1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 3

Genome-based phylogeny of the genera and and description of subsp. subsp. nov. and subsp. subsp. nov. Free

Abstract

The genera and are closely related members of the family . The genus consists of the species originally separated from the genus by gene analysis. Due to the high similarity of the 16S rRNA genes between species of both genera, the taxonomic status is here re-evaluated by a genome-based approach. Based on a core genome phylogeny and genome relatedness indices, it is shown that the taxonomy and nomenclature given for the basonym is more appropriate. Therefore, we propose to use this name in preference. Furthermore, the species status of and was reassessed. Both species are related at subspecies level by digital DNA–DNA hybridization (dDDH) analysis. Additionally, average amino acid identity (AAI) and average nucleotide identity (ANI) do not support a separate species status, and therefore it is proposed to classify as a subspecies of . Consequently, both species are being renamed subsp. subsp. nov. and subsp. subsp. nov., respectively. The genome relatedness indices revealed a close relationship of the genomospecies 5 with subsp. . Thus, it has been assigned to the same subspecies.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Cosenzaea , Genome-based phylogeny , Proteus , Proteus terrae subsp. cibarius subsp. nov and Proteus terrae subsp. terrae subsp. nov
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004651
2021-01-27
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/71/3/ijsem004651.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004651&mimeType=html&fmt=ahah

References

  1. Hauser G. ÜBer Fäulnissbakterien Und Deren Beziehungen Zur Septicämie. Ein Beitrag Zur Morphologie Der Spaltpilze Leipzig: Vogel; 1885
     [Google Scholar]
  2. O'Hara CM, Brenner FW, Miller JM. Classification, identification, and clinical significance of Proteus, Providencia, and Morganella . Clin Microbiol Rev 2000; 13:534–546 [View Article][PubMed]
     [Google Scholar]
  3. Drzewiecka D. Significance and roles of Proteus spp. bacteria in natural environments. Microb Ecol 2016; 72:741–758 [View Article][PubMed]
     [Google Scholar]
  4. Brenner DJ, Farmer JJ, Fanning GR, Steigerwalt AG, Klykken P et al. Deoxyribonucleic acid relatedness of Proteus and Providencia species. Int J Syst Bacteriol 1978; 28:269–282 [View Article]
     [Google Scholar]
  5. Cosenza BJ, Podgwaite JD. A new species of Proteus isolated from larvae of the gypsy moth Porthetria dispar (L.). Antonie van Leeuwenhoek 1966; 32:187–191 [View Article][PubMed]
     [Google Scholar]
  6. Hickman FW, Steigerwalt AG, Farmer JJ, Brenner DJ. Identification of Proteus penneri sp. nov., formerly known as Proteus vulgaris indole negative or as Proteus vulgaris biogroup 1. J Clin Microbiol 1982; 15:1097–1102 [View Article][PubMed]
     [Google Scholar]
  7. O'Hara CM, Brenner FW, Steigerwalt AG, Hill BC, Holmes B et al. Classification of Proteus vulgaris biogroup 3 with recognition of Proteus hauseri sp. nov., nom. rev. and unnamed Proteus genomospecies 4, 5 and 6. Int J Syst Evol Microbiol 2000; 50 Pt 5:1869–1875 [View Article][PubMed]
     [Google Scholar]
  8. Giammanco GM, Grimont PAD, Grimont F, Lefevre M, Giammanco G et al. Phylogenetic analysis of the genera Proteus, Morganella and Providencia by comparison of rpoB gene sequences of type and clinical strains suggests the reclassification of Proteus myxofaciens in a new genus, Cosenzaea gen. nov., as Cosenzaea myxofaciens comb. nov. Int J Syst Evol Microbiol 2011; 61:1638–1644 [View Article][PubMed]
     [Google Scholar]
  9. Adeolu M, Alnajar S, Naushad S, S Gupta R. 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][PubMed]
     [Google Scholar]
  10. Behrendt U, Augustin J, Spröer C, Gelbrecht J, Schumann P et al. Taxonomic characterisation of Proteus terrae sp. nov., a N2O-producing, nitrate-ammonifying soil bacterium. Antonie van Leeuwenhoek 2015; 108:1457–1468 [View Article][PubMed]
     [Google Scholar]
  11. Hyun D-W, Jung M-J, Kim M-S, Shin N-R, Kim PS et al. Proteus cibarius sp. nov., a swarming bacterium from Jeotgal, a traditional Korean fermented seafood, and emended description of the genus Proteus . Int J Syst Evol Microbiol 2016; 66:2158–2164 [View Article][PubMed]
     [Google Scholar]
  12. Dai H, Wang Y, Fang Y, Huang Z, Kan B et al. Proteus alimentorum sp. nov., isolated from pork and lobster in Ma'anshan City, China. Int J Syst Evol Microbiol 2018; 68:1390–1395 [View Article][PubMed]
     [Google Scholar]
  13. Dai H, Wang Y, Fang Y, Xiao T, Huang Z et al. Proteus columbae sp. nov., isolated from a pigeon in Ma'anshan, China. Int J Syst Evol Microbiol 2018; 68:552–557 [View Article][PubMed]
     [Google Scholar]
  14. Dai H, Chen A, Wang Y, Lu B, Wang Y et al. Proteus faecis sp. nov., and Proteus cibi sp. nov., two new species isolated from food and clinical samples in China. Int J Syst Evol Microbiol 2019; 69:852–858 [View Article][PubMed]
     [Google Scholar]
  15. 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]
  16. Parks DH, Chuvochina M, Chaumeil P-A, Rinke C, Mussig AJ. A complete domain-to-species taxonomy for bacteria and archaea. Nat Biotechnol 2020
     [Google Scholar]
  17. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article][PubMed]
     [Google Scholar]
  18. Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol 2011; 7:e1002195 [View Article][PubMed]
     [Google Scholar]
  19. 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]
  20. Zheng J, Wittouck S, Salvetti E, Franz CMAP, Harris HMB et al. A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae . Int J Syst Evol Microbiol 2020; 70:2782–2858 [View Article][PubMed]
     [Google Scholar]
  21. Palmer M, Steenkamp ET, Coetzee MPA, Avontuur JR, Chan W-Y et al. Mixta gen. nov., a new genus in the Erwiniaceae . Int J Syst Evol Microbiol 2018; 68:1396–1407 [View Article][PubMed]
     [Google Scholar]
  22. Xu L, Sun C, Fang C, Oren A, Xu X-W. Genomic-based taxonomic classification of the family Erythrobacteraceae . Int J Syst Evol Microbiol 2020; 70:4470–4495 [View Article][PubMed]
     [Google Scholar]
  23. 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]
  24. Yoon SH, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
     [Google Scholar]
  25. 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]
  26. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the bacteria and archaea. Int J Syst Evol Microbiol 2014; 64:316–324 [View Article][PubMed]
     [Google Scholar]
  27. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article][PubMed]
     [Google Scholar]
  28. 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]
  29. Kim M, Oh H-S, Park S-C, 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]
  30. 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]
  31. Palmer M, Steenkamp ET, Blom J, Hedlund BP, Venter SN. All ANIs are not created equal: implications for prokaryotic species boundaries and integration of ANIs into polyphasic taxonomy. Int J Syst Evol Microbiol 2020; 70:2937–2948 [View Article][PubMed]
     [Google Scholar]
  32. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
     [Google Scholar]
  33. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article][PubMed]
     [Google Scholar]
  34. Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V et al. Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 2014; 9:2 [View Article][PubMed]
     [Google Scholar]
  35. Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2016; 66:1603–1606 [View Article][PubMed]
     [Google Scholar]
  36. Oren A, Garrity GM. Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 66, part 6, of the IJSEM. Int J Syst Evol Microbiol 2016; 66:3765–3767 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004651
Loading
Genome-based phylogeny of the genera Proteus and Cosenzaea and description of Proteus terrae subsp. terrae subsp. nov. and Proteus terrae subsp. cibarius subsp. nov.
Int J Syst Evol Microbiol 71, 004651 (2021); https://doi.org/10.1099/ijsem.0.004651
/content/journal/ijsem/10.1099/ijsem.0.004651
/content/journal/ijsem/10.1099/ijsem.0.004651
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

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