1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 8

sp. nov., isolated from an abscess of a hospital patient Free

Abstract

A strain of an obligately anaerobic, Gram-stain-negative rod-shaped bacterium is described by phenotypical, biochemical and genotypical characterization. This strain A2879 was isolated from an abscess swab of a patient sampled during routine care at hospital. Phylogenetic analyses (full-length 16S rRNA gene and whole-genome sequence) revealed the strain to belong to the genus , but to be distant from recognized species, with the closest relationship to . Unambiguous identification also proved possible by MALDI-TOF MS. The genomic DNA G+C content was 41.5 mol%. Strain A2879 was moderately saccharolytic and proteolytic. The most abundant cellular long-chain fatty acids were anteiso-C and iso-C. In view of these data, strain A2879 is considered to represent a novel species within the genus , for which the name sp. nov. is proposed. The type strain is A2879 (=DSM 108027=CCOS 1233=CCUG72808). As this strain has been isolated from a clinical sample, it is considered relevant for human medicine and health in general, and in particular for the fields of clinical microbiology and infectious diseases. This description will enable routine and research laboratories alike to easily identify the novel taxon, allowing its role in the context of human health and disease or microbiota to be further elucidated.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Bacteroidetes , microbiome , new , phylogenomic treeing , Prevotellaceae and WGS
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004316
2020-07-31
2024-04-23
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/8/4576.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004316&mimeType=html&fmt=ahah

References

  1. Ley RE. Gut microbiota in 2015: Prevotella in the gut: choose carefully. Nat Rev Gastroenterol Hepatol 2016; 13:69–70 [View Article][PubMed]
     [Google Scholar]
  2. Larsen JM. The immune response to Prevotella bacteria in chronic inflammatory disease. Immunology 2017; 151:363–374 [View Article][PubMed]
     [Google Scholar]
  3. De Filippis F, Pasolli E, Tett A, Tarallo S, Naccarati A et al. Distinct genetic and functional traits of human intestinal Prevotella copri strains are associated with different habitual diets. Cell Host Microbe 2019; 25:444–453 [View Article][PubMed]
     [Google Scholar]
  4. Carlier J-P, 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]
  5. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
     [Google Scholar]
  6. 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]
  7. 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]
  8. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article][PubMed]
     [Google Scholar]
  9. Hahnke RL, Meier-Kolthoff JP, García-López M, Mukherjee S, Huntemann M et al. Genome-based taxonomic classification of Bacteroidetes . Front Microbiol 2016; 7:2003 [View Article][PubMed]
     [Google Scholar]
  10. 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]
  11. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
     [Google Scholar]
  12. 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]
  13. 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]
  14. 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]
  15. 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]
  16. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article][PubMed]
     [Google Scholar]
  17. Auch AF, Klenk H-P, 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]
  18. 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]
  19. 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]
  20. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
     [Google Scholar]
  21. Afgan E, Baker D, Batut B, van den Beek M, Bouvier D et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res 2018; 46:W537–W544 [View Article][PubMed]
     [Google Scholar]
  22. Ankenbrand MJ, Keller A. bcgTree: automatized phylogenetic tree building from bacterial core genomes. Genome 2016; 59:783–791 [View Article][PubMed]
     [Google Scholar]
  23. 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]
  24. 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]
  25. 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]
  26. 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]
  27. Watabe J, Benno J, Mitsuoka T. Taxonomic study of Bacteroides oralis and related organisms and proposal of Bacteroides veroralis sp. nov. Int J Syst Evol Microbiol 1983; 33: [View Article]
     [Google Scholar]
  28. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article][PubMed]
     [Google Scholar]
  29. Oren A, Garrity GM, Parte AC. Why are so many effectively published names of prokaryotic taxa never validated?. Int J Syst Evol Microbiol 2018; 68:2125–2129 [View Article][PubMed]
     [Google Scholar]
  30. Wu CC, Johnson JL, Moore WE, Moore LV. Emended descriptions of Prevotella denticola, Prevotella loescheii, Prevotella veroralis, and Prevotella melaninogenica . Int J Syst Bacteriol 1992; 42:536–541 [View Article][PubMed]
     [Google Scholar]
  31. Downes J, Hooper SJ, Wilson MJ, Wade WG. Prevotella histicola sp. nov., isolated from the human oral cavity. Int J Syst Evol Microbiol 2008; 58:1788–1791 [View Article][PubMed]
     [Google Scholar]
  32. 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]
  33. 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]
  34. 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]
  35. Hedberg ME, Israelsson A, Moore ERB, Svensson-Stadler L, Wai SN et al. Prevotella jejuni sp. nov., isolated from the small intestine of a child with coeliac disease. Int J Syst Evol Microbiol 2013; 63:4218–4223 [View Article][PubMed]
     [Google Scholar]
  36. Downes J, Wade WG. Prevotella fusca sp. nov. and Prevotella scopos sp. nov., isolated from the human oral cavity. Int J Syst Evol Microbiol 2011; 61:854–858 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004316
Loading
Prevotella vespertina sp. nov., isolated from an abscess of a hospital patient
Int J Syst Evol Microbiol 70, 4576 (2020); https://doi.org/10.1099/ijsem.0.004316
/content/journal/ijsem/10.1099/ijsem.0.004316
/content/journal/ijsem/10.1099/ijsem.0.004316
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