sp. nov., isolated from a wound of a patient Free

Abstract

A strain of an obligately anaerobic, Gram-stain-negative rod-shaped bacterium is described by phenotypical, biochemical and genotypical characterization. Strain A2672 was isolated from a wound of a patient sampled during routine care at hospital. Phylogenetic analysis was based on full-length 16S rRNA gene sequence analysis and revealed the strain to belong to the genus , but to be distant from known species, with the closest relationship to The genomic DNA G+C content was 44.0 mol%. Strain A2672 was moderately saccharolytic and proteolytic. The most abundant cellular long-chain fatty acids were anteiso-C and iso-C. In view of these characteristics as well as whole-genome sequence analysis, strain A2672 is considered to represent a novel species within the genus , for which the name sp. nov. is proposed. The type strain is A2672 (=DSM 108033=CCOS 1231=CCUG 72809).

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2019-12-01
2024-03-29
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References

  1. Shah HN, Collins DM. Prevotella, a new genus to include Bacteroides melaninogenicus and related species formerly classified in the genus Bacteroides . Int J Syst Bacteriol 1990; 40:205–208 [View Article][PubMed]
    [Google Scholar]
  2. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature ( bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article][PubMed]
    [Google Scholar]
  3. Euzéby J, Parte AC. LPSN - Genus Prevotella . http://www.bacterio.net/prevotella.html
  4. Nakata H, Kanda H, Nakakita Y, Kaneko T, Tsuchiya Y. Prevotella cerevisiae sp. nov., beer-spoilage obligate anaerobic bacteria isolated from brewery wastewater. Int J Syst Evol Microbiol 2019; 69:1789–1793 [View Article][PubMed]
    [Google Scholar]
  5. Efimov BA, Chaplin AV, Shcherbakova VA, Suzina NE, Podoprigora IV et al. Prevotella rara sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2018; 68:3818–3825 [View Article][PubMed]
    [Google Scholar]
  6. Buhl M, Willmann M, Liese J, Autenrieth IB, Marschal M. Prevotella colorans sp. nov., isolated from a human wound. Int J Syst Evol Microbiol 2016; 66:3005–3009 [View Article][PubMed]
    [Google Scholar]
  7. Robertson D, Smith AJ. The microbiology of the acute dental abscess. J Med Microbiol 2009; 58:155–162 [View Article][PubMed]
    [Google Scholar]
  8. Le Moal G, Landron C, Grollier G, Bataille B, Roblot F et al. Characteristics of brain abscess with isolation of anaerobic bacteria. Scand J Infect Dis 2003; 35:318–321 [View Article][PubMed]
    [Google Scholar]
  9. Mehmood M, Jaffar NA, Nazim M, Khasawneh FA. Bacteremic skin and soft tissue infection caused by Prevotella loescheii . BMC Infect Dis 2014; 14:162 [View Article][PubMed]
    [Google Scholar]
  10. Carlier JP, K'ouas G, Bonne I, Lozniewski A, Mory F. Oribacterium sinus gen. nov., sp. nov., within the family 'Lachnospiraceae' (phylum Firmicutes). Int J Syst Evol Microbiol 2004; 54:1611–1615 [View Article][PubMed]
    [Google Scholar]
  11. Haft DH, Dicuccio M, Badretdin A, Brover V, Chetvernin V et al. RefSeq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res 2018; 46:D851–D860 [View Article][PubMed]
    [Google Scholar]
  12. Yoon SH, Ha SM, 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]
  13. McWilliam H, Li W, Uludag M, Squizzato S, Park YM et al. Analysis tool web services from the EMBL-EBI. Nucleic Acids Res 2013; 41:W597–W600 [View Article][PubMed]
    [Google Scholar]
  14. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  15. 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]
  16. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  17. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article][PubMed]
    [Google Scholar]
  18. Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nat Biotechnol 2018; 36:566–569 [View Article][PubMed]
    [Google Scholar]
  19. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  20. Auch AF, Klenk HP, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2:142–148 [View Article][PubMed]
    [Google Scholar]
  21. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
    [Google Scholar]
  22. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  23. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
    [Google Scholar]
  24. Ankenbrand MJ, Keller A. bcgTree: automatized phylogenetic tree building from bacterial core genomes. Genome 2016; 59:783–791 [View Article][PubMed]
    [Google Scholar]
  25. 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]
  26. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article][PubMed]
    [Google Scholar]
  27. Avgustin G, Wallace RJ, Flint HJ. Phenotypic diversity among ruminal isolates of Prevotella ruminicola: proposal of Prevotella brevis sp. nov., Prevotella bryantii sp. nov., and Prevotella albensis sp. nov. and redefinition of Prevotella ruminicola . Int J Syst Bacteriol 1997; 47:284–288 [View Article][PubMed]
    [Google Scholar]
  28. Willems A, Collins MD. 16S rRNA gene similarities indicate that Hallella seregens (Moore and Moore) and Mitsuokella dentalis (Haapsalo et al.) are genealogically highly related and are members of the genus Prevotella: emended description of the genus Prevotella (Shah and Collins) and description of Prevotella dentalis comb. nov. Int J Syst Bacteriol 1995; 45:832–836 [View Article][PubMed]
    [Google Scholar]
  29. Johnson JL, Holdeman LV. Bacteroides intermedius comb. nov. and descriptions of Bacteroides corporis sp. nov. and Bacteroides levii sp. nov. Int J Syst Bacteriol 1983; 33:15–25 [View Article]
    [Google Scholar]
  30. Holdeman LV, Johnson JL. Bacteroides disiens sp. nov. and Bacteroides bivius sp. nov. from human clinical infections. Int J Syst Bacteriol 1977; 27:337–345 [View Article]
    [Google Scholar]
  31. Kerttula AM, Carlson P, Sarkonen N, Hall V, Könönen E. Enzymatic/biochemical analysis of Actinomyces with commercial test kits with an emphasis on newly described species. Anaerobe 2005; 11:99–108 [View Article][PubMed]
    [Google Scholar]
  32. Sarkonen N, Könönen E, Summanen P, Könönen M, Jousimies-Somer H. Phenotypic identification of Actinomyces and related species isolated from human sources. J Clin Microbiol 2001; 39:3955–3961 [View Article][PubMed]
    [Google Scholar]
  33. Conrads G, Nagy E, Könönen E. Bacteroides, Porphyromonas, Prevotella, Fusobacterium, and other anaerobic Gram-negative rods. In Carroll, Landry, McAdam, Patel. (editors) Manual of Clinical Microbiology, 12th ed. American Society of Microbiology; pp. 995–1023
    [Google Scholar]
  34. Holdeman LV, Johnson JL. Description of Bacteroides loescheii sp. nov. and emendation of the descriptions of Bacteroides melaninogenicus (Oliver and Wherry) Roy and Kelly 1939 and Bacteroides denticola Shah and Collins 1981. Int J Syst Bacteriol 1982; 32:399–409 [View Article]
    [Google Scholar]
  35. Hayashi H, Shibata K, Sakamoto M, Tomita S, Benno Y. Prevotella copri sp. nov. and Prevotella stercorea sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2007; 57:941–946 [View Article][PubMed]
    [Google Scholar]
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