1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 74, Issue 9

Reclassification of Moore . 1976 (Approved Lists 1980) into a novel genus as gen. nov., comb. nov. No Access

Abstract

The reclassification of Moore . 1976 (Approved Lists 1980) as gen. nov., comb. nov. is proposed within the family . This reclassification is based on differences revealed through the analysis of 16S rRNA, , , and genes, as well as genome sequences, distinguishing it from other species. Comparative analysis showed that exhibited digital DNA–DNA hybridization (dDDH) values of 19.40–27.20% and average nucleotide identities based on (ANIb) values of 67.06–67.64% with other species. These values are significantly below the species delineation thresholds (dDDH, 70%; ANIb, 95–96%), justifying the proposed reclassification. Additionally, the results of the average amino acid identity (AAI) analysis indicated that this species shares 59.22–60.17% AAI with the other species of the genus , which is below the AAI threshold (65%) for a genus boundary. In addition, biochemical and morphological characteristics also support the proposal that this species is different from other species of the genus . The type strain is ATCC 29175 (DSM 2876=T9-40A).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA , Butyrivibrio , Eshraghiella , genome analysis , Lachnospiraceae and reclassification
© 2024 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006509
2024-09-03
2024-09-15
Loading full text...

Full text loading...

References

  1. Bryant MP, Small N. The anaerobic monotrichous butyric acid-producing curved rod-shaped bacteria of the rumen. J Bacteriol 1956; 72:16–21 [View Article] [PubMed]
     [Google Scholar]
  2. LPSN 2024 https://lpsn.dsmz.de/
  3. LPSN Genus: Cellfalcicula; 2024 https://lpsn.dsmz.de/genus/cellfalcicula
  4. Hespell RB, Wolf R, Bothast RJ. Fermentation of xylans by Butyrivibrio fibrisolvens and other ruminal bacteria. Appl Environ Microbiol 1987; 53:2849–2853 [View Article] [PubMed]
     [Google Scholar]
  5. Stewart C, Flint H, Bryant M. The rumen bacteria. In The Rumen Microbial Ecosystem Springer; 1997 pp 10–72
     [Google Scholar]
  6. Kopečný J, Zorec M, Mrázek J, Kobayashi Y, Marinšek-Logar R. Butyrivibrio hungatei sp. nov. and Pseudobutyrivibrio xylanivorans sp. nov., butyrate-producing bacteria from the rumen. Int J Syst Evol Microbiol 2003; 53:201–209 [View Article] [PubMed]
     [Google Scholar]
  7. Polan CE, McNeill JJ, Tove SB. Biohydrogenation of unsaturated fatty acids by rumen bacteria. J Bacteriol 1964; 88:1056–1064 [View Article] [PubMed]
     [Google Scholar]
  8. Wallace RJ, Chaudhary LC, McKain N, McEwan NR, Richardson AJ et al. Clostridium proteoclasticum: a ruminal bacterium that forms stearic acid from linoleic acid. FEMS Microbiol Lett 2006; 265:195–201
     [Google Scholar]
  9. Hazlewood GP, Orpin CG, Greenwood Y, Black ME. Isolation of proteolytic rumen bacteria by use of selective medium containing leaf fraction 1 protein (ribulosebisphosphate carboxylase). Appl Environ Microbiol 1983; 45:1780–1784 [View Article] [PubMed]
     [Google Scholar]
  10. Wallace R, Brammall ML. The role of different species of bacteria in the hydrolysis of protein in the rumen. Microbiology 1985; 131:821–832
     [Google Scholar]
  11. Cotta MA, Hespell RB. Proteolytic activity of the ruminal bacterium Butyrivibrio fibrisolvens. Appl Environ Microbiol 1986; 52:51–58 [View Article] [PubMed]
     [Google Scholar]
  12. LPSN Genus: Butyrivibrio; 2024 https://lpsn.dsmz.de/genus/butyrivibrio
  13. Cheng KJ, Costerton JW. Ultrastructure of Butyrivibrio fibrisolvens: a Gram-positive bacterium. J Bacteriol 1977; 129:1506–1512 [View Article] [PubMed]
     [Google Scholar]
  14. Moore WC, Johnson J, Holdeman L. Emendation of Bacteroidaceae and Butyrivibrio and descriptions of Desulfomonas gen. nov. and ten new species in the genera Desulfomonas, Butyrivibrio, Eubacterium, Clostridium, and Ruminococcus. Int J Syst Evol Microbiol 1976; 26:238–252
     [Google Scholar]
  15. Attwood G, Reilly K, Patel B. Clostridium proteoclasticum sp. nov., a novel proteolytic bacterium from the bovine rumen. Int J Syst Evol Microbiol 1996; 46:753–758
     [Google Scholar]
  16. Moon CD, Pacheco DM, Kelly WJ, Leahy SC, Li D et al. Reclassification of Clostridium proteoclasticum as Butyrivibrio proteoclasticus comb. nov., a butyrate-producing ruminal bacterium. Int J Syst Evol Microbiol 2008; 58:2041–2045 [View Article] [PubMed]
     [Google Scholar]
  17. Yoon S-H, 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]
  18. 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]
  19. Jeon Y-S, Chung H, Park S, Hur I, Lee J-H et al. jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences. Bioinformatics 2005; 21:3171–3173 [View Article] [PubMed]
     [Google Scholar]
  20. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731–2739 [View Article] [PubMed]
     [Google Scholar]
  21. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
     [Google Scholar]
  22. 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]
  23. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
     [Google Scholar]
  24. 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]
  25. 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]
  26. 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; 14:1–14 [View Article] [PubMed]
     [Google Scholar]
  27. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131
     [Google Scholar]
  28. Teeling H, Meyerdierks A, Bauer M, Amann R, Glöckner FO. Application of tetranucleotide frequencies for the assignment of genomic fragments. Environ Microbiol 2004; 6:938–947 [View Article] [PubMed]
     [Google Scholar]
  29. Gomila M, Peña A, Mulet M, Lalucat J, García-Valdés E. Phylogenomics and systematics in Pseudomonas. Front Microbiol 2015; 6:214 [View Article] [PubMed]
     [Google Scholar]
  30. Kim D, Park S, Chun J. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 2021; 59:476–480 [View Article] [PubMed]
     [Google Scholar]
  31. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J 2017; 11:2399–2406 [View Article] [PubMed]
     [Google Scholar]
  32. Vacca M, Celano G, Calabrese FM, Portincasa P, Gobbetti M et al. The controversial role of human gut Lachnospiraceae. Microorganisms 2020; 8:573 [View Article] [PubMed]
     [Google Scholar]
  33. Willems A, Amat-Marco M, Collins MD. Phylogenetic analysis of Butyrivibrio strains reveals three distinct groups of species within the Clostridium subphylum of the Gram-positive bacteria. Int J Syst Evol Microbiol 1996; 46:195–199
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006509
Loading
Reclassification of Butyrivibrio crossotus Moore et al. 1976 (Approved Lists 1980) into a novel genus as Eshraghiella crossota gen. nov., comb. nov.
Int J Syst Evol Microbiol 74, 006509 (2024); https://doi.org/10.1099/ijsem.0.006509
/content/journal/ijsem/10.1099/ijsem.0.006509
/content/journal/ijsem/10.1099/ijsem.0.006509
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

EXCEL

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