubMed]
     [Google Scholar]
  59. Singh B, Gupta RS. Conserved inserts in the Hsp60 (GroEL) and Hsp70 (DnaK) proteins are essential for cellular growth. Mol Genet Genomics 2009; 281:361–373 [View Article] [PubMed]
     [Google Scholar]
  60. Wong SY, Paschos A, Gupta RS, Schellhorn HE. Insertion/deletion-based approach for the detection of Escherichia coli O157:H7 in freshwater environments. Environ Sci Technol 2014; 48:11462–11470 [View Article] [PubMed]
     [Google Scholar]
  61. Yoon JH, Kim IG, Kang KH, Oh TK, Park YH. Bacillus hwajinpoensis sp. nov. and an unnamed Bacillus genomospecies, novel members of Bacillus rRNA group 6 isolated from sea water of the east sea and the yellow sea in Korea. Int J Syst Evol Microbiol 2004; 54:803–808 [View Article] [PubMed]
     [Google Scholar]
  62. Ivanova EP, Alexeeva YA, Zhukova NV, Gorshkova NM, Buljan V et al. Bacillus algicola sp. nov., a novel filamentous organism isolated from brown alga fucus evanescens. Syst Appl Microbiol 2004; 27:301–307 [View Article] [PubMed]
     [Google Scholar]
  63. Chen Y-G, Zhang Y-Q, He J-W, Klenk H-P, Xiao J-Q et al. Bacillus hemicentroti sp. nov., a moderate halophile isolated from a sea urchin. Int J Syst Evol Microbiol 2011; 61(pt 12):2950–2955 [View Article] [PubMed]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006757
Loading
Phylogenomic studies and molecular markers clarifying the evolutionary relationships and classification of Pseudalkalibacillus species: proposal for the family Guptibacillaceae fam. nov. harbouring the genera Guptibacillus gen. nov. and Exobacillus gen. nov.
Int J Syst Evol Microbiol 75, 006757 (2025); https://doi.org/10.1099/ijsem.0.006757
/content/journal/ijsem/10.1099/ijsem.0.006757
/content/journal/ijsem/10.1099/ijsem.0.006757
Loading

Data & Media loading...

Supplements

Loading data from figshare Loading data from figshare

Most cited Most Cited RSS feed

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